From ee4e3f3a58c41913bab52af4cd257fc9d8c329da Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 13 Sep 2023 15:59:16 +0200
Subject: [PATCH 01/79] add the input box

---
 omero_figure/templates/figure/index.html   |    4 +-
 package-lock.json                          | 3536 +++++++++++++++++++-
 src/js/views/right_panel_view.js           |    5 +-
 src/templates/channel_slider_template.html |    3 +
 4 files changed, 3538 insertions(+), 10 deletions(-)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index 6eae81088..9e5e5a310 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -1070,12 +1070,12 @@ <h5>Example Label</h5>
                     <div class='clearfix'></div>
                     <div class='tab-footer'>
                         <div class="col-sm-2 no-padding">
-                            <h5>Zoom</h5>
+                            <h5>Zoom %</h5>
                         </div>
                         <div class="col-sm-8 no-padding">
                             <div id="vp_zoom_slider"></div>
                         </div>
-                        <div id="vp_zoom_value" class="col-sm-2" style="padding: 8px 0 0; text-align:right"></div>
+                        <input id="vp_zoom_value" type="number" size="4"></input>
                         <div class='clearfix'></div>
                         <div id="reset-zoom-view">
                             <!-- button added by ZoomView render() -->
diff --git a/package-lock.json b/package-lock.json
index c9d4b70cb..c771a5d02 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,8 +1,3530 @@
 {
   "name": "omero-figure",
   "version": "0.0.0",
-  "lockfileVersion": 1,
+  "lockfileVersion": 2,
   "requires": true,
+  "packages": {
+    "": {
+      "name": "omero-figure",
+      "version": "0.0.0",
+      "license": "AGPL-3.0",
+      "dependencies": {
+        "@openmicroscopy/shape-editor": "^4.0.0"
+      },
+      "devDependencies": {
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+        "grunt-cli": "^1.3.2",
+        "grunt-contrib-concat": "^0.5.0",
+        "grunt-contrib-copy": "^0.8.1",
+        "grunt-contrib-jshint": "~3.2.0",
+        "grunt-contrib-jst": "^2.0.0",
+        "grunt-contrib-watch": "^1.1.0",
+        "grunt-replace": "^2.0.2"
+      }
+    },
+    "node_modules/@openmicroscopy/shape-editor": {
+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/@openmicroscopy/shape-editor/-/shape-editor-4.0.0.tgz",
+      "integrity": "sha1-EoHNj1pG6WAayo8R9L4bahLFPoU="
+    },
+    "node_modules/abbrev": {
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+      "resolved": "https://registry.npmjs.org/abbrev/-/abbrev-1.1.1.tgz",
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+        "body": "^5.1.0",
+        "debug": "^3.1.0",
+        "faye-websocket": "~0.10.0",
+        "livereload-js": "^2.3.0",
+        "object-assign": "^4.1.0",
+        "qs": "^6.4.0"
+      }
+    },
+    "node_modules/to-object-path": {
+      "version": "0.3.0",
+      "resolved": "https://registry.npmjs.org/to-object-path/-/to-object-path-0.3.0.tgz",
+      "integrity": "sha1-KXWIt7Dn4KwI4E5nL4XB9JmeF68=",
+      "dev": true,
+      "dependencies": {
+        "kind-of": "^3.0.2"
+      },
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/to-object-path/node_modules/kind-of": {
+      "version": "3.2.2",
+      "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-3.2.2.tgz",
+      "integrity": "sha512-NOW9QQXMoZGg/oqnVNoNTTIFEIid1627WCffUBJEdMxYApq7mNE7CpzucIPc+ZQg25Phej7IJSmX3hO+oblOtQ==",
+      "dev": true,
+      "dependencies": {
+        "is-buffer": "^1.1.5"
+      },
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/to-regex": {
+      "version": "3.0.2",
+      "resolved": "https://registry.npmjs.org/to-regex/-/to-regex-3.0.2.tgz",
+      "integrity": "sha512-FWtleNAtZ/Ki2qtqej2CXTOayOH9bHDQF+Q48VpWyDXjbYxA4Yz8iDB31zXOBUlOHHKidDbqGVrTUvQMPmBGBw==",
+      "dev": true,
+      "dependencies": {
+        "define-property": "^2.0.2",
+        "extend-shallow": "^3.0.2",
+        "regex-not": "^1.0.2",
+        "safe-regex": "^1.1.0"
+      },
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/to-regex-range": {
+      "version": "2.1.1",
+      "resolved": "https://registry.npmjs.org/to-regex-range/-/to-regex-range-2.1.1.tgz",
+      "integrity": "sha1-fIDBe53+vlmeJzZ+DU3VWQFB2zg=",
+      "dev": true,
+      "dependencies": {
+        "is-number": "^3.0.0",
+        "repeat-string": "^1.6.1"
+      },
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/unc-path-regex": {
+      "version": "0.1.2",
+      "resolved": "https://registry.npmjs.org/unc-path-regex/-/unc-path-regex-0.1.2.tgz",
+      "integrity": "sha1-5z3T17DXxe2G+6xrCufYxqadUPo=",
+      "dev": true,
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/underscore.string": {
+      "version": "3.3.6",
+      "resolved": "https://registry.npmjs.org/underscore.string/-/underscore.string-3.3.6.tgz",
+      "integrity": "sha512-VoC83HWXmCrF6rgkyxS9GHv8W9Q5nhMKho+OadDJGzL2oDYbYEppBaCMH6pFlwLeqj2QS+hhkw2kpXkSdD1JxQ==",
+      "dev": true,
+      "dependencies": {
+        "sprintf-js": "^1.1.1",
+        "util-deprecate": "^1.0.2"
+      },
+      "engines": {
+        "node": "*"
+      }
+    },
+    "node_modules/underscore.string/node_modules/sprintf-js": {
+      "version": "1.1.2",
+      "resolved": "https://registry.npmjs.org/sprintf-js/-/sprintf-js-1.1.2.tgz",
+      "integrity": "sha512-VE0SOVEHCk7Qc8ulkWw3ntAzXuqf7S2lvwQaDLRnUeIEaKNQJzV6BwmLKhOqT61aGhfUMrXeaBk+oDGCzvhcug==",
+      "dev": true
+    },
+    "node_modules/union-value": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/union-value/-/union-value-1.0.1.tgz",
+      "integrity": "sha512-tJfXmxMeWYnczCVs7XAEvIV7ieppALdyepWMkHkwciRpZraG/xwT+s2JN8+pr1+8jCRf80FFzvr+MpQeeoF4Xg==",
+      "dev": true,
+      "dependencies": {
+        "arr-union": "^3.1.0",
+        "get-value": "^2.0.6",
+        "is-extendable": "^0.1.1",
+        "set-value": "^2.0.1"
+      },
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/unset-value": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/unset-value/-/unset-value-1.0.0.tgz",
+      "integrity": "sha1-g3aHP30jNRef+x5vw6jtDfyKtVk=",
+      "dev": true,
+      "dependencies": {
+        "has-value": "^0.3.1",
+        "isobject": "^3.0.0"
+      },
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/unset-value/node_modules/has-value": {
+      "version": "0.3.1",
+      "resolved": "https://registry.npmjs.org/has-value/-/has-value-0.3.1.tgz",
+      "integrity": "sha1-ex9YutpiyoJ+wKIHgCVlSEWZXh8=",
+      "dev": true,
+      "dependencies": {
+        "get-value": "^2.0.3",
+        "has-values": "^0.1.4",
+        "isobject": "^2.0.0"
+      },
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/unset-value/node_modules/has-value/node_modules/isobject": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/isobject/-/isobject-2.1.0.tgz",
+      "integrity": "sha1-8GVWEJaj8dou9GJy+BXIQNh+DIk=",
+      "dev": true,
+      "dependencies": {
+        "isarray": "1.0.0"
+      },
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/unset-value/node_modules/has-values": {
+      "version": "0.1.4",
+      "resolved": "https://registry.npmjs.org/has-values/-/has-values-0.1.4.tgz",
+      "integrity": "sha1-bWHeldkd/Km5oCCJrThL/49it3E=",
+      "dev": true,
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/unset-value/node_modules/isarray": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/isarray/-/isarray-1.0.0.tgz",
+      "integrity": "sha1-u5NdSFgsuhaMBoNJV6VKPgcSTxE=",
+      "dev": true
+    },
+    "node_modules/urix": {
+      "version": "0.1.0",
+      "resolved": "https://registry.npmjs.org/urix/-/urix-0.1.0.tgz",
+      "integrity": "sha1-2pN/emLiH+wf0Y1Js1wpNQZ6bHI=",
+      "deprecated": "Please see https://github.com/lydell/urix#deprecated",
+      "dev": true
+    },
+    "node_modules/use": {
+      "version": "3.1.1",
+      "resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz",
+      "integrity": "sha512-cwESVXlO3url9YWlFW/TA9cshCEhtu7IKJ/p5soJ/gGpj7vbvFrAY/eIioQ6Dw23KjZhYgiIo8HOs1nQ2vr/oQ==",
+      "dev": true,
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/util-deprecate": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz",
+      "integrity": "sha1-RQ1Nyfpw3nMnYvvS1KKJgUGaDM8=",
+      "dev": true
+    },
+    "node_modules/v8flags": {
+      "version": "3.1.3",
+      "resolved": "https://registry.npmjs.org/v8flags/-/v8flags-3.1.3.tgz",
+      "integrity": "sha512-amh9CCg3ZxkzQ48Mhcb8iX7xpAfYJgePHxWMQCBWECpOSqJUXgY26ncA61UTV0BkPqfhcy6mzwCIoP4ygxpW8w==",
+      "dev": true,
+      "dependencies": {
+        "homedir-polyfill": "^1.0.1"
+      },
+      "engines": {
+        "node": ">= 0.10"
+      }
+    },
+    "node_modules/websocket-driver": {
+      "version": "0.7.4",
+      "resolved": "https://registry.npmjs.org/websocket-driver/-/websocket-driver-0.7.4.tgz",
+      "integrity": "sha512-b17KeDIQVjvb0ssuSDF2cYXSg2iztliJ4B9WdsuB6J952qCPKmnVq4DyW5motImXHDC1cBT/1UezrJVsKw5zjg==",
+      "dev": true,
+      "dependencies": {
+        "http-parser-js": ">=0.5.1",
+        "safe-buffer": ">=5.1.0",
+        "websocket-extensions": ">=0.1.1"
+      },
+      "engines": {
+        "node": ">=0.8.0"
+      }
+    },
+    "node_modules/websocket-extensions": {
+      "version": "0.1.4",
+      "resolved": "https://registry.npmjs.org/websocket-extensions/-/websocket-extensions-0.1.4.tgz",
+      "integrity": "sha512-OqedPIGOfsDlo31UNwYbCFMSaO9m9G/0faIHj5/dZFDMFqPTcx6UwqyOy3COEaEOg/9VsGIpdqn62W5KhoKSpg==",
+      "dev": true,
+      "engines": {
+        "node": ">=0.8.0"
+      }
+    },
+    "node_modules/which": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
+      "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==",
+      "dev": true,
+      "dependencies": {
+        "isexe": "^2.0.0"
+      },
+      "bin": {
+        "node-which": "bin/node-which"
+      },
+      "engines": {
+        "node": ">= 8"
+      }
+    },
+    "node_modules/wrappy": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
+      "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=",
+      "dev": true
+    }
+  },
   "dependencies": {
     "@openmicroscopy/shape-editor": {
       "version": "4.0.0",
@@ -2532,18 +6054,18 @@
         }
       }
     },
-    "string-template": {
-      "version": "0.2.1",
-      "resolved": "https://registry.npmjs.org/string-template/-/string-template-0.2.1.tgz",
-      "integrity": "sha512-Yptehjogou2xm4UJbxJ4CxgZx12HBfeystp0y3x7s4Dj32ltVVG1Gg8YhKjHZkHicuKpZX/ffilA8505VbUbpw==",
-      "dev": true
-    },
     "string_decoder": {
       "version": "0.10.31",
       "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-0.10.31.tgz",
       "integrity": "sha512-ev2QzSzWPYmy9GuqfIVildA4OdcGLeFZQrq5ys6RtiuF+RQQiZWr8TZNyAcuVXyQRYfEO+MsoB/1BuQVhOJuoQ==",
       "dev": true
     },
+    "string-template": {
+      "version": "0.2.1",
+      "resolved": "https://registry.npmjs.org/string-template/-/string-template-0.2.1.tgz",
+      "integrity": "sha512-Yptehjogou2xm4UJbxJ4CxgZx12HBfeystp0y3x7s4Dj32ltVVG1Gg8YhKjHZkHicuKpZX/ffilA8505VbUbpw==",
+      "dev": true
+    },
     "strip-ansi": {
       "version": "0.3.0",
       "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-0.3.0.tgz",
diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index c91641e52..1c355390e 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -633,6 +633,8 @@
                 value: self.zoom_avg,
                 slide: function(event, ui) {
                     self.update_img_css(ui.value, 0, 0);
+                    $('#vp_zoom_value').value(ui.value);
+                    console.log($("#vp_zoom_value"))
                 },
                 stop: function( event, ui ) {
                     self.zoom_avg = ui.value;
@@ -649,6 +651,7 @@
                 }
             });
             this.$vp_zoom_value = $("#vp_zoom_value");
+            
 
             // We nest the ZoomView so we can update it on update_img_css
             this.zmView = new ZoomView({models: this.models,
@@ -768,7 +771,7 @@
                     offset_y = dy;
                 }
                 this.$vp_img.css( this.models.head().get_vp_img_css(zoom, frame_w, frame_h, offset_x, offset_y) );
-                this.$vp_zoom_value.text(zoom + "%");
+                this.$vp_zoom_value.text(zoom);
 
                 if (save) {
                     if (typeof dx === "undefined") dx = 0;  // rare crazy-dragging case!
diff --git a/src/templates/channel_slider_template.html b/src/templates/channel_slider_template.html
index e2ef76a7c..6377d91dd 100644
--- a/src/templates/channel_slider_template.html
+++ b/src/templates/channel_slider_template.html
@@ -44,6 +44,9 @@
                 <li><a data-color="FF00FF" href="#">
                     <span style="background-color:#f0f">&nbsp &nbsp &nbsp</span>&nbsp Magenta
                 </a></li>
+                <li><a data-color="00FFFF" href="#">
+                    <span style="background-color:#0ff">&nbsp &nbsp &nbsp</span>&nbsp Cyan
+                </a></li>
                 <li class="divider"></li>
                 <li><a data-color="lutpicker" href="#">
                     <span class="lutBg">&nbsp &nbsp &nbsp</span>&nbsp Lookup Tables

From b15ee0a0923bf3f7bd2b617dc2a049cfabe0a9a1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 13 Sep 2023 16:01:31 +0200
Subject: [PATCH 02/79] add cyan color to drop down menu for LUT

---
 src/templates/channel_slider_template.html | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/templates/channel_slider_template.html b/src/templates/channel_slider_template.html
index e2ef76a7c..6377d91dd 100644
--- a/src/templates/channel_slider_template.html
+++ b/src/templates/channel_slider_template.html
@@ -44,6 +44,9 @@
                 <li><a data-color="FF00FF" href="#">
                     <span style="background-color:#f0f">&nbsp &nbsp &nbsp</span>&nbsp Magenta
                 </a></li>
+                <li><a data-color="00FFFF" href="#">
+                    <span style="background-color:#0ff">&nbsp &nbsp &nbsp</span>&nbsp Cyan
+                </a></li>
                 <li class="divider"></li>
                 <li><a data-color="lutpicker" href="#">
                     <span class="lutBg">&nbsp &nbsp &nbsp</span>&nbsp Lookup Tables

From 81238b7aa5a10780b5c4a4aebbd65f6527e1a5e2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 13 Sep 2023 16:02:49 +0200
Subject: [PATCH 03/79] retracts back the Cyan LUT color

---
 src/templates/channel_slider_template.html | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/templates/channel_slider_template.html b/src/templates/channel_slider_template.html
index 6377d91dd..e2ef76a7c 100644
--- a/src/templates/channel_slider_template.html
+++ b/src/templates/channel_slider_template.html
@@ -44,9 +44,6 @@
                 <li><a data-color="FF00FF" href="#">
                     <span style="background-color:#f0f">&nbsp &nbsp &nbsp</span>&nbsp Magenta
                 </a></li>
-                <li><a data-color="00FFFF" href="#">
-                    <span style="background-color:#0ff">&nbsp &nbsp &nbsp</span>&nbsp Cyan
-                </a></li>
                 <li class="divider"></li>
                 <li><a data-color="lutpicker" href="#">
                     <span class="lutBg">&nbsp &nbsp &nbsp</span>&nbsp Lookup Tables

From 5deb683dacc609db8e791d56925dd7164f1ba321 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 15 Sep 2023 14:30:54 +0200
Subject: [PATCH 04/79] try to add listener ==> fail for now

---
 .vscode/launch.json                      |  7 +++++
 omero_figure/templates/figure/index.html |  4 ++-
 src/js/views/channel_slider_view.js      |  9 +++---
 src/js/views/right_panel_view.js         | 37 ++++++++++++++++++++----
 4 files changed, 46 insertions(+), 11 deletions(-)
 create mode 100644 .vscode/launch.json

diff --git a/.vscode/launch.json b/.vscode/launch.json
new file mode 100644
index 000000000..5c7247b40
--- /dev/null
+++ b/.vscode/launch.json
@@ -0,0 +1,7 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": []
+}
\ No newline at end of file
diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index 9e5e5a310..ee92351e3 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -1075,7 +1075,9 @@ <h5>Zoom %</h5>
                         <div class="col-sm-8 no-padding">
                             <div id="vp_zoom_slider"></div>
                         </div>
-                        <input id="vp_zoom_value" type="number" size="4"></input>
+                    
+                        <input id="vp_zoom_value"  type="number" size="4"/>
+                        
                         <div class='clearfix'></div>
                         <div id="reset-zoom-view">
                             <!-- button added by ZoomView render() -->
diff --git a/src/js/views/channel_slider_view.js b/src/js/views/channel_slider_view.js
index df2b4ce6b..e514d953b 100644
--- a/src/js/views/channel_slider_view.js
+++ b/src/js/views/channel_slider_view.js
@@ -18,11 +18,11 @@ var ChannelSliderView = Backbone.View.extend({
     events: {
         "keyup .ch_start": "handle_channel_input",
         "keyup .ch_end": "handle_channel_input",
-        "click .channel-btn": "toggle_channel",
-        "click .dropdown-menu a": "pick_color",
+        //"click .channel-btn": "toggle_channel",
+        //"click .dropdown-menu a": "pick_color",
     },
 
-    pick_color: function(e) {
+   /* pick_color: function(e) {
         var color = e.currentTarget.getAttribute('data-color'),
             $colorbtn = $(e.currentTarget).parent().parent(),
             oldcolor = $(e.currentTarget).attr('data-oldcolor'),
@@ -54,7 +54,7 @@ var ChannelSliderView = Backbone.View.extend({
             this.set_color(idx, color);
         }
         return false;
-    },
+    },*/
 
     set_color: function(idx, color) {
         if (this.models) {
@@ -138,6 +138,7 @@ var ChannelSliderView = Backbone.View.extend({
     },
 
     handle_channel_input: function(event) {
+        console.log("Emter the channel input handle method")
         if (event.type === "keyup" && event.which !== 13) {
             return;     // Ignore keyups except 'Enter'
         }
diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index 1c355390e..de5550f00 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -623,8 +623,12 @@
                 self.listenTo(m,
                     'change:channels change:theZ change:theT',
                     self.rerender_image_change);
+              //  self.listenTo(m, "change:$vp_zoom_value", self.handle_user_zoom)/
             });
 
+            //document.getElementById("vp_zoom_value").addEventListener("keyup", (event) => {self.handle_user_zoom} );*/
+
+           // $('#vp_zoom_value').mouseup(handle_user_zoom)
 
             $("#vp_zoom_slider").slider({
                 // NB: these values are updated on render()
@@ -633,8 +637,8 @@
                 value: self.zoom_avg,
                 slide: function(event, ui) {
                     self.update_img_css(ui.value, 0, 0);
-                    $('#vp_zoom_value').value(ui.value);
-                    console.log($("#vp_zoom_value"))
+                   // $('#vp_zoom_value').val(ui.value);
+                    console.log("je passe par ici")
                 },
                 stop: function( event, ui ) {
                     self.zoom_avg = ui.value;
@@ -665,6 +669,7 @@
             "mousedown .vp_img": "mousedown",
             "mousemove .vp_img": "mousemove",
             "mouseup .vp_img": "mouseup",
+            //"keyup .vp_zoom_value": "handle_user_zoom",
         },
 
         mousedown: function(event) {
@@ -705,6 +710,26 @@
             return false;
         },
 
+        handle_user_zoom: function(event){
+            console.log("event OK !")
+            if (event.type === "keyup" && event.which !== 13) {
+                console.log("Ignore my command")
+                return;     // Ignore keyups except 'Enter'
+            }
+
+            var value = event.target.getAttribute('value')
+            console.log("value : "+value)
+            console.log("this.min : "+this.min)
+            console.log("this.max_zoom : "+this.max_zoom)
+            if (value < this.min) value = this.min;
+            if(value > this.max_zoom) value = this.max_zoom
+
+            $("#vp_zoom_slider").slider({'value': value,
+            'max': this.max_zoom});
+
+            this.update_img_css(value, 0, 0);
+        },
+
         // if the panel is rotated by css, drag events need to be corrected
         correct_rotation: function(dx, dy) {
             if (dx === 0 && dy === 0) {
@@ -716,7 +741,7 @@
                 ang1 = Math.PI + ang1;
             }
             var angr = this.r * (Math.PI/180),  // deg -> rad
-                ang2 = ang1 - angr;
+                ang2 = ang1 - angr;pick_color
             dx = Math.cos(ang2) * length;
             dy = Math.sin(ang2) * length;
             return {'dx': dx, 'dy': dy};
@@ -728,7 +753,7 @@
             $( "#vp_zoom_slider" ).slider( "destroy" );
             $("#vp_z_slider").slider("destroy");
             $("#vp_t_slider").slider("destroy");
-            this.$vp_zoom_value.text('');
+            this.$vp_zoom_value.val();
 
             if (this.zmView) {
                 this.zmView.remove();
@@ -771,7 +796,7 @@
                     offset_y = dy;
                 }
                 this.$vp_img.css( this.models.head().get_vp_img_css(zoom, frame_w, frame_h, offset_x, offset_y) );
-                this.$vp_zoom_value.text(zoom);
+                this.$vp_zoom_value.val(zoom);
 
                 if (save) {
                     if (typeof dx === "undefined") dx = 0;  // rare crazy-dragging case!
@@ -1023,7 +1048,7 @@
             this.$vp_frame = $(".vp_frame", this.$el);  // cache for later
             this.$vp_img = $(".vp_img", this.$el);
             this.zoom_avg = zoom >> 0;
-            this.$vp_zoom_value.text(this.zoom_avg + "%");
+            this.$vp_zoom_value.val(this.zoom_avg);
             // zoom may be > 1000 if set by 'crop'
 
             // We want to be able to zoom Big images to 'actual size' in viewport

From 6431dc6ba97cea1d8b8f67d5c7e26a189b970d80 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 15 Sep 2023 16:04:59 +0200
Subject: [PATCH 05/79] Mimic channel slider view events

---
 Dockerfile                          |  5 +++++
 src/js/views/channel_slider_view.js |  9 ++++-----
 src/js/views/right_panel_view.js    | 16 +++-------------
 3 files changed, 12 insertions(+), 18 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index f719ae83b..7e065e462 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -13,4 +13,9 @@ RUN /opt/omero/web/venv3/bin/pip install -e .
 
 RUN echo "config set omero.web.application_server development" >> /opt/omero/web/config/01-default-webapps.omero
 RUN echo "config set omero.web.debug true" >> /opt/omero/web/config/01-default-webapps.omero
+
+COPY . /home/figure/src
+
+WORKDIR /home/figure/src
+
 USER omero-web
diff --git a/src/js/views/channel_slider_view.js b/src/js/views/channel_slider_view.js
index e514d953b..df2b4ce6b 100644
--- a/src/js/views/channel_slider_view.js
+++ b/src/js/views/channel_slider_view.js
@@ -18,11 +18,11 @@ var ChannelSliderView = Backbone.View.extend({
     events: {
         "keyup .ch_start": "handle_channel_input",
         "keyup .ch_end": "handle_channel_input",
-        //"click .channel-btn": "toggle_channel",
-        //"click .dropdown-menu a": "pick_color",
+        "click .channel-btn": "toggle_channel",
+        "click .dropdown-menu a": "pick_color",
     },
 
-   /* pick_color: function(e) {
+    pick_color: function(e) {
         var color = e.currentTarget.getAttribute('data-color'),
             $colorbtn = $(e.currentTarget).parent().parent(),
             oldcolor = $(e.currentTarget).attr('data-oldcolor'),
@@ -54,7 +54,7 @@ var ChannelSliderView = Backbone.View.extend({
             this.set_color(idx, color);
         }
         return false;
-    },*/
+    },
 
     set_color: function(idx, color) {
         if (this.models) {
@@ -138,7 +138,6 @@ var ChannelSliderView = Backbone.View.extend({
     },
 
     handle_channel_input: function(event) {
-        console.log("Emter the channel input handle method")
         if (event.type === "keyup" && event.which !== 13) {
             return;     // Ignore keyups except 'Enter'
         }
diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index de5550f00..1f4ea0b64 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -623,13 +623,8 @@
                 self.listenTo(m,
                     'change:channels change:theZ change:theT',
                     self.rerender_image_change);
-              //  self.listenTo(m, "change:$vp_zoom_value", self.handle_user_zoom)/
             });
 
-            //document.getElementById("vp_zoom_value").addEventListener("keyup", (event) => {self.handle_user_zoom} );*/
-
-           // $('#vp_zoom_value').mouseup(handle_user_zoom)
-
             $("#vp_zoom_slider").slider({
                 // NB: these values are updated on render()
                 max: 1000,
@@ -637,8 +632,7 @@
                 value: self.zoom_avg,
                 slide: function(event, ui) {
                     self.update_img_css(ui.value, 0, 0);
-                   // $('#vp_zoom_value').val(ui.value);
-                    console.log("je passe par ici")
+                    $('#vp_zoom_value').val(ui.value);
                 },
                 stop: function( event, ui ) {
                     self.zoom_avg = ui.value;
@@ -669,7 +663,7 @@
             "mousedown .vp_img": "mousedown",
             "mousemove .vp_img": "mousemove",
             "mouseup .vp_img": "mouseup",
-            //"keyup .vp_zoom_value": "handle_user_zoom",
+            "keyup .vp_zoom_value": "handle_user_zoom",
         },
 
         mousedown: function(event) {
@@ -711,16 +705,12 @@
         },
 
         handle_user_zoom: function(event){
-            console.log("event OK !")
             if (event.type === "keyup" && event.which !== 13) {
-                console.log("Ignore my command")
                 return;     // Ignore keyups except 'Enter'
             }
 
             var value = event.target.getAttribute('value')
-            console.log("value : "+value)
-            console.log("this.min : "+this.min)
-            console.log("this.max_zoom : "+this.max_zoom)
+
             if (value < this.min) value = this.min;
             if(value > this.max_zoom) value = this.max_zoom
 

From 4f99b4c0a12f045f3ef8a5845dec32cd0a4f5580 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 15 Sep 2023 16:06:07 +0200
Subject: [PATCH 06/79] Remove dockerfile changes

---
 Dockerfile | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 7e065e462..de638a3a9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -10,12 +10,6 @@ RUN npm install -g grunt-cli && npm install grunt --save-dev
 RUN $(npm bin)/grunt build
 RUN /opt/omero/web/venv3/bin/pip install -e .
 
-
 RUN echo "config set omero.web.application_server development" >> /opt/omero/web/config/01-default-webapps.omero
 RUN echo "config set omero.web.debug true" >> /opt/omero/web/config/01-default-webapps.omero
-
-COPY . /home/figure/src
-
-WORKDIR /home/figure/src
-
 USER omero-web

From 5f621d2112c0b8464fda88d4b4ab13f8768e2236 Mon Sep 17 00:00:00 2001
From: Rdornier <64911638+Rdornier@users.noreply.github.com>
Date: Fri, 15 Sep 2023 16:53:43 +0200
Subject: [PATCH 07/79] Delete .vscode directory

---
 .vscode/launch.json | 7 -------
 1 file changed, 7 deletions(-)
 delete mode 100644 .vscode/launch.json

diff --git a/.vscode/launch.json b/.vscode/launch.json
deleted file mode 100644
index 5c7247b40..000000000
--- a/.vscode/launch.json
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-    // Use IntelliSense to learn about possible attributes.
-    // Hover to view descriptions of existing attributes.
-    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
-    "version": "0.2.0",
-    "configurations": []
-}
\ No newline at end of file

From f394fe1d0ac778c70869fcebb18c3806a48d0bb1 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Mon, 18 Sep 2023 22:27:19 +0100
Subject: [PATCH 08/79] Fix event handling of manual-zoom-level

---
 omero_figure/templates/figure/index.html |  2 +-
 src/js/views/right_panel_view.js         | 22 ++++++++++++++++------
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index ee92351e3..6506966f7 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -1076,7 +1076,7 @@ <h5>Zoom %</h5>
                             <div id="vp_zoom_slider"></div>
                         </div>
                     
-                        <input id="vp_zoom_value"  type="number" size="4"/>
+                        <input id="vp_zoom_value" type="number" size="4"/>
                         
                         <div class='clearfix'></div>
                         <div id="reset-zoom-view">
diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index 1f4ea0b64..1b9ea89e6 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -656,6 +656,11 @@
                                         figureModel: this.figureModel}); // auto-renders on init
             $("#reset-zoom-view").append(this.zmView.el);
 
+            // Listen for events on zoom input field
+            $("#vp_zoom_value").on("keyup", function(event){
+                this.handle_user_zoom(event);
+            }.bind(this));
+
             this.render();
         },
 
@@ -663,7 +668,6 @@
             "mousedown .vp_img": "mousedown",
             "mousemove .vp_img": "mousemove",
             "mouseup .vp_img": "mouseup",
-            "keyup .vp_zoom_value": "handle_user_zoom",
         },
 
         mousedown: function(event) {
@@ -709,13 +713,18 @@
                 return;     // Ignore keyups except 'Enter'
             }
 
-            var value = event.target.getAttribute('value')
+            var value = event.target.value;
+            if (isNaN(value)) {
+                return;
+            }
+
+            var minVal = $("#vp_zoom_slider").slider("option", "min");
+            var maxVal = $("#vp_zoom_slider").slider("option", "max");
 
-            if (value < this.min) value = this.min;
-            if(value > this.max_zoom) value = this.max_zoom
+            if (value < minVal) value = minVal;
+            if (value > maxVal) value = maxVal;
 
-            $("#vp_zoom_slider").slider({'value': value,
-            'max': this.max_zoom});
+            $("#vp_zoom_slider").slider({'value': value});
 
             this.update_img_css(value, 0, 0);
         },
@@ -743,6 +752,7 @@
             $( "#vp_zoom_slider" ).slider( "destroy" );
             $("#vp_z_slider").slider("destroy");
             $("#vp_t_slider").slider("destroy");
+            $("#vp_zoom_value").off();
             this.$vp_zoom_value.val();
 
             if (this.zmView) {

From ceecb87f1687e9888afca33dbd675f5455631c3b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 19 Sep 2023 10:20:01 +0200
Subject: [PATCH 09/79] update the figure view

---
 src/js/views/right_panel_view.js | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index 1b9ea89e6..e0f166043 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -727,6 +727,19 @@
             $("#vp_zoom_slider").slider({'value': value});
 
             this.update_img_css(value, 0, 0);
+
+            this.zoom_avg = value;
+            var to_save = {'zoom': value};
+            if (value == 100) {
+                to_save.dx = 0;
+                to_save.dy = 0;
+            }
+            this.models.forEach(function(m){
+                m.save(to_save);
+            });
+            // we don't listenTo zoom change...
+            this.rerender_image_change();
+
         },
 
         // if the panel is rotated by css, drag events need to be corrected

From e39e71e4e9ea6fa2904d6c88579bc911a5488e8a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 19 Sep 2023 10:39:15 +0200
Subject: [PATCH 10/79] add comments

---
 src/js/views/right_panel_view.js | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index e0f166043..1a7c0ae7e 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -713,21 +713,26 @@
                 return;     // Ignore keyups except 'Enter'
             }
 
+            // get the current entered value 
             var value = event.target.value;
             if (isNaN(value)) {
                 return;
             }
 
+            // get min/max and restrict the user input between min/max
             var minVal = $("#vp_zoom_slider").slider("option", "min");
             var maxVal = $("#vp_zoom_slider").slider("option", "max");
 
             if (value < minVal) value = minVal;
             if (value > maxVal) value = maxVal;
 
+            // update the slider position
             $("#vp_zoom_slider").slider({'value': value});
 
+            // update the preview image
             this.update_img_css(value, 0, 0);
 
+            // update the figure image
             this.zoom_avg = value;
             var to_save = {'zoom': value};
             if (value == 100) {
@@ -737,9 +742,8 @@
             this.models.forEach(function(m){
                 m.save(to_save);
             });
-            // we don't listenTo zoom change...
-            this.rerender_image_change();
 
+            this.rerender_image_change();
         },
 
         // if the panel is rotated by css, drag events need to be corrected

From f6467991155f2f0273adaf06437ec008bc04b399 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 19 Sep 2023 11:23:21 +0200
Subject: [PATCH 11/79] Fix bug due to wrong copy-paste

---
 src/js/views/right_panel_view.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index 1a7c0ae7e..2ccd1a4b6 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -703,6 +703,7 @@
                     dx = xy.dx;
                     dy = xy.dy;
                 }
+                console.log(this.zoom_avg)
                 this.update_img_css(this.zoom_avg, dx, dy);
             }
             return false;
@@ -757,7 +758,7 @@
                 ang1 = Math.PI + ang1;
             }
             var angr = this.r * (Math.PI/180),  // deg -> rad
-                ang2 = ang1 - angr;pick_color
+                ang2 = ang1 - angr;
             dx = Math.cos(ang2) * length;
             dy = Math.sin(ang2) * length;
             return {'dx': dx, 'dy': dy};

From cfa8ab166fe66b2d2e3bbb07bc5b33350dc56d6e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 19 Sep 2023 11:24:50 +0200
Subject: [PATCH 12/79] Remove console log

---
 src/js/views/right_panel_view.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index 2ccd1a4b6..08409f1e7 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -703,7 +703,6 @@
                     dx = xy.dx;
                     dy = xy.dy;
                 }
-                console.log(this.zoom_avg)
                 this.update_img_css(this.zoom_avg, dx, dy);
             }
             return false;

From 5f01e1020aa08ed54af01f7a88cad2841dbb2cde Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 20 Sep 2023 13:45:02 +0200
Subject: [PATCH 13/79] Fix issue #512

---
 src/js/views/modal_views.js | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/src/js/views/modal_views.js b/src/js/views/modal_views.js
index db1ef93ca..ff032b265 100644
--- a/src/js/views/modal_views.js
+++ b/src/js/views/modal_views.js
@@ -281,7 +281,7 @@
                     // 'width': data.size.width,
                     // 'height': data.size.height,
                     'sizeZ': data.size.z,
-                    'theZ': data.rdefs.defaultZ,
+                    //'theZ': data.rdefs.defaultZ,
                     'sizeT': data.size.t,
                     // 'theT': data.rdefs.defaultT,
                     'channels': data.channels,
@@ -380,6 +380,26 @@
                 } else {
                     json.comp.sizeT = true;
                 }
+
+                // special message for sizeZ
+                if (json.selImg.sizeZ != json.newImg.sizeZ) {
+                    // check if any existing images have theZ > new.sizeZ
+                    var tooSmallZ = false;
+                    sel.forEach(function(o){
+                        if (o.get('theZ') > json.newImg.sizeZ) tooSmallZ = true;
+                    });
+                    if (tooSmallZ) {
+                        json.messages.push({"text": "New Image has fewer slices than needed. Check after update.",
+                            "status": "danger"});
+                    } else {
+                        json.messages.push({"text":"Mismatch of slices: should be OK.",
+                            "status": "success"});
+                    }
+                    json.comp.sizeZ = false;
+                } else {
+                    json.comp.sizeZ = true;
+                }
+
                 // compare channels
                 json.comp.channels = json.ok(true);
                 var selC = json.selImg.channels,

From e3634df5fdbc7c751a606bc058410406d6402818 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 20 Sep 2023 14:50:06 +0200
Subject: [PATCH 14/79] Fix bug on setting theZ

---
 src/js/views/modal_views.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/js/views/modal_views.js b/src/js/views/modal_views.js
index ff032b265..46a34beb8 100644
--- a/src/js/views/modal_views.js
+++ b/src/js/views/modal_views.js
@@ -281,7 +281,7 @@
                     // 'width': data.size.width,
                     // 'height': data.size.height,
                     'sizeZ': data.size.z,
-                    //'theZ': data.rdefs.defaultZ,
+                    'theZ': data.rdefs.defaultZ,
                     'sizeT': data.size.t,
                     // 'theT': data.rdefs.defaultT,
                     'channels': data.channels,
@@ -398,6 +398,7 @@
                     json.comp.sizeZ = false;
                 } else {
                     json.comp.sizeZ = true;
+                    json.newImg['theZ'] = json.selImg['theZ']
                 }
 
                 // compare channels

From e637f66f5cdd6368e8cf8cb2ea2d5a28d07eb40d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 20 Sep 2023 15:19:39 +0200
Subject: [PATCH 15/79] Fix issue #511

---
 src/js/views/modal_views.js | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/js/views/modal_views.js b/src/js/views/modal_views.js
index 46a34beb8..cceff120b 100644
--- a/src/js/views/modal_views.js
+++ b/src/js/views/modal_views.js
@@ -292,7 +292,9 @@
                     'datasetName': data.meta.datasetName,
                     'pixel_size_x': data.pixel_size.valueX,
                     'pixel_size_y': data.pixel_size.valueY,
+                    'pixel_size_z': data.pixel_size.valueZ,
                     'pixel_size_x_unit': data.pixel_size.unitX,
+                    'pixel_size_z_unit':data.pixel_size.unitZ,
                     'pixel_size_x_symbol': data.pixel_size.symbolX,
                     'deltaT': data.deltaT,
                 };

From de9f97d0564d4d6266632e73fa6c2af4ceae5947 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 20 Sep 2023 17:29:02 +0200
Subject: [PATCH 16/79] Add cyan color to label and scalebar dropdown menus

---
 src/templates/labels_form_inner_template.html | 3 +++
 src/templates/scalebar_form_template.html     | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/src/templates/labels_form_inner_template.html b/src/templates/labels_form_inner_template.html
index efb061fc7..10cb5c07c 100644
--- a/src/templates/labels_form_inner_template.html
+++ b/src/templates/labels_form_inner_template.html
@@ -146,6 +146,9 @@
             <li><a href="#">
                 <span data-color="FF00FF" style="background-color:#f0f">&nbsp &nbsp &nbsp</span>&nbsp Magenta
             </a></li>
+            <li><a href="#">
+                <span data-color="00FFFF" style="background-color:#0ff">&nbsp &nbsp &nbsp</span>&nbsp Cyan
+            </a></li>
             <li class="divider"></li>
             <li><a data-color="colorpicker" data-oldcolor="<%= l.color %>" href="#">
                 <span class="colorpickerOption">&nbsp &nbsp &nbsp</span>&nbsp More Colors...
diff --git a/src/templates/scalebar_form_template.html b/src/templates/scalebar_form_template.html
index 21f3c95a9..3fed4e074 100644
--- a/src/templates/scalebar_form_template.html
+++ b/src/templates/scalebar_form_template.html
@@ -99,6 +99,9 @@
                     <li><a href="#">
                         <span data-color="FF00FF" style="background-color:#f0f">&nbsp &nbsp &nbsp</span>&nbsp Magenta
                     </a></li>
+                    <li><a href="#">
+                        <span data-color="00FFFF" style="background-color:#0ff">&nbsp &nbsp &nbsp</span>&nbsp Cyan
+                    </a></li>
                 </ul>
             </div>
         </div>

From a8fea4679c1062aa88557a7c5bb72e48fb424281 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 27 Sep 2023 08:32:59 +0200
Subject: [PATCH 17/79] fix bug on value type ; convert string to int

---
 src/js/views/right_panel_view.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index 08409f1e7..e17113229 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -631,11 +631,11 @@
                 min: 100,
                 value: self.zoom_avg,
                 slide: function(event, ui) {
-                    self.update_img_css(ui.value, 0, 0);
-                    $('#vp_zoom_value').val(ui.value);
+                    self.update_img_css(parseInt(ui.value), 0, 0);
+                    $('#vp_zoom_value').val(parseInt(ui.value));
                 },
                 stop: function( event, ui ) {
-                    self.zoom_avg = ui.value;
+                    self.zoom_avg = parseInt(ui.value);
                     var to_save = {'zoom': ui.value};
                     if (ui.value === 100) {
                         to_save.dx = 0;
@@ -714,7 +714,7 @@
             }
 
             // get the current entered value 
-            var value = event.target.value;
+            var value = parseInt(event.target.value);
             if (isNaN(value)) {
                 return;
             }

From 9559d19a2b95ff4ea10f354a30866aacf918591c Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 27 Sep 2023 20:23:39 +0100
Subject: [PATCH 18/79] Use same logic for theZ and theT for setId()

---
 src/js/models/panel_model.js | 6 ++++--
 src/js/views/modal_views.js  | 9 ++++-----
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 7e3c02a67..8d2495e0d 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -90,7 +90,6 @@
             var newData = {'imageId': data.imageId,
                 'name': data.name,
                 'sizeZ': data.sizeZ,
-                'theZ': data.theZ,
                 'sizeT': data.sizeT,
                 'orig_width': data.orig_width,
                 'orig_height': data.orig_height,
@@ -106,10 +105,13 @@
                 'deltaT': data.deltaT,
             };
 
-            // theT is not changed unless we have to...
+            // theT and theZ are not changed unless we have to...
             if (this.get('theT') >= newData.sizeT) {
                 newData.theT = newData.sizeT - 1;
             }
+            if (this.get('theZ') >= newData.sizeZ) {
+                newData.theZ = newData.sizeZ - 1;
+            }
 
             // Make sure dx and dy are not outside the new image
             if (Math.abs(this.get('dx')) > newData.orig_width/2) {
diff --git a/src/js/views/modal_views.js b/src/js/views/modal_views.js
index cceff120b..21d3dc1f7 100644
--- a/src/js/views/modal_views.js
+++ b/src/js/views/modal_views.js
@@ -349,8 +349,8 @@
             json.selThumbSrc = WEBGATEWAYINDEX + "render_thumbnail/" + json.selImg.imageId + "/";
 
             // minor attributes ('info' only)
-            var attrs = ["sizeZ", "orig_width", "orig_height"],
-                attrName = ['Z size', 'Width', 'Height'];
+            var attrs = ["orig_width", "orig_height"],
+                attrName = ['Width', 'Height'];
 
             if (this.newImg) {
                 json.newImg = this.newImg;
@@ -391,16 +391,15 @@
                         if (o.get('theZ') > json.newImg.sizeZ) tooSmallZ = true;
                     });
                     if (tooSmallZ) {
-                        json.messages.push({"text": "New Image has fewer slices than needed. Check after update.",
+                        json.messages.push({"text": "New Image has fewer Z slices than needed. Check after update.",
                             "status": "danger"});
                     } else {
-                        json.messages.push({"text":"Mismatch of slices: should be OK.",
+                        json.messages.push({"text":"Mismatch of Z slices: should be OK.",
                             "status": "success"});
                     }
                     json.comp.sizeZ = false;
                 } else {
                     json.comp.sizeZ = true;
-                    json.newImg['theZ'] = json.selImg['theZ']
                 }
 
                 // compare channels

From 472aa0ee3e0e3a1c0ab1ae1cf863b83f2124c5e9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 28 Sep 2023 08:12:51 +0200
Subject: [PATCH 19/79] remove parseInt from slide and stop functions

---
 src/js/views/right_panel_view.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index e17113229..e5e2c764a 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -631,11 +631,11 @@
                 min: 100,
                 value: self.zoom_avg,
                 slide: function(event, ui) {
-                    self.update_img_css(parseInt(ui.value), 0, 0);
-                    $('#vp_zoom_value').val(parseInt(ui.value));
+                    self.update_img_css(ui.value, 0, 0);
+                    $('#vp_zoom_value').val(ui.value);
                 },
-                stop: function( event, ui ) {
-                    self.zoom_avg = parseInt(ui.value);
+                stop: function(event, ui) {
+                    self.zoom_avg = ui.value;
                     var to_save = {'zoom': ui.value};
                     if (ui.value === 100) {
                         to_save.dx = 0;

From 01cffd070449836d58ac97504829b2c36e10e716 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 29 Sep 2023 08:11:58 +0200
Subject: [PATCH 20/79] Handle look and feel

---
 omero_figure/static/figure/css/figure.css | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/omero_figure/static/figure/css/figure.css b/omero_figure/static/figure/css/figure.css
index 332b65788..ad108bb5c 100644
--- a/omero_figure/static/figure/css/figure.css
+++ b/omero_figure/static/figure/css/figure.css
@@ -233,6 +233,11 @@
         height: 14px;
         border-radius: 5px;
     }
+    #vp_zoom_value {
+        float: right;
+        width: 50px;
+        margin-top: 5px;
+    }
     .toggle_channel {
         border-radius: 6px 6px 6px 6px;
         margin: 2px;

From e86749e612b9ac9227ca741127f1831752b891b8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Mon, 2 Oct 2023 10:45:15 +0200
Subject: [PATCH 21/79] Add right vertical choice in drop-down list

---
 src/js/views/right_panel_view.js              | 2 +-
 src/templates/labels_form_inner_template.html | 7 ++++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index c91641e52..53dca6857 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -507,7 +507,7 @@
         render: function() {
 
             var self = this,
-                positions = {'top':{}, 'bottom':{}, 'left':{}, 'leftvert':{}, 'right':{},
+                positions = {'top':{}, 'bottom':{}, 'left':{}, 'leftvert':{}, 'right':{},'rightvert':{},
                     'topleft':{}, 'topright':{}, 'bottomleft':{}, 'bottomright':{}};
             this.models.forEach(function(m){
                 // group labels by position
diff --git a/src/templates/labels_form_inner_template.html b/src/templates/labels_form_inner_template.html
index efb061fc7..a0298f252 100644
--- a/src/templates/labels_form_inner_template.html
+++ b/src/templates/labels_form_inner_template.html
@@ -74,7 +74,7 @@
         <button type="button" class="label-position btn btn-default btn-sm dropdown-toggle" 
                 title="Position" data-toggle="dropdown">
             <span data-position="<%= position %>" class="labelicon-<%= position %> glyphicon 
-                <% if (_.contains(['top','bottom','left','leftvert','right'],position)) print('glyphicon-log-out'); else {print('glyphicon-new-window')} %>"></span>
+                <% if (_.contains(['top','bottom','left','leftvert','right','rightvert'],position)) print('glyphicon-log-out'); else {print('glyphicon-new-window')} %>"></span>
             <span class="caret"></span>
         </button>
         <ul class="dropdown-menu" role="menu">
@@ -112,6 +112,11 @@
             <li><a href="#">
                 <span data-position="right" class="labelicon-right glyphicon glyphicon-log-out"></span> Right</a>
             </li>
+            <li><a href="#">
+                <span data-position="rightvert" class="labelicon-rightvert glyphicon glyphicon-log-out"></span> 
+                Right vertical
+            </a>
+        </li>
             <li><a href="#">
                 <span data-position="bottom" class="labelicon-bottom glyphicon glyphicon-log-out"></span> Bottom</a>
             </li>

From b170e220d7a6c0492b717e0d96d078ae9f8cf9db Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Mon, 2 Oct 2023 11:13:32 +0200
Subject: [PATCH 22/79] Update bounding box size + add rightvert to the panel
 view

---
 src/js/models/panel_model.js | 12 +++++++++++-
 src/js/views/panel_view.js   |  6 +++---
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 7e3c02a67..b65e860fa 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -877,7 +877,17 @@
 
         getBoundingBoxRight: function() {
             // Ignore right (horizontal) labels since we don't know how long they are
-            return this.get('x') + this.get('width');
+            // but include right vertical labels
+            var labels = this.get("labels");
+            var x = this.get('x') + this.get('width');
+            // get labels by position
+            var right_labels = labels.filter(function(l) {return l.position === 'rightvert'});
+            // offset by font-size of each
+            x = right_labels.reduce(function(prev, l){
+                return prev + (LINE_HEIGHT * l.size);
+            }, x);
+
+            return x;
         },
 
         getBoundingBoxBottom: function() {
diff --git a/src/js/views/panel_view.js b/src/js/views/panel_view.js
index ca9f1599f..8a7a1a766 100644
--- a/src/js/views/panel_view.js
+++ b/src/js/views/panel_view.js
@@ -171,7 +171,7 @@
                 self = this,
                 positions = {
                     'top':[], 'bottom':[], 'left':[], 'right':[],
-                    'leftvert':[],
+                    'leftvert':[],'rightvert':[],
                     'topleft':[], 'topright':[],
                     'bottomleft':[], 'bottomright':[]
                 };
@@ -182,7 +182,7 @@
                 var ljson = $.extend(true, {}, l);
                 // If label is same color as page (and is outside of panel)
                 if (ljson.color.toLowerCase() == self.page_color.toLowerCase() &&
-                        ["top", "bottom", "left", "right", "leftvert"].indexOf(l.position) > -1 ) {
+                        ["top", "bottom", "left", "right", "leftvert", "rightvert"].indexOf(l.position) > -1 ) {
                     // If black -> white, otherwise -> black
                     if (ljson.color === '000000') {
                         ljson.color = 'ffffff';
@@ -249,7 +249,7 @@
             _.each(positions, function(lbls, p) {
                 var json = {'position':p, 'labels':lbls};
                 if (lbls.length === 0) return;
-                if (p == 'leftvert') {  // vertical
+                if (p == 'leftvert'|| p == 'rightvert') {  // vertical
                     html += self.label_vertical_template(json);
                 } else if (p == 'left' || p == 'right') {
                     html += self.label_table_template(json);

From 85bd8c36fe6d6d0409fb7452922c8446c704e415 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Mon, 2 Oct 2023 13:29:00 +0200
Subject: [PATCH 23/79] Add css labels

---
 omero_figure/static/figure/css/figure.css      | 18 ++++++++++++++++++
 src/js/views/panel_view.js                     |  7 ++++++-
 .../labels/label_right_vertical_template.html  |  8 ++++++++
 3 files changed, 32 insertions(+), 1 deletion(-)
 create mode 100644 src/templates/labels/label_right_vertical_template.html

diff --git a/omero_figure/static/figure/css/figure.css b/omero_figure/static/figure/css/figure.css
index 332b65788..7f78579ee 100644
--- a/omero_figure/static/figure/css/figure.css
+++ b/omero_figure/static/figure/css/figure.css
@@ -344,6 +344,9 @@
     .left_vlabels>div {
         margin-bottom: 5px;
     }
+    .right_vlabels>div {
+        margin-bottom: 5px;
+    }
     .label_middle, .label_middle table, .label_middle td {
         height:100%;
         width:10000px;
@@ -362,11 +365,26 @@
         -webkit-transform: rotate(-90deg);
         transform: rotate(-90deg);
     }
+    .right_vlabels{
+        position: absolute;
+        left: 100%;
+        height: 300%;
+        top: -100%;
+        width: 300%;
+        text-align: center;
+        -webkit-transform: rotate(90deg);
+        transform: rotate(90deg);
+    }
     .left_vlabels>div {
         position: absolute;
         bottom:0;
         width:100%;
     }
+    .right_vlabels>div {
+        position: absolute;
+        bottom:0;
+        width:100%;
+    }
 
     .previewIdChange .glyphicon-ok {
         color: #0f0;
diff --git a/src/js/views/panel_view.js b/src/js/views/panel_view.js
index 8a7a1a766..3bbfa4f5f 100644
--- a/src/js/views/panel_view.js
+++ b/src/js/views/panel_view.js
@@ -7,6 +7,7 @@
         template: JST["src/templates/figure_panel_template.html"],
         label_template: JST["src/templates/labels/label_template.html"],
         label_vertical_template: JST["src/templates/labels/label_vertical_template.html"],
+        label_right_vertical_template: JST["src/templates/labels/label_right_vertical_template.html"],
         label_table_template: JST["src/templates/labels/label_table_template.html"],
         scalebar_template: JST["src/templates/scalebar_panel_template.html"],
 
@@ -76,6 +77,7 @@
 
             // container needs to be square for rotation to vertical
             $('.left_vlabels', this.$el).css('width', 3 * h + 'px');
+            $('.right_vlabels', this.$el).css('width', 3 * h + 'px');
 
             // update the img within the panel
             var zoom = this.model.get('zoom'),
@@ -249,8 +251,10 @@
             _.each(positions, function(lbls, p) {
                 var json = {'position':p, 'labels':lbls};
                 if (lbls.length === 0) return;
-                if (p == 'leftvert'|| p == 'rightvert') {  // vertical
+                if (p == 'leftvert') {  // vertical
                     html += self.label_vertical_template(json);
+                } else if (p == 'rightvert') {
+                    html += self.label_right_vertical_template(json);
                 } else if (p == 'left' || p == 'right') {
                     html += self.label_table_template(json);
                 } else {
@@ -261,6 +265,7 @@
 
             // need to force update of vertical labels layout
             $('.left_vlabels', self.$el).css('width', 3 * self.$el.height() + 'px');
+            $('.right_vlabels', self.$el).css('width', 3 * self.$el.height() + 'px');
 
             return this;
         },
diff --git a/src/templates/labels/label_right_vertical_template.html b/src/templates/labels/label_right_vertical_template.html
new file mode 100644
index 000000000..61ed50c16
--- /dev/null
+++ b/src/templates/labels/label_right_vertical_template.html
@@ -0,0 +1,8 @@
+
+<div class="label_layout right_vlabels">
+    <div>
+        <% _.each(labels, function(l, i) { %>
+            <div style='color:#<%= l.color %>; font-size:<%= l.size %>px'><%= l.text %></div>
+        <% }); %>
+    </div>
+</div>

From 82731799272aea8fbfacf45253c17c3ab1c02236 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Mon, 2 Oct 2023 17:23:22 +0200
Subject: [PATCH 24/79] Add right and bottom buttons

---
 omero_figure/templates/figure/index.html | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index 6eae81088..b03178650 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -865,6 +865,9 @@ <h5>Example Label</h5>
                         <button type="button" class="aleft btn btn-default btn-sm" title="Align Left" disabled="disabled">
                             <span class="glyphicon glyphicon-align-left"></span>
                         </button>
+                        <button type="button" class="aleft btn btn-default btn-sm" title="Align Right" disabled="disabled">
+                            <span class="glyphicon glyphicon-align-right"></span>
+                        </button>
                         <button type="button" class="agrid btn btn-default btn-sm" title="Align To Grid" disabled="disabled">
                             <span class="glyphicon glyphicon-th"></span>
                         </button>
@@ -890,6 +893,9 @@ <h5>Example Label</h5>
                         <button type="button" class="atop btn btn-default btn-sm rotate-font" title="Align Top" disabled="disabled">
                             <span class="glyphicon glyphicon-align-right"></span>
                         </button>
+                        <button type="button" class="atop btn btn-default btn-sm rotate-font" title="Align Bottom" disabled="disabled">
+                            <span class="glyphicon glyphicon-align-left"></span>
+                        </button>
                         <button type="button" class="btn btn-default btn-sm dropdown-toggle" title="Align Sizes"
                             disabled="disabled" data-toggle="dropdown">
                             <span class="glyphicon glyphicon-fullscreen"></span>

From abbf9abc22f2ceb8d23a85dce2c61fb5e43d2171 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 3 Oct 2023 08:38:44 +0200
Subject: [PATCH 25/79] make the right and bottom alignment

---
 omero_figure/templates/figure/index.html |  4 ++--
 src/js/models/figure_model.js            | 27 ++++++++++++++++++++++++
 src/js/views/figure_view.js              | 12 +++++++++++
 3 files changed, 41 insertions(+), 2 deletions(-)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index b03178650..380c44cfa 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -865,7 +865,7 @@ <h5>Example Label</h5>
                         <button type="button" class="aleft btn btn-default btn-sm" title="Align Left" disabled="disabled">
                             <span class="glyphicon glyphicon-align-left"></span>
                         </button>
-                        <button type="button" class="aleft btn btn-default btn-sm" title="Align Right" disabled="disabled">
+                        <button type="button" class="aright btn btn-default btn-sm" title="Align Right" disabled="disabled">
                             <span class="glyphicon glyphicon-align-right"></span>
                         </button>
                         <button type="button" class="agrid btn btn-default btn-sm" title="Align To Grid" disabled="disabled">
@@ -893,7 +893,7 @@ <h5>Example Label</h5>
                         <button type="button" class="atop btn btn-default btn-sm rotate-font" title="Align Top" disabled="disabled">
                             <span class="glyphicon glyphicon-align-right"></span>
                         </button>
-                        <button type="button" class="atop btn btn-default btn-sm rotate-font" title="Align Bottom" disabled="disabled">
+                        <button type="button" class="abottom btn btn-default btn-sm rotate-font" title="Align Bottom" disabled="disabled">
                             <span class="glyphicon glyphicon-align-left"></span>
                         </button>
                         <button type="button" class="btn btn-default btn-sm dropdown-toggle" title="Align Sizes"
diff --git a/src/js/models/figure_model.js b/src/js/models/figure_model.js
index cced4e8cc..4502fe917 100644
--- a/src/js/models/figure_model.js
+++ b/src/js/models/figure_model.js
@@ -610,6 +610,20 @@
             });
         },
 
+        
+        align_right: function() {
+            var selected = this.getSelected(),
+                x_vals = [];
+            selected.forEach(function(p){
+                x_vals.push(p.get('x'));
+            });
+            var max_x = Math.max.apply(window, x_vals);
+
+            selected.forEach(function(p){
+                p.save('x', max_x);
+            });
+        },
+
         align_top: function() {
             var selected = this.getSelected(),
                 y_vals = [];
@@ -623,6 +637,19 @@
             });
         },
 
+        align_bottom: function() {
+            var selected = this.getSelected(),
+                y_vals = [];
+            selected.forEach(function(p){
+                y_vals.push(p.get('y'));
+            });
+            var max_y = Math.max.apply(window, y_vals);
+
+            selected.forEach(function(p){
+                p.save('y', max_y);
+            });
+        },
+
         align_grid: function(gridGap) {
             var sel = this.getSelected(),
                 top_left = this.get_top_left_panel(sel),
diff --git a/src/js/views/figure_view.js b/src/js/views/figure_view.js
index 1c4bd3da0..ed06b905d 100644
--- a/src/js/views/figure_view.js
+++ b/src/js/views/figure_view.js
@@ -867,6 +867,8 @@
             "click .aleft": "align_left",
             "click .agrid": "align_grid",
             "click .atop": "align_top",
+            "click .aright": "align_right",
+            "click .abottom": "align_bottom",
 
             "click .awidth": "align_width",
             "click .aheight": "align_height",
@@ -917,6 +919,16 @@
             this.model.align_top();
         },
 
+        align_right: function(event) {
+            event.preventDefault();
+            this.model.align_right();
+        },
+
+        align_bottom: function(event) {
+            event.preventDefault();
+            this.model.align_bottom();
+        },
+
         custom_grid_gap: function() {
             let current = $("#custom_grid_gap").attr("value");
             // simple propmt to ask user for custom grid gap

From dcecb7606bc82ca224a8d0e4aa2e224d92f9def2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 3 Oct 2023 09:26:59 +0200
Subject: [PATCH 26/79] Add z-offset option in labels

---
 src/js/models/panel_model.js | 36 ++++++++++++++++++++++++++++++++++--
 src/js/views/panel_view.js   |  4 ++++
 2 files changed, 38 insertions(+), 2 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 7e3c02a67..28c2d86b6 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -353,6 +353,38 @@
             return text;
         },
 
+        get_z_label_text: function(format, ref_idx, dec_prec) {
+            var text = "";
+            if (this.get('z_projection')) {
+                var start = this.get('z_start'),
+                    end = this.get('z_end');
+                if (format === "pixel") {
+                    text = "" + (start+1) + " - " + (end+1);
+                } else if (format === "unit") {
+                    start = (start * z_size).toFixed(dec_prec)
+                    end = (end * z_size).toFixed(dec_prec)
+                    text = ""+ start +" "+ z_symbol
+                           + " - " + end +" "+ z_symbol
+                }
+            }
+            else {
+                var theZ = this.get('theZ'),
+                deltaZ = this.get('deltaZ')[theZ] || 0;
+
+                if (ref_idx) {
+                    var shift = this.get('deltaZ')[parseInt(ref_idx)-1];
+                    deltaZ = shift==null ? deltaZ : deltaZ-shift;
+                }
+
+                if (format === "pixel") {
+                    text = "" + (theZ + 1);
+                } else if (format === "unit") {
+                    text = ""+ (deltaZ * z_size).toFixed(dec_prec) +" "+ z_symbol
+                }
+            }
+            return text
+        },
+
         get_view_label_text: function(property, format, dec_prec) {
             if (format === "px") format = "pixel";
 
@@ -375,7 +407,7 @@
             dec_prec = dec_prec==null ? 2 : dec_prec; // 2 is the default precision
 
             var text = "";
-            if (property === "z") {
+            /*if (property === "z") {
                 if (this.get('z_projection')) {
                     var start = this.get('z_start'),
                         end = this.get('z_end');
@@ -397,7 +429,7 @@
                     }
                 }
                 return text
-            }
+            }*/
 
             var value = this.getViewportAsRect()[property];
             if (property === "rotation") {
diff --git a/src/js/views/panel_view.js b/src/js/views/panel_view.js
index ca9f1599f..7066b15cf 100644
--- a/src/js/views/panel_view.js
+++ b/src/js/views/panel_view.js
@@ -226,6 +226,10 @@
                             format = prop_nf[1] ? prop_nf[1] : "pixel";
                             precision = param_dict["precision"] !== undefined ? param_dict["precision"] : 2; // decimal places default to 2
                             label_value = self.model.get_view_label_text(prop_nf[0], format, precision);
+                        } else if (['z'].includes(prop_nf[0])){
+                            format = prop_nf[1] ? prop_nf[1] : "pixel";
+                            precision = param_dict["precision"] !== undefined ? param_dict["precision"] : 2; // decimal places default to 2
+                            label_value = self.model.get_z_label_text(format, param_dict["offset"], precision);
                         } else if (['channels', 'c'].includes(prop_nf[0])) {
                             label_value = self.model.get_channels_label_text();
                         }

From 18e9ee52c4f2c8957e115b745d1300ccf692d8e9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 3 Oct 2023 10:00:55 +0200
Subject: [PATCH 27/79] Integrate the z-offset in the existing functions and
 fix bugs

---
 src/js/models/panel_model.js | 49 +++++++++---------------------------
 src/js/views/panel_view.js   |  6 +----
 2 files changed, 13 insertions(+), 42 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 28c2d86b6..459e1a42d 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -353,39 +353,7 @@
             return text;
         },
 
-        get_z_label_text: function(format, ref_idx, dec_prec) {
-            var text = "";
-            if (this.get('z_projection')) {
-                var start = this.get('z_start'),
-                    end = this.get('z_end');
-                if (format === "pixel") {
-                    text = "" + (start+1) + " - " + (end+1);
-                } else if (format === "unit") {
-                    start = (start * z_size).toFixed(dec_prec)
-                    end = (end * z_size).toFixed(dec_prec)
-                    text = ""+ start +" "+ z_symbol
-                           + " - " + end +" "+ z_symbol
-                }
-            }
-            else {
-                var theZ = this.get('theZ'),
-                deltaZ = this.get('deltaZ')[theZ] || 0;
-
-                if (ref_idx) {
-                    var shift = this.get('deltaZ')[parseInt(ref_idx)-1];
-                    deltaZ = shift==null ? deltaZ : deltaZ-shift;
-                }
-
-                if (format === "pixel") {
-                    text = "" + (theZ + 1);
-                } else if (format === "unit") {
-                    text = ""+ (deltaZ * z_size).toFixed(dec_prec) +" "+ z_symbol
-                }
-            }
-            return text
-        },
-
-        get_view_label_text: function(property, format, dec_prec) {
+        get_view_label_text: function(property, format, ref_idx, dec_prec) {
             if (format === "px") format = "pixel";
 
             if (property === "w") property = "width";
@@ -407,7 +375,7 @@
             dec_prec = dec_prec==null ? 2 : dec_prec; // 2 is the default precision
 
             var text = "";
-            /*if (property === "z") {
+            if (property === "z") {
                 if (this.get('z_projection')) {
                     var start = this.get('z_start'),
                         end = this.get('z_end');
@@ -421,15 +389,22 @@
                     }
                 }
                 else {
-                    var theZ = this.get('theZ');
+                    var theZ = this.get('theZ'),
+                    sizeZ = this.get('sizeZ');
+
+                    var deltaZ = theZ;
+                    if (ref_idx) {
+                        var shift = theZ + parseInt(ref_idx)
+                        deltaZ = shift < 0 ? 0 : (shift > sizeZ ? sizeZ : shift);
+                    }
                     if (format === "pixel") {
                         text = "" + (theZ + 1);
                     } else if (format === "unit") {
-                        text = ""+ (theZ * z_size).toFixed(dec_prec) +" "+ z_symbol
+                        text = ""+ (deltaZ * z_size).toFixed(dec_prec) +" "+ z_symbol
                     }
                 }
                 return text
-            }*/
+            }
 
             var value = this.getViewportAsRect()[property];
             if (property === "rotation") {
diff --git a/src/js/views/panel_view.js b/src/js/views/panel_view.js
index 7066b15cf..ded7973f7 100644
--- a/src/js/views/panel_view.js
+++ b/src/js/views/panel_view.js
@@ -225,11 +225,7 @@
                         } else if (['x', 'y', 'z', 'width', 'height', 'w', 'h', 'rotation', 'rot'].includes(prop_nf[0])){
                             format = prop_nf[1] ? prop_nf[1] : "pixel";
                             precision = param_dict["precision"] !== undefined ? param_dict["precision"] : 2; // decimal places default to 2
-                            label_value = self.model.get_view_label_text(prop_nf[0], format, precision);
-                        } else if (['z'].includes(prop_nf[0])){
-                            format = prop_nf[1] ? prop_nf[1] : "pixel";
-                            precision = param_dict["precision"] !== undefined ? param_dict["precision"] : 2; // decimal places default to 2
-                            label_value = self.model.get_z_label_text(format, param_dict["offset"], precision);
+                            label_value = self.model.get_view_label_text(prop_nf[0], format, param_dict["offset"], precision);  
                         } else if (['channels', 'c'].includes(prop_nf[0])) {
                             label_value = self.model.get_channels_label_text();
                         }

From b3061c7bb3a78f8eeb4a7ec8bbaa2f0ed38c9020 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 3 Oct 2023 10:09:55 +0200
Subject: [PATCH 28/79] extend offset beyond z-limits

---
 src/js/models/panel_model.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 459e1a42d..1f0a27f88 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -394,8 +394,8 @@
 
                     var deltaZ = theZ;
                     if (ref_idx) {
-                        var shift = theZ + parseInt(ref_idx)
-                        deltaZ = shift < 0 ? 0 : (shift > sizeZ ? sizeZ : shift);
+                        var shift = parseInt(ref_idx)
+                        deltaZ = shift == null ? theZ : theZ + shift;
                     }
                     if (format === "pixel") {
                         text = "" + (theZ + 1);

From 64c7983da8dc558db860db5e0ded3b5855932973 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 3 Oct 2023 10:16:09 +0200
Subject: [PATCH 29/79] Clean code

---
 src/js/models/panel_model.js | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 1f0a27f88..044e4c070 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -389,10 +389,9 @@
                     }
                 }
                 else {
-                    var theZ = this.get('theZ'),
-                    sizeZ = this.get('sizeZ');
-
+                    var theZ = this.get('theZ');
                     var deltaZ = theZ;
+                    
                     if (ref_idx) {
                         var shift = parseInt(ref_idx)
                         deltaZ = shift == null ? theZ : theZ + shift;

From c48a1ef217deb307071ad2f9c98ff694919e411e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 6 Oct 2023 08:22:59 +0200
Subject: [PATCH 30/79] fix case where offset is NaN

---
 src/js/models/panel_model.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 044e4c070..683525ca7 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -394,7 +394,9 @@
                     
                     if (ref_idx) {
                         var shift = parseInt(ref_idx)
-                        deltaZ = shift == null ? theZ : theZ + shift;
+                        if(!isNaN(shift)){
+                            deltaZ = theZ + shift;
+                        }
                     }
                     if (format === "pixel") {
                         text = "" + (theZ + 1);

From 1bd2e901ac1d2d8bd785202ab275325e72af1247 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 6 Oct 2023 08:34:36 +0200
Subject: [PATCH 31/79] Fix bug when images don't have the same dimensions

---
 src/js/models/figure_model.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/js/models/figure_model.js b/src/js/models/figure_model.js
index 4502fe917..fe6050b9e 100644
--- a/src/js/models/figure_model.js
+++ b/src/js/models/figure_model.js
@@ -615,12 +615,12 @@
             var selected = this.getSelected(),
                 x_vals = [];
             selected.forEach(function(p){
-                x_vals.push(p.get('x'));
+                x_vals.push(p.get('x') + p.get('width'));
             });
             var max_x = Math.max.apply(window, x_vals);
 
             selected.forEach(function(p){
-                p.save('x', max_x);
+                p.save('x', max_x - p.get('width'));
             });
         },
 
@@ -641,12 +641,12 @@
             var selected = this.getSelected(),
                 y_vals = [];
             selected.forEach(function(p){
-                y_vals.push(p.get('y'));
+                y_vals.push(p.get('y') + p.get('height'));
             });
             var max_y = Math.max.apply(window, y_vals);
 
             selected.forEach(function(p){
-                p.save('y', max_y);
+                p.save('y', max_y - p.get('height'));
             });
         },
 

From 06f4bb5ce17119ea23fcee62b0e6f1372d62513b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 6 Oct 2023 10:18:29 +0200
Subject: [PATCH 32/79] Add right vertical to Figure_to_pdf script

---
 docs/figure_file_format.rst                   |  2 +-
 .../omero/figure_scripts/Figure_To_Pdf.py     | 33 +++++++++++++++----
 2 files changed, 28 insertions(+), 7 deletions(-)

diff --git a/docs/figure_file_format.rst b/docs/figure_file_format.rst
index 3218d2483..e56e5ee9f 100644
--- a/docs/figure_file_format.rst
+++ b/docs/figure_file_format.rst
@@ -105,7 +105,7 @@ Optional settings for each panel::
     ],
 
     // labels on the panel
-    // positions are: top, left, right, leftvert, bottom, topleft, topright, bottomleft, bottomright
+    // positions are: top, left, right, leftvert, rightvert, bottom, topleft, topright, bottomleft, bottomright
     "labels": [
         {
             "text": "GFP-INCENP",
diff --git a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
index a4652c9ff..1c24f142c 100644
--- a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
+++ b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
@@ -1153,7 +1153,7 @@ def draw_labels(self, panel, page):
 
         # group by 'position':
         positions = {'top': [], 'bottom': [], 'left': [],
-                     'leftvert': [], 'right': [],
+                     'leftvert': [], 'right': [], 'rightvert': [],
                      'topleft': [], 'topright': [],
                      'bottomleft': [], 'bottomright': []}
 
@@ -1310,7 +1310,7 @@ def draw_labels(self, panel, page):
             page_color = self.figure_json.get('page_color', 'ffffff').lower()
             label_color = l['color'].lower()
             label_on_page = pos in ('left', 'right', 'top',
-                                    'bottom', 'leftvert')
+                                    'bottom', 'leftvert', 'rightvert')
             if label_on_page:
                 if label_color == '000000' and page_color == '000000':
                     l['color'] = 'ffffff'
@@ -1395,7 +1395,14 @@ def draw_lab(label, lx, ly, align='left'):
                 labels.reverse()
                 for l in labels:
                     lx = lx - l['size'] - spacer
-                    draw_lab(l, lx, ly, align='vertical')
+                    draw_lab(l, lx, ly, align='left-vertical')
+            elif key == 'rightvert':
+                lx = x + width + spacer
+                ly = y + (height/2)
+                labels.reverse()
+                for l in labels:
+                    lx = lx + l['size'] + spacer
+                    draw_lab(l, lx, ly, align='right-vertical')
 
     def draw_scalebar(self, panel, region_width, page):
         """
@@ -2024,7 +2031,7 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
             x = x - para_width
         elif (align == "left"):
             pass
-        elif align == 'vertical':
+        elif align == 'left-vertical':
             # Switch axes
             c.rotate(90)
             px = x
@@ -2033,6 +2040,15 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
             # Align center
             alignment = TA_CENTER
             x = x - (para_width/2)
+        elif align == 'right-vertical':
+            # Switch axes
+            c.rotate(-90)
+            px = x
+            x = y
+            y = -px
+            # Align center
+            alignment = TA_CENTER
+            x = x + (para_width/2)
 
         # set fully opaque background color to avoid transparent text
         c.setFillColorRGB(0, 0, 0, 1)
@@ -2050,8 +2066,10 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
         para.drawOn(c, x, y - h + int(fontsize * 0.25))
 
         # Rotate back again
-        if align == 'vertical':
+        if align == 'left-vertical':
             c.rotate(-90)
+        elif align == 'right-vertical':
+            c.rotate(90)
 
     def draw_scalebar_line(self, x, y, x2, y2, width, rgb):
         """ Adds line to PDF. Overwritten for TIFF below """
@@ -2308,9 +2326,12 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
 
         temp_label = self.draw_temp_label(text, fontsize, rgb)
 
-        if align == "vertical":
+        if align == "left-vertical":
             temp_label = temp_label.rotate(90, expand=True)
             y = y - (temp_label.size[1]/2)
+        elif align == "right-vertical":
+            temp_label = temp_label.rotate(-90, expand=True)
+            y = y - (temp_label.size[1]/2)
         elif align == "center":
             x = x - (temp_label.size[0] / 2)
         elif align == "right":

From c023b75f9af397487b857ca15d0f8951831f2f36 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 10 Oct 2023 08:42:41 +0200
Subject: [PATCH 33/79] Fix bug in alignment

---
 omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
index 1c24f142c..aa0adfea5 100644
--- a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
+++ b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
@@ -2044,11 +2044,11 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
             # Switch axes
             c.rotate(-90)
             px = x
-            x = y
-            y = -px
+            x = -y
+            y = px
             # Align center
             alignment = TA_CENTER
-            x = x + (para_width/2)
+            x = x - (para_width/2)
 
         # set fully opaque background color to avoid transparent text
         c.setFillColorRGB(0, 0, 0, 1)

From 88c9e38a1f531f0870df71f77dc28aa4a1a26573 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 10 Oct 2023 08:54:00 +0200
Subject: [PATCH 34/79] Fix figure title shadowed issue

---
 omero_figure/static/figure/css/figure.css | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/omero_figure/static/figure/css/figure.css b/omero_figure/static/figure/css/figure.css
index 332b65788..ade21209d 100644
--- a/omero_figure/static/figure/css/figure.css
+++ b/omero_figure/static/figure/css/figure.css
@@ -123,7 +123,7 @@
         line-height: 20px;
         padding: 12px;
         position: absolute;
-        right: 450px;
+        right: 520px;
         text-align: center;
         height: 100%;
     }
@@ -705,6 +705,10 @@
     .navbar>div.container {
         max-width: 100%;
     }
+    #alignment-toolbars {
+        padding-right: 0;
+        margin-right: -20px;
+    }
     /** Add my class to boost size of font icons **/
     .icon-buttons {
         margin-right: 20px;

From 26bef019c116224b3192b20e7eea89a794b4af05 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 17 Oct 2023 22:07:27 +0100
Subject: [PATCH 35/79] Use font.getbbox() instead of font.getsize()

Since font.getsize() is removed in Pillow 10
---
 omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
index a4652c9ff..215ae3aff 100644
--- a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
+++ b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
@@ -573,7 +573,7 @@ def draw_shape_label(self, shape, bounds):
         except Exception:
             font = ImageFont.load(
                 '%s/pilfonts/B%0.2d.pil' % (self.GATEWAYPATH, size))
-        textsize = font.getsize(text)
+        textsize = font.getbbox(text)[2:]
         xy = (center[0] - textsize[0] / 2.0, center[1] - textsize[1] / 2.0)
         self.draw.text(xy, text, fill=rgba, font=font)
 
@@ -2230,7 +2230,7 @@ def draw_temp_label(self, text, fontsize, rgb):
         heights = []
         for t in tokens:
             font = self.get_font(fontsize, t['bold'], t['italics'])
-            txt_w, txt_h = font.getsize(t['text'])
+            txt_w, txt_h = font.getbbox(t['text'])[2:]
             widths.append(txt_w)
             heights.append(txt_h)
 
@@ -2243,7 +2243,7 @@ def draw_temp_label(self, text, fontsize, rgb):
         w = 0
         for t in tokens:
             font = self.get_font(fontsize, t['bold'], t['italics'])
-            txt_w, txt_h = font.getsize(t['text'])
+            txt_w, txt_h = font.getbbox(t['text'])[2:]
             textdraw.text((w, 0), t['text'], font=font, fill=rgb)
             w += txt_w
         return temp_label

From e857ab224e255adeef21c50b9cd19c02ae988eee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 18 Oct 2023 08:28:14 +0200
Subject: [PATCH 36/79] Add label left shifting

---
 omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
index aa0adfea5..254a3a476 100644
--- a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
+++ b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
@@ -2332,6 +2332,7 @@ def draw_text(self, text, x, y, fontsize, rgb, align="center"):
         elif align == "right-vertical":
             temp_label = temp_label.rotate(-90, expand=True)
             y = y - (temp_label.size[1]/2)
+            x = x - temp_label.size[0]
         elif align == "center":
             x = x - (temp_label.size[0] / 2)
         elif align == "right":

From 15df5dc1c09feda3ff37c994474db5c8b7c96cb0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 18 Oct 2023 17:19:35 +0200
Subject: [PATCH 37/79] Add z-offset value to the label

---
 src/js/models/panel_model.js | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 683525ca7..cca3b2eae 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -400,8 +400,14 @@
                     }
                     if (format === "pixel") {
                         text = "" + (theZ + 1);
+                        if (!isNaN(shift)){
+                            text += " off: "+shift
+                        }
                     } else if (format === "unit") {
                         text = ""+ (deltaZ * z_size).toFixed(dec_prec) +" "+ z_symbol
+                        if (!isNaN(shift)){
+                            text += " off: "+shift
+                        }
                     }
                 }
                 return text

From d8e76016734eb2553cdae946fd74655022362d46 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 18 Oct 2023 17:25:15 +0200
Subject: [PATCH 38/79] Refactor

---
 src/js/models/panel_model.js | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index cca3b2eae..037d73ab1 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -391,23 +391,22 @@
                 else {
                     var theZ = this.get('theZ');
                     var deltaZ = theZ;
-                    
+                    var shift;
+
                     if (ref_idx) {
-                        var shift = parseInt(ref_idx)
+                        shift = parseInt(ref_idx)
                         if(!isNaN(shift)){
                             deltaZ = theZ + shift;
                         }
                     }
                     if (format === "pixel") {
                         text = "" + (theZ + 1);
-                        if (!isNaN(shift)){
-                            text += " off: "+shift
-                        }
+                        
                     } else if (format === "unit") {
                         text = ""+ (deltaZ * z_size).toFixed(dec_prec) +" "+ z_symbol
-                        if (!isNaN(shift)){
-                            text += " off: "+shift
-                        }
+                    }
+                    if (!isNaN(shift)){
+                        text += " off: "+shift
                     }
                 }
                 return text

From 7212b38c196567b04cbc0b23d1949452016a2a4d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 18 Oct 2023 18:00:30 +0200
Subject: [PATCH 39/79] Add Time offset to label

---
 src/js/models/panel_model.js | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 037d73ab1..cfe19ec02 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -294,7 +294,9 @@
                 deltaT = this.get('deltaT')[theT] || 0,
                 text = "", h, m, s;
 
+            var shiftIdx;
             if (ref_idx) {
+                shiftIdx = parseInt(ref_idx)
                 var shift = this.get('deltaT')[parseInt(ref_idx)-1];
                 deltaT = shift==null ? deltaT : deltaT-shift;
             }
@@ -331,6 +333,10 @@
             if (["0"+dec_str+" s", "0"+dec_str+" mins", "0:00"+dec_str, "0:00:00"+dec_str].indexOf(text) > -1) {
                 isNegative = false;
             }
+
+            if(!isNaN(shiftIdx)){
+                text += " off: "+shiftIdx   
+            }
             return (isNegative ? '-' : '') + text;
         },
 

From 6bb1381aadf8f285a05ec016c799b9b22f9b78e9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 19 Oct 2023 08:48:01 +0200
Subject: [PATCH 40/79] Remove addings in label; modified the index label
 accordingly to the offset and fix bug on time offset

---
 src/js/models/panel_model.js | 19 +++++++------------
 1 file changed, 7 insertions(+), 12 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index cfe19ec02..14bc6fad7 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -297,8 +297,8 @@
             var shiftIdx;
             if (ref_idx) {
                 shiftIdx = parseInt(ref_idx)
-                var shift = this.get('deltaT')[parseInt(ref_idx)-1];
-                deltaT = shift==null ? deltaT : deltaT-shift;
+                var shift = this.get('deltaT')[shiftIdx];
+                deltaT = shift==null ? deltaT : shift;
             }
             var isNegative = (deltaT < 0);
             deltaT = Math.abs(deltaT);
@@ -306,7 +306,9 @@
             var padlen = dec_prec>0 ? dec_prec+3 : 2;
             if (format === "index") {
                 isNegative = false;
-                text = "" + (theT + 1);
+                if(!isNaN(shiftIdx) && shiftIdx > 0)
+                    text = "" + (theT + shiftIdx + 1);
+                else text = "" + (theT + 1);
             } else if (['milliseconds', 'ms'].includes(format)) {
                 text = (deltaT*1000).toFixed(dec_prec) + " ms";
             } else if (['seconds', 'secs', 's'].includes(format)) {
@@ -334,9 +336,6 @@
                 isNegative = false;
             }
 
-            if(!isNaN(shiftIdx)){
-                text += " off: "+shiftIdx   
-            }
             return (isNegative ? '-' : '') + text;
         },
 
@@ -397,23 +396,19 @@
                 else {
                     var theZ = this.get('theZ');
                     var deltaZ = theZ;
-                    var shift;
 
                     if (ref_idx) {
-                        shift = parseInt(ref_idx)
+                        var shift = parseInt(ref_idx)
                         if(!isNaN(shift)){
                             deltaZ = theZ + shift;
                         }
                     }
                     if (format === "pixel") {
-                        text = "" + (theZ + 1);
+                        text = "" + (deltaZ + 1);
                         
                     } else if (format === "unit") {
                         text = ""+ (deltaZ * z_size).toFixed(dec_prec) +" "+ z_symbol
                     }
-                    if (!isNaN(shift)){
-                        text += " off: "+shift
-                    }
                 }
                 return text
             }

From ec9b9791002ceb6b8541009611a927b5da473b9b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 20 Oct 2023 08:33:32 +0200
Subject: [PATCH 41/79] Add z symbol

---
 src/js/views/modal_views.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/js/views/modal_views.js b/src/js/views/modal_views.js
index 21d3dc1f7..2961a5db0 100644
--- a/src/js/views/modal_views.js
+++ b/src/js/views/modal_views.js
@@ -296,6 +296,7 @@
                     'pixel_size_x_unit': data.pixel_size.unitX,
                     'pixel_size_z_unit':data.pixel_size.unitZ,
                     'pixel_size_x_symbol': data.pixel_size.symbolX,
+                    'pixel_size_z_symbol': data.pixel_size.symbolZ,
                     'deltaT': data.deltaT,
                 };
                 self.newImg = newImg;

From 21907249e35f04525e40d76e1947641e19be48a3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 20 Oct 2023 09:47:25 +0200
Subject: [PATCH 42/79] Correct bug on positive offset

---
 src/js/models/panel_model.js | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 14bc6fad7..5f6ac15ee 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -297,8 +297,8 @@
             var shiftIdx;
             if (ref_idx) {
                 shiftIdx = parseInt(ref_idx)
-                var shift = this.get('deltaT')[shiftIdx];
-                deltaT = shift==null ? deltaT : shift;
+                var shift = this.get('deltaT')[shiftIdx - 1];
+                deltaT = shift==null ? deltaT : deltaT - shift;
             }
             var isNegative = (deltaT < 0);
             deltaT = Math.abs(deltaT);
@@ -307,7 +307,7 @@
             if (format === "index") {
                 isNegative = false;
                 if(!isNaN(shiftIdx) && shiftIdx > 0)
-                    text = "" + (theT + shiftIdx + 1);
+                    text = "" + (theT - shiftIdx + 1);
                 else text = "" + (theT + 1);
             } else if (['milliseconds', 'ms'].includes(format)) {
                 text = (deltaT*1000).toFixed(dec_prec) + " ms";
@@ -397,16 +397,20 @@
                     var theZ = this.get('theZ');
                     var deltaZ = theZ;
 
+                    var shift;
                     if (ref_idx) {
-                        var shift = parseInt(ref_idx)
-                        if(!isNaN(shift)){
-                            deltaZ = theZ + shift;
-                        }
+                        shift = parseInt(ref_idx)
                     }
                     if (format === "pixel") {
+                        if(!isNaN(shift)){
+                            deltaZ = theZ - shift;
+                        }
                         text = "" + (deltaZ + 1);
                         
                     } else if (format === "unit") {
+                        if(!isNaN(shift)){
+                            deltaZ = theZ - shift + 1;
+                        }
                         text = ""+ (deltaZ * z_size).toFixed(dec_prec) +" "+ z_symbol
                     }
                 }

From 90522d79f5b3f8e6d1d9257f1ebc676b1e06e193 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 27 Oct 2023 14:38:54 +0200
Subject: [PATCH 43/79] remove offset +1

---
 src/js/models/panel_model.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 5f6ac15ee..17789fd88 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -405,11 +405,11 @@
                         if(!isNaN(shift)){
                             deltaZ = theZ - shift;
                         }
-                        text = "" + (deltaZ + 1);
+                        text = "" + (deltaZ);
                         
                     } else if (format === "unit") {
                         if(!isNaN(shift)){
-                            deltaZ = theZ - shift + 1;
+                            deltaZ = theZ - shift;
                         }
                         text = ""+ (deltaZ * z_size).toFixed(dec_prec) +" "+ z_symbol
                     }

From ffd83e9f002892164815be88036714b3a224d8a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 27 Oct 2023 14:57:14 +0200
Subject: [PATCH 44/79] Update figure to pdf script

---
 omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
index a4652c9ff..6647cb0a3 100644
--- a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
+++ b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
@@ -1265,9 +1265,13 @@ def draw_labels(self, panel, page):
                         else:
                             the_z = panel['theZ'] if panel['theZ'] else 0
                             if format == "pixel":
+                                if offset is not None and 1 <= offset:
+                                    the_z -= offset
                                 label_value = str(the_z + 1)
                             elif (format == "unit" and size_z
                                   and the_z < size_z):
+                                if offset is not None and 1 <= offset:
+                                    the_z -= offset
                                 z_pos = "%.*f" % (precision,
                                                   (the_z * pixel_size_z))
                                 label_value = (z_pos + " " + z_symbol)

From 8a28043791f69a0f4a0c9f326bbc5404fa858678 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 27 Oct 2023 15:05:06 +0200
Subject: [PATCH 45/79] Fix offsets

---
 src/js/models/panel_model.js | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 17789fd88..ef8be58ea 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -401,16 +401,12 @@
                     if (ref_idx) {
                         shift = parseInt(ref_idx)
                     }
+                    if(!isNaN(shift)){
+                        deltaZ = theZ - shift;
+                    }
                     if (format === "pixel") {
-                        if(!isNaN(shift)){
-                            deltaZ = theZ - shift;
-                        }
-                        text = "" + (deltaZ);
-                        
+                        text = "" + (deltaZ + 1);
                     } else if (format === "unit") {
-                        if(!isNaN(shift)){
-                            deltaZ = theZ - shift;
-                        }
                         text = ""+ (deltaZ * z_size).toFixed(dec_prec) +" "+ z_symbol
                     }
                 }

From 035da8f937c681f1783cd27c5c69dc53973766d7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 27 Oct 2023 15:12:26 +0200
Subject: [PATCH 46/79] Add Z tips

---
 omero_figure/templates/figure/index.html | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index 6eae81088..a63d5b692 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -595,6 +595,16 @@ <h4>Dynamic properties</h4>
                             <td>Time: [time.seconds; precision=2; offset=3]</td>
                             <td>Time: -0.06 s</td>
                         </tr>
+                        <tr>
+                            <th>Z slice with units position <br/>relative to the 3rd frame</th>
+                            <td>Z: [z.unit; offset=3]</td>
+                            <td>Z: -3.00 &#181;m </td>
+                        </tr>
+                        <tr>
+                            <th>Z slice with index position <br/>relative to the 3rd frame</th>
+                            <td>Z: [z.pixel; offset=3]</td>
+                            <td>Z: -3 </td>
+                        </tr>
                         <tr>
                             <th>Image ID</th>
                             <td>Image ID: [image.id]</td>

From b548f8289313f46511ead98be1bb021e12a59e56 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 27 Oct 2023 15:25:42 +0200
Subject: [PATCH 47/79] coming back to the first behavior for time offset

---
 src/js/models/panel_model.js | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index ef8be58ea..7ae5c9428 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -294,10 +294,8 @@
                 deltaT = this.get('deltaT')[theT] || 0,
                 text = "", h, m, s;
 
-            var shiftIdx;
             if (ref_idx) {
-                shiftIdx = parseInt(ref_idx)
-                var shift = this.get('deltaT')[shiftIdx - 1];
+                var shift = this.get('deltaT')[parseInt(ref_idx) - 1];
                 deltaT = shift==null ? deltaT : deltaT - shift;
             }
             var isNegative = (deltaT < 0);
@@ -306,9 +304,7 @@
             var padlen = dec_prec>0 ? dec_prec+3 : 2;
             if (format === "index") {
                 isNegative = false;
-                if(!isNaN(shiftIdx) && shiftIdx > 0)
-                    text = "" + (theT - shiftIdx + 1);
-                else text = "" + (theT + 1);
+                text = "" + (theT + 1);
             } else if (['milliseconds', 'ms'].includes(format)) {
                 text = (deltaT*1000).toFixed(dec_prec) + " ms";
             } else if (['seconds', 'secs', 's'].includes(format)) {

From 7f49a6e942a8c3b7b15da8e0736960f4bcb44409 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 27 Oct 2023 15:39:11 +0200
Subject: [PATCH 48/79] Enable time index offset

---
 src/js/models/panel_model.js | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 7e3c02a67..21db57e90 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -294,9 +294,11 @@
                 deltaT = this.get('deltaT')[theT] || 0,
                 text = "", h, m, s;
 
+            var shiftIdx;
             if (ref_idx) {
-                var shift = this.get('deltaT')[parseInt(ref_idx)-1];
-                deltaT = shift==null ? deltaT : deltaT-shift;
+                shiftIdx = parseInt(ref_idx)
+                var shift = this.get('deltaT')[shiftIdx - 1];
+                deltaT = shift==null ? deltaT : deltaT - shift;
             }
             var isNegative = (deltaT < 0);
             deltaT = Math.abs(deltaT);
@@ -304,7 +306,9 @@
             var padlen = dec_prec>0 ? dec_prec+3 : 2;
             if (format === "index") {
                 isNegative = false;
-                text = "" + (theT + 1);
+                if(!isNaN(shiftIdx) && !(this.get('deltaT')[shiftIdx - 1] == null))
+                    text = "" + (theT - shiftIdx + 1);
+                else text = "" + (theT + 1);
             } else if (['milliseconds', 'ms'].includes(format)) {
                 text = (deltaT*1000).toFixed(dec_prec) + " ms";
             } else if (['seconds', 'secs', 's'].includes(format)) {

From bc59a7002ab836d521f1dc9458512b6e4068aa33 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 9 Nov 2023 11:03:11 +0000
Subject: [PATCH 49/79] set explicitly ubuntu version

---
 .github/workflows/publish_pypi.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 81eccda37..920566544 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -5,7 +5,7 @@ on: push
 jobs:
   build-n-publish:
     name: Build and publish Python distribution to PyPI
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4

From e1cf2b7940040d26b6fc057b9e83e21a2d62af01 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 9 Nov 2023 11:03:43 +0000
Subject: [PATCH 50/79] set python to 3.9

---
 .github/workflows/publish_pypi.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 920566544..c6cd33037 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -9,6 +9,8 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
       - name: Build a binary wheel and a source tarball
         run: |
           python -mpip install wheel

From 0da40e82e4cee29c00035241911f29efadc92f2b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 9 Nov 2023 14:13:08 +0100
Subject: [PATCH 51/79] Add zoom label template

---
 src/templates/labels_form_inner_template.html | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/templates/labels_form_inner_template.html b/src/templates/labels_form_inner_template.html
index efb061fc7..166d52749 100644
--- a/src/templates/labels_form_inner_template.html
+++ b/src/templates/labels_form_inner_template.html
@@ -52,6 +52,9 @@
                     <li  title="Add a label that shows the current Z-index">
                         <a href="#" data-label="Z: [z.pixel]">Z (pixel or unit)</a>
                     </li>
+                    <li  title="Add a label that shows the current Zoom level">
+                        <a href="#" data-label="[zoom]">Zoom level (%)</a>
+                    </li>
                 </ul>
             </div>
         <% } %>

From 33bde73061ed0ef1b6085cac6a1a6f41e5b1a5cc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 9 Nov 2023 14:34:12 +0100
Subject: [PATCH 52/79] Add zoom label on figure

---
 src/js/models/panel_model.js | 7 +++++++
 src/js/views/panel_view.js   | 2 ++
 2 files changed, 9 insertions(+)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 7e3c02a67..72df926f2 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -104,6 +104,7 @@
                 'pixel_size_x_unit': data.pixel_size_x_unit,
                 'pixel_size_z_unit': data.pixel_size_z_unit,
                 'deltaT': data.deltaT,
+                'zoom':data.zoom,
             };
 
             // theT is not changed unless we have to...
@@ -334,6 +335,12 @@
             return (isNegative ? '-' : '') + text;
         },
 
+        get_zoom_label_text: function() {
+            var text = "" + this.get('zoom') + " %"
+            return text;
+        },
+
+
         get_name_label_text: function(property, format) {
             var text = "";
             if (property === "image") {
diff --git a/src/js/views/panel_view.js b/src/js/views/panel_view.js
index ca9f1599f..49265570c 100644
--- a/src/js/views/panel_view.js
+++ b/src/js/views/panel_view.js
@@ -228,6 +228,8 @@
                             label_value = self.model.get_view_label_text(prop_nf[0], format, precision);
                         } else if (['channels', 'c'].includes(prop_nf[0])) {
                             label_value = self.model.get_channels_label_text();
+                        } else if (['zoom'].includes(prop_nf[0])) {
+                            label_value = self.model.get_zoom_label_text();
                         }
 
                         //If label_value hasn't been created (invalid prop_nf[0])

From 2b4539d06bbeea95cb675bd071abbce311893699 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 9 Nov 2023 14:40:07 +0100
Subject: [PATCH 53/79] Modify Figure-to-pdf script

---
 omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
index a4652c9ff..1cc703b10 100644
--- a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
+++ b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
@@ -1299,6 +1299,8 @@ def draw_labels(self, panel, page):
                             label_value.append(channel["label"])
                     label_value = " ".join(label_value)
 
+                elif  prop_nf[0] in ["zoom"]:
+                    label_value = str(panel["zoom"]) + " %"
                 new_text.append(label_value if label_value else item.group())
                 last_idx = item.end()
 

From 1eabc040f61f4a687bfc6b831d161529154868d0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 9 Nov 2023 14:43:41 +0100
Subject: [PATCH 54/79] Add documentation in teh tips

---
 omero_figure/templates/figure/index.html | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index 6eae81088..4a5d4cfe2 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -605,6 +605,11 @@ <h4>Dynamic properties</h4>
                             <td>Dataset ID: [dataset.id]</td>
                             <td>Dataset ID: 1654</td>
                         </tr>
+                        <tr>
+                            <th>Zoom</th>
+                            <td>[zoom] %</td>
+                            <td>100 %</td>
+                        </tr>
                     </table>
                     <h4>Legend</h4>
                     <p>The figure legend will be included in the PDF info page when the figure is

From 804c456c3ef34350515ddb6210eda5a320bab6cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 9 Nov 2023 14:59:49 +0100
Subject: [PATCH 55/79] Suppress the extra space

---
 omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
index 1cc703b10..b01e80bc8 100644
--- a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
+++ b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
@@ -1299,7 +1299,7 @@ def draw_labels(self, panel, page):
                             label_value.append(channel["label"])
                     label_value = " ".join(label_value)
 
-                elif  prop_nf[0] in ["zoom"]:
+                elif prop_nf[0] in ["zoom"]:
                     label_value = str(panel["zoom"]) + " %"
                 new_text.append(label_value if label_value else item.group())
                 last_idx = item.end()

From c191664aee01c833bb127842be53cf9db581ed1f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 9 Nov 2023 15:30:12 +0100
Subject: [PATCH 56/79] Add radio button to choose all or single key

---
 omero_figure/templates/figure/index.html | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index 6eae81088..41a0d312e 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -698,8 +698,14 @@ <h4 class="modal-title" id="addImagesLabel">Labels from Key-Value Pairs</h4>
                 </div>
                 <form class="labelsFromMapAnnsForm" role="form">
                     <div class="modal-body">
-                        <p>Choose Key
-                            <small class="text-muted">(shows numbers of images)</small>:</p>
+                        <div>                                                    
+                            <input type="radio" id="all-keys" name="kvpChoice" value="all-keys" />
+                            <label for="all-keys">All Keys </label>
+              
+                            <input type="radio" id="single-key" name="kvpChoice" value="one-key" checked />
+                            <label for="one-key">Choose Key <small class="text-muted">(shows numbers of images)</small>:</label>
+                        </div>
+                    
                         <select>
                         </select>
                         <div class="checkbox">

From aa8d7529bb758a6366397178b9f00ad5f0be4d9e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 9 Nov 2023 16:11:08 +0100
Subject: [PATCH 57/79] set all keys as label if selected

---
 omero_figure/templates/figure/index.html |  2 +-
 src/js/views/labels_from_maps_modal.js   | 27 ++++++++++++++++++------
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index 41a0d312e..36986579d 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -702,7 +702,7 @@ <h4 class="modal-title" id="addImagesLabel">Labels from Key-Value Pairs</h4>
                             <input type="radio" id="all-keys" name="kvpChoice" value="all-keys" />
                             <label for="all-keys">All Keys </label>
               
-                            <input type="radio" id="single-key" name="kvpChoice" value="one-key" checked />
+                            <input type="radio" id="single-key" name="kvpChoice" value="single-key" checked />
                             <label for="one-key">Choose Key <small class="text-muted">(shows numbers of images)</small>:</label>
                         </div>
                     
diff --git a/src/js/views/labels_from_maps_modal.js b/src/js/views/labels_from_maps_modal.js
index 2da09d12b..4150f022c 100644
--- a/src/js/views/labels_from_maps_modal.js
+++ b/src/js/views/labels_from_maps_modal.js
@@ -54,13 +54,26 @@ var LabelFromMapsModal = Backbone.View.extend({
         event.preventDefault();
         if (this.isLoading) return;
 
-        var key = $('select', this.el).val();
+        var radios = $("input[name='kvpChoice']")
+        var choice
+        for (var i = 0, length = radios.length; i < length; i++) {
+            if (radios[i].checked) {
+                choice = radios[i].value;
+                break;
+            }
+        }
+        console.log(choice)
+        var key;
+        if(choice === "single-key"){
+            key = $('select', this.el).val();
+        }
+
         var includeKey = $("input[name='includeKey']").is(':checked');
         var labelSize = this.options.size || "12";
         var labelPosition = this.options.position || "top";
         var labelColor = this.options.color || "000000";
 
-        var imageValues = this.annotations.reduce(function(prev, t){
+        var imageKeyValues = this.annotations.reduce(function(prev, t){
             var iid = t.link.parent.id;
             if (!prev[iid]) {
                 prev[iid] = [];
@@ -68,8 +81,8 @@ var LabelFromMapsModal = Backbone.View.extend({
             t.values.forEach(function(kv) {
                 var value = kv[1];
                 // If key matches, add to values for the image (no duplicates)
-                if (kv[0] === key && prev[iid].indexOf(value) === -1) {
-                    prev[iid].push(value);
+                if ((choice === "all-keys" || (kv[0] === key)) && prev[iid].indexOf(value) === -1) {
+                    prev[iid].push(kv);
                 }
             });
             return prev;
@@ -77,10 +90,10 @@ var LabelFromMapsModal = Backbone.View.extend({
 
         this.model.getSelected().forEach(function(p){
             var iid = p.get('imageId');
-            if (imageValues[iid]) {
-                var labels = imageValues[iid].map(function(value){
+            if (imageKeyValues[iid]) {
+                var labels = imageKeyValues[iid].map(function(value){
                     return {
-                        'text': includeKey ? (key + ': ' + value) : value,
+                        'text': includeKey ? (value[0] + ': ' + value[1]) : value[1],
                         'size': labelSize,
                         'position': labelPosition,
                         'color': labelColor,

From d8c626ec8e76ce2c77b70a0a24e2d65b150c3506 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 9 Nov 2023 17:26:26 +0100
Subject: [PATCH 58/79] Escape underscores to not be interprated as markdown

---
 src/js/models/panel_model.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 7e3c02a67..df0c87dd6 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -259,7 +259,7 @@
                     // If channel has LUT, make grey (visible on black/white bg)
                     var chColor = c.color.endsWith('lut') ? 'BBBBBB' : c.color;
                     newLabels.push({
-                        'text': c.label,
+                        'text': c.label.replaceAll("_","\\_"),
                         'size': options.size,
                         'position': options.position,
                         'color': options.color || chColor
@@ -277,7 +277,7 @@
                     else text = text + " " + c.label
                 }
             });
-            return text ? text : " ";
+            return text ? text.replaceAll("_","\\_") : " ";
         },
 
         getDeltaT: function() {
@@ -986,7 +986,7 @@
                     if (!prev[iid]) {
                         prev[iid] = {};
                     }
-                    prev[iid][t.id] = t.textValue;
+                    prev[iid][t.id] = t.textValue.replaceAll("_","\\_");
                     return prev;
                 }, {});
                 // Apply tags to panels

From 73f6477d0ab41b52eb4159519b5ccf9832291c01 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 9 Nov 2023 17:41:04 +0100
Subject: [PATCH 59/79] Escape underscores to not be interpreted as markdown

---
 src/js/views/labels_from_maps_modal.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/js/views/labels_from_maps_modal.js b/src/js/views/labels_from_maps_modal.js
index 4150f022c..2ac9e2e59 100644
--- a/src/js/views/labels_from_maps_modal.js
+++ b/src/js/views/labels_from_maps_modal.js
@@ -93,7 +93,7 @@ var LabelFromMapsModal = Backbone.View.extend({
             if (imageKeyValues[iid]) {
                 var labels = imageKeyValues[iid].map(function(value){
                     return {
-                        'text': includeKey ? (value[0] + ': ' + value[1]) : value[1],
+                        'text': includeKey ? (value[0].replaceAll("_","\\_") + ': ' + value[1].replaceAll("_","\\_")) : value[1].replaceAll("_","\\_"),
                         'size': labelSize,
                         'position': labelPosition,
                         'color': labelColor,

From 4eb62d8d4e42a25d955380f224bf36e09325c30f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 10 Nov 2023 08:39:06 +0100
Subject: [PATCH 60/79] replace underscore on key-value labels

---
 src/js/views/labels_from_maps_modal.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/js/views/labels_from_maps_modal.js b/src/js/views/labels_from_maps_modal.js
index 2da09d12b..461dedf31 100644
--- a/src/js/views/labels_from_maps_modal.js
+++ b/src/js/views/labels_from_maps_modal.js
@@ -80,7 +80,7 @@ var LabelFromMapsModal = Backbone.View.extend({
             if (imageValues[iid]) {
                 var labels = imageValues[iid].map(function(value){
                     return {
-                        'text': includeKey ? (key + ': ' + value) : value,
+                        'text': includeKey ? (key.replaceAll("_","\\_") + ': ' + value.replaceAll("_","\\_")) : value.replaceAll("_","\\_"),
                         'size': labelSize,
                         'position': labelPosition,
                         'color': labelColor,

From 87e87750b7ff9e25795d4b6600ffa735053b994c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 10 Nov 2023 10:24:32 +0100
Subject: [PATCH 61/79] remove duplicate labels when editing and add new

---
 src/js/models/panel_model.js | 29 ++++++++++++++++++++++++++---
 1 file changed, 26 insertions(+), 3 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 7e3c02a67..50e60a78d 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -241,13 +241,35 @@
             var oldLabs = this.get("labels");
             // Need to clone the list of labels...
             var labs = [];
-            for (var i=0; i<oldLabs.length; i++) {
+            /*for (var i=0; i<oldLabs.length; i++) {
                 labs.push( $.extend(true, {}, oldLabs[i]) );
+            }*/
+           var newLabKey = []
+            for (var i=0; i<labels.length; i++) {
+                newLabKey.push(this.get_label_key(labels[i]));
+            }
+
+            for (var i=0; i<oldLabs.length; i++) {
+                lbl = oldLabs[i];
+
+                lbl_key = this.get_label_key(lbl);
+                // for existing label that matches...
+                console.log(labels)
+                console.log(lbl)
+                console.log(newLabKey)
+                console.log(lbl_key)
+                console.log(newLabKey.includes(lbl_key))
+                if (!newLabKey.includes(lbl_key)) {
+                    // otherwise leave un-edited
+                    labs.push( $.extend(true, {}, lbl));
+                }
             }
+
             // ... then add new labels ...
             for (var j=0; j<labels.length; j++) {
                 labs.push( $.extend(true, {}, labels[j]) );
             }
+
             // ... so that we get the changed event triggering OK
             this.save('labels', labs);
         },
@@ -424,16 +446,17 @@
             var oldLabs = this.get('labels');
             // Need to clone the list of labels...
             var labs = [],
-                lbl, lbl_key;
+                lbl, lbl_key, replaced = false;
             for (var i=0; i<oldLabs.length; i++) {
                 lbl = oldLabs[i];
                 lbl_key = this.get_label_key(lbl);
                 // for existing label that matches...
                 if (labels_map.hasOwnProperty(lbl_key)) {
-                    if (labels_map[lbl_key]) {
+                    if (labels_map[lbl_key] && !replaced) {
                         // replace with the new label
                         lbl = $.extend(true, {}, labels_map[lbl_key]);
                         labs.push( lbl );
+                        replaced = true
                     }
                     // else 'false' are ignored (deleted)
                 } else {

From b4d142f17463c3c3b3f7a4eeefe65d2457218307 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 10 Nov 2023 14:08:48 +0100
Subject: [PATCH 62/79] remove duplicates after adding them on the figure when
 editing

---
 src/js/models/panel_model.js     | 17 +++--------------
 src/js/views/right_panel_view.js | 14 +++++++++++---
 2 files changed, 14 insertions(+), 17 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 50e60a78d..b3468047b 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -241,24 +241,15 @@
             var oldLabs = this.get("labels");
             // Need to clone the list of labels...
             var labs = [];
-            /*for (var i=0; i<oldLabs.length; i++) {
-                labs.push( $.extend(true, {}, oldLabs[i]) );
-            }*/
-           var newLabKey = []
+            var newLabKey = [];
             for (var i=0; i<labels.length; i++) {
                 newLabKey.push(this.get_label_key(labels[i]));
             }
 
             for (var i=0; i<oldLabs.length; i++) {
                 lbl = oldLabs[i];
-
                 lbl_key = this.get_label_key(lbl);
                 // for existing label that matches...
-                console.log(labels)
-                console.log(lbl)
-                console.log(newLabKey)
-                console.log(lbl_key)
-                console.log(newLabKey.includes(lbl_key))
                 if (!newLabKey.includes(lbl_key)) {
                     // otherwise leave un-edited
                     labs.push( $.extend(true, {}, lbl));
@@ -442,21 +433,19 @@
         // labels_map is {labelKey: {size:s, text:t, position:p, color:c}} or {labelKey: false} to delete
         // where labelKey specifies the label to edit. "l.text + '_' + l.size + '_' + l.color + '_' + l.position"
         edit_labels: function(labels_map) {
-
             var oldLabs = this.get('labels');
             // Need to clone the list of labels...
             var labs = [],
-                lbl, lbl_key, replaced = false;
+                lbl, lbl_key;
             for (var i=0; i<oldLabs.length; i++) {
                 lbl = oldLabs[i];
                 lbl_key = this.get_label_key(lbl);
                 // for existing label that matches...
                 if (labels_map.hasOwnProperty(lbl_key)) {
-                    if (labels_map[lbl_key] && !replaced) {
+                    if (labels_map[lbl_key]) {
                         // replace with the new label
                         lbl = $.extend(true, {}, labels_map[lbl_key]);
                         labs.push( lbl );
-                        replaced = true
                     }
                     // else 'false' are ignored (deleted)
                 } else {
diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index c91641e52..83e464c22 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -483,7 +483,6 @@
 
         // Use the label 'key' to specify which labels to update
         handle_label_edit: function(event) {
-
             var $form = $(event.target),
                 label_text = $('.label-text', $form).val(),
                 font_size = $('.font-size', $form).text().trim(),
@@ -497,7 +496,6 @@
 
             var newlbls = {};
             newlbls[key] = new_label;
-
             this.models.forEach(function(m){
                 m.edit_labels(newlbls);
             });
@@ -524,15 +522,25 @@
 
             // Render template for each position and append to $el
             var html = "";
+            var filteredLbls = []
             _.each(positions, function(lbls, p) {
-
                 lbls = _.map(lbls, function(label, key){ return label; });
 
                 var json = {'position':p, 'labels':lbls};
                 if (lbls.length === 0) return;
+                console.log(lbls)
+                lbls.forEach(function(lbl){
+                    filteredLbls.push(lbl)
+                })
+                
                 json.inner_template = self.inner_template;
                 html += self.template(json);
             });
+           
+            this.models.forEach(function(m){
+                m.save('labels', filteredLbls);
+            })
+
             self.$el.append(html);
 
             return this;

From a35a596f62038f2703a0a95707ff1c4dc603aae2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 14 Nov 2023 16:05:13 +0100
Subject: [PATCH 63/79] fix description in info panel

---
 omero_figure/templates/figure/index.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index a63d5b692..b6a6ed0f7 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -596,14 +596,14 @@ <h4>Dynamic properties</h4>
                             <td>Time: -0.06 s</td>
                         </tr>
                         <tr>
-                            <th>Z slice with units position <br/>relative to the 3rd frame</th>
+                            <th>Z index with units <br/> (first plane is Z: 0.00 &#181;m), <br/>offset by 3 times the Z pixel size</th>
                             <td>Z: [z.unit; offset=3]</td>
                             <td>Z: -3.00 &#181;m </td>
                         </tr>
                         <tr>
-                            <th>Z slice with index position <br/>relative to the 3rd frame</th>
+                            <th>Z index with (first plane is Z: 1) <br/>offset by 3</th>
                             <td>Z: [z.pixel; offset=3]</td>
-                            <td>Z: -3 </td>
+                            <td>Z: -2 </td>
                         </tr>
                         <tr>
                             <th>Image ID</th>

From 3a6bbd273d9607a7b703534da443c66d4d3b3e1e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 15 Nov 2023 13:13:18 +0100
Subject: [PATCH 64/79] Fix naming typo

---
 omero_figure/templates/figure/index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index e79624c71..9be0176c1 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -703,7 +703,7 @@ <h4 class="modal-title" id="addImagesLabel">Labels from Key-Value Pairs</h4>
                             <label for="all-keys">All Keys </label>
               
                             <input type="radio" id="single-key" name="kvpChoice" value="single-key" checked />
-                            <label for="one-key">Choose Key <small class="text-muted">(shows numbers of images)</small>:</label>
+                            <label for="single-key">Choose Key <small class="text-muted">(shows numbers of images)</small>:</label>
                         </div>
                     
                         <select>

From 1c3b8e2458cc4460ac618a3e5913ab247d8d3133 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Thu, 16 Nov 2023 10:49:22 +0100
Subject: [PATCH 65/79] Fix undo break by removing duplicates in edit_labels

---
 src/js/models/panel_model.js     | 14 +++++++++++++-
 src/js/views/right_panel_view.js | 10 ----------
 2 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index d52cd9ce8..3561340ad 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -456,8 +456,20 @@
                     labs.push( lbl );
                 }
             }
+
+            // filter unique keys only to remove duplicates
+            var filtered_lbls_map = {}
+            for (var i=0; i<labs.length; i++) {
+                filtered_lbls_map[this.get_label_key(labs[i])] = i
+            }
+        
+            var filtered_lbls = [] 
+            _.each(Object.values(filtered_lbls_map), function(idx){
+                filtered_lbls.push(labs[idx])
+            })
+
             // ... so that we get the changed event triggering OK
-            this.save('labels', labs);
+            this.save('labels', filtered_lbls);
         },
 
         save_channel: function(cIndex, attr, value) {
diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index 749e33516..76eb0544e 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -522,25 +522,15 @@
 
             // Render template for each position and append to $el
             var html = "";
-            var filteredLbls = []
             _.each(positions, function(lbls, p) {
                 lbls = _.map(lbls, function(label, key){ return label; });
 
                 var json = {'position':p, 'labels':lbls};
                 if (lbls.length === 0) return;
-                console.log(lbls)
-                lbls.forEach(function(lbl){
-                    filteredLbls.push(lbl)
-                })
                 
                 json.inner_template = self.inner_template;
                 html += self.template(json);
             });
-           
-            this.models.forEach(function(m){
-                m.save('labels', filteredLbls);
-            })
-
             self.$el.append(html);
 
             return this;

From a0c9ecb0e5b335211e9ed5a404792bf39c701773 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 21 Nov 2023 08:24:09 +0100
Subject: [PATCH 66/79] Fix bug on label sorting

---
 src/js/models/panel_model.js | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 3561340ad..720e21e1e 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -243,24 +243,24 @@
             var oldLabs = this.get("labels");
             // Need to clone the list of labels...
             var labs = [];
-            var newLabKey = [];
-            for (var i=0; i<labels.length; i++) {
-                newLabKey.push(this.get_label_key(labels[i]));
-            }
+            var oldLabKeys = [];
 
+            // Keep old labels unchanged...
             for (var i=0; i<oldLabs.length; i++) {
-                lbl = oldLabs[i];
-                lbl_key = this.get_label_key(lbl);
-                // for existing label that matches...
-                if (!newLabKey.includes(lbl_key)) {
-                    // otherwise leave un-edited
-                    labs.push( $.extend(true, {}, lbl));
-                }
+                var lbl = oldLabs[i];
+                var lbl_key = this.get_label_key(lbl);
+                oldLabKeys.push(lbl_key);
+                labs.push( $.extend(true, {}, lbl));
             }
 
             // ... then add new labels ...
             for (var j=0; j<labels.length; j++) {
-                labs.push( $.extend(true, {}, labels[j]) );
+                var lbl = labels[j];
+                var lbl_key = this.get_label_key(lbl);
+                if (!oldLabKeys.includes(lbl_key)) {
+                    // otherwise leave un-edited
+                    labs.push( $.extend(true, {}, lbl));
+                }
             }
 
             // ... so that we get the changed event triggering OK

From 8c3caa64a346083dbcd0139aa640311e0e7f0a6a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 21 Nov 2023 08:27:09 +0100
Subject: [PATCH 67/79] Remove whitespace lines

---
 src/js/models/panel_model.js     | 3 +--
 src/js/views/right_panel_view.js | 4 +++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index 720e21e1e..0ad93a692 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -252,7 +252,6 @@
                 oldLabKeys.push(lbl_key);
                 labs.push( $.extend(true, {}, lbl));
             }
-
             // ... then add new labels ...
             for (var j=0; j<labels.length; j++) {
                 var lbl = labels[j];
@@ -262,7 +261,6 @@
                     labs.push( $.extend(true, {}, lbl));
                 }
             }
-
             // ... so that we get the changed event triggering OK
             this.save('labels', labs);
         },
@@ -435,6 +433,7 @@
         // labels_map is {labelKey: {size:s, text:t, position:p, color:c}} or {labelKey: false} to delete
         // where labelKey specifies the label to edit. "l.text + '_' + l.size + '_' + l.color + '_' + l.position"
         edit_labels: function(labels_map) {
+            
             var oldLabs = this.get('labels');
             // Need to clone the list of labels...
             var labs = [],
diff --git a/src/js/views/right_panel_view.js b/src/js/views/right_panel_view.js
index 76eb0544e..a8fecf58a 100644
--- a/src/js/views/right_panel_view.js
+++ b/src/js/views/right_panel_view.js
@@ -483,6 +483,7 @@
 
         // Use the label 'key' to specify which labels to update
         handle_label_edit: function(event) {
+
             var $form = $(event.target),
                 label_text = $('.label-text', $form).val(),
                 font_size = $('.font-size', $form).text().trim(),
@@ -496,6 +497,7 @@
 
             var newlbls = {};
             newlbls[key] = new_label;
+
             this.models.forEach(function(m){
                 m.edit_labels(newlbls);
             });
@@ -523,11 +525,11 @@
             // Render template for each position and append to $el
             var html = "";
             _.each(positions, function(lbls, p) {
+
                 lbls = _.map(lbls, function(label, key){ return label; });
 
                 var json = {'position':p, 'labels':lbls};
                 if (lbls.length === 0) return;
-                
                 json.inner_template = self.inner_template;
                 html += self.template(json);
             });

From 68f10d8a37a74fc601e031185592ecaf4b30a655 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 21 Nov 2023 08:29:57 +0100
Subject: [PATCH 68/79] Fix typo

---
 omero_figure/templates/figure/index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index b6a6ed0f7..296ef91b1 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -601,7 +601,7 @@ <h4>Dynamic properties</h4>
                             <td>Z: -3.00 &#181;m </td>
                         </tr>
                         <tr>
-                            <th>Z index with (first plane is Z: 1) <br/>offset by 3</th>
+                            <th>Z index (first plane is Z: 1) <br/>offset by 3</th>
                             <td>Z: [z.pixel; offset=3]</td>
                             <td>Z: -2 </td>
                         </tr>

From 9e6bcfef5f2890a0e0bb09e5178ffcf187a0b3ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Tue, 21 Nov 2023 08:39:59 +0100
Subject: [PATCH 69/79] Fix type for zoom info in the tips

---
 omero_figure/templates/figure/index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index 4a5d4cfe2..4e08093fd 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -607,7 +607,7 @@ <h4>Dynamic properties</h4>
                         </tr>
                         <tr>
                             <th>Zoom</th>
-                            <td>[zoom] %</td>
+                            <td>[zoom]</td>
                             <td>100 %</td>
                         </tr>
                     </table>

From 9729834782824e9c35cc1566ea8ee45608ad8c90 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 22 Nov 2023 14:17:12 +0100
Subject: [PATCH 70/79] Remove console.log and shorten the choice

---
 src/js/views/labels_from_maps_modal.js | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/src/js/views/labels_from_maps_modal.js b/src/js/views/labels_from_maps_modal.js
index 2ac9e2e59..a7387320f 100644
--- a/src/js/views/labels_from_maps_modal.js
+++ b/src/js/views/labels_from_maps_modal.js
@@ -54,15 +54,7 @@ var LabelFromMapsModal = Backbone.View.extend({
         event.preventDefault();
         if (this.isLoading) return;
 
-        var radios = $("input[name='kvpChoice']")
-        var choice
-        for (var i = 0, length = radios.length; i < length; i++) {
-            if (radios[i].checked) {
-                choice = radios[i].value;
-                break;
-            }
-        }
-        console.log(choice)
+        var choice = $("input[name='kvpChoice']:checked").val();
         var key;
         if(choice === "single-key"){
             key = $('select', this.el).val();

From 598f278607d0c79e12cf7539a472fd6b8ddf6b2f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 22 Nov 2023 16:06:05 +0100
Subject: [PATCH 71/79] Remove conflicting line

---
 src/js/views/labels_from_maps_modal.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/js/views/labels_from_maps_modal.js b/src/js/views/labels_from_maps_modal.js
index 461dedf31..463e2a7eb 100644
--- a/src/js/views/labels_from_maps_modal.js
+++ b/src/js/views/labels_from_maps_modal.js
@@ -80,7 +80,7 @@ var LabelFromMapsModal = Backbone.View.extend({
             if (imageValues[iid]) {
                 var labels = imageValues[iid].map(function(value){
                     return {
-                        'text': includeKey ? (key.replaceAll("_","\\_") + ': ' + value.replaceAll("_","\\_")) : value.replaceAll("_","\\_"),
+                        'text': includeKey ? (value[0].replaceAll("_","\\_") + ': ' + value[1].replaceAll("_","\\_")) : value[1].replaceAll("_","\\_"),
                         'size': labelSize,
                         'position': labelPosition,
                         'color': labelColor,

From 62795429799f43c5d0182fbabcb44e2c31143ae8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 22 Nov 2023 16:07:37 +0100
Subject: [PATCH 72/79] Fix merge conflicts

---
 src/js/views/labels_from_maps_modal.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/js/views/labels_from_maps_modal.js b/src/js/views/labels_from_maps_modal.js
index a7387320f..121f77b25 100644
--- a/src/js/views/labels_from_maps_modal.js
+++ b/src/js/views/labels_from_maps_modal.js
@@ -85,7 +85,7 @@ var LabelFromMapsModal = Backbone.View.extend({
             if (imageKeyValues[iid]) {
                 var labels = imageKeyValues[iid].map(function(value){
                     return {
-                        'text': includeKey ? (value[0].replaceAll("_","\\_") + ': ' + value[1].replaceAll("_","\\_")) : value[1].replaceAll("_","\\_"),
+                        'text': includeKey ? (key.replaceAll("_","\\_") + ': ' + value.replaceAll("_","\\_")) : value.replaceAll("_","\\_"),
                         'size': labelSize,
                         'position': labelPosition,
                         'color': labelColor,

From 06d2d50615e9257b61ecd463bf0b604949de1be6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Wed, 22 Nov 2023 16:27:45 +0100
Subject: [PATCH 73/79] shorten the filtering and remove Object.values()

---
 src/js/models/panel_model.js | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/src/js/models/panel_model.js b/src/js/models/panel_model.js
index b23379b02..ebdeabeed 100644
--- a/src/js/models/panel_model.js
+++ b/src/js/models/panel_model.js
@@ -463,16 +463,12 @@
                 }
             }
 
-            // filter unique keys only to remove duplicates
-            var filtered_lbls_map = {}
-            for (var i=0; i<labs.length; i++) {
-                filtered_lbls_map[this.get_label_key(labs[i])] = i
-            }
-        
-            var filtered_lbls = [] 
-            _.each(Object.values(filtered_lbls_map), function(idx){
-                filtered_lbls.push(labs[idx])
-            })
+            // Extract all the keys (even duplicates)
+            var keys = labs.map(lbl => this.get_label_key(lbl));
+
+            // get all unique labels based on filtering keys 
+            //(i.e removing duplicate keys based on the index of the first occurrence of the value)
+            var filtered_lbls = labs.filter((lbl, index) => index == keys.indexOf(this.get_label_key(lbl)));
 
             // ... so that we get the changed event triggering OK
             this.save('labels', filtered_lbls);

From b5f107a0d6559bcee19da026c6b25fb96f579e4a Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Thu, 23 Nov 2023 11:38:52 +0000
Subject: [PATCH 74/79] Fix missing pixel_size_z_symbol in Figure_To_Pdf.py

---
 omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
index f8065b094..8409d46f0 100644
--- a/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
+++ b/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
@@ -1247,6 +1247,7 @@ def draw_labels(self, panel, page):
                         z_symbol = panel.get('pixel_size_z_symbol')
                         if pixel_size_z is None:
                             pixel_size_z = 0
+                        if z_symbol is None:
                             z_symbol = "\xB5m"
 
                         if ("z_projection" in panel.keys()

From bae750e8570dedd49533108385b309ea7c5f42ee Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Fri, 24 Nov 2023 14:46:20 +0000
Subject: [PATCH 75/79] Avoid errors marshalling pixel_size data

---
 omero_figure/views.py | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/omero_figure/views.py b/omero_figure/views.py
index d7b1358a9..efd8523a5 100644
--- a/omero_figure/views.py
+++ b/omero_figure/views.py
@@ -121,15 +121,19 @@ def img_data_json(request, image_id, conn=None, **kwargs):
 
     if units_support:
         # Add extra parameters with units data
+        if 'pixel_size' not in rv:
+            rv['pixel_size'] = {}
         # NB ['pixel_size']['x'] will have size in MICROMETER
         px = image.getPrimaryPixels().getPhysicalSizeX()
-        rv['pixel_size']['valueX'] = px.getValue()
-        rv['pixel_size']['symbolX'] = px.getSymbol()
-        rv['pixel_size']['unitX'] = str(px.getUnit())
+        if px is not None:
+            rv['pixel_size']['valueX'] = px.getValue()
+            rv['pixel_size']['symbolX'] = px.getSymbol()
+            rv['pixel_size']['unitX'] = str(px.getUnit())
         py = image.getPrimaryPixels().getPhysicalSizeY()
-        rv['pixel_size']['valueY'] = py.getValue()
-        rv['pixel_size']['symbolY'] = py.getSymbol()
-        rv['pixel_size']['unitY'] = str(py.getUnit())
+        if py is not None:
+            rv['pixel_size']['valueY'] = py.getValue()
+            rv['pixel_size']['symbolY'] = py.getSymbol()
+            rv['pixel_size']['unitY'] = str(py.getUnit())
         pz = image.getPrimaryPixels().getPhysicalSizeZ()
         if pz is not None:
             rv['pixel_size']['valueZ'] = pz.getValue()

From ecdaa70243b9fa74d7132bc50d060f2eac2bd39c Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Fri, 24 Nov 2023 14:47:56 +0000
Subject: [PATCH 76/79] Handle data.Exception value: show error message

---
 src/js/models/figure_model.js | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/js/models/figure_model.js b/src/js/models/figure_model.js
index fe6050b9e..937b94b7f 100644
--- a/src/js/models/figure_model.js
+++ b/src/js/models/figure_model.js
@@ -459,6 +459,11 @@
                 dataType: dataType,
                 // work with the response
                 success: function( data ) {
+                    if (data.Exception) {
+                        // If something went wrong, show error and don't add to figure
+                        alert(`Image loading from ${imgDataUrl} included an Error: ${data.Exception}`);
+                        return;
+                    }
 
                     self.set('loading_count', self.get('loading_count') - 1);
 

From 504a5d60d934258c9887551a8f9f69fbe294e707 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Fri, 24 Nov 2023 17:00:12 +0000
Subject: [PATCH 77/79] Also handle ConcurrencyException

---
 src/js/models/figure_model.js | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/js/models/figure_model.js b/src/js/models/figure_model.js
index 937b94b7f..dc00d5316 100644
--- a/src/js/models/figure_model.js
+++ b/src/js/models/figure_model.js
@@ -459,9 +459,10 @@
                 dataType: dataType,
                 // work with the response
                 success: function( data ) {
-                    if (data.Exception) {
+                    if (data.Exception || data.ConcurrencyException) {
                         // If something went wrong, show error and don't add to figure
-                        alert(`Image loading from ${imgDataUrl} included an Error: ${data.Exception}`);
+                        message = data.Exception || "ConcurrencyException"
+                        alert(`Image loading from ${imgDataUrl} included an Error: ${message}`);
                         return;
                     }
 

From e94f7874cc6daa3b5d2c91232661899707b9a818 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 1 Dec 2023 08:31:26 +0100
Subject: [PATCH 78/79] Fix bug on key-values import

---
 src/js/views/labels_from_maps_modal.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/js/views/labels_from_maps_modal.js b/src/js/views/labels_from_maps_modal.js
index 121f77b25..a7387320f 100644
--- a/src/js/views/labels_from_maps_modal.js
+++ b/src/js/views/labels_from_maps_modal.js
@@ -85,7 +85,7 @@ var LabelFromMapsModal = Backbone.View.extend({
             if (imageKeyValues[iid]) {
                 var labels = imageKeyValues[iid].map(function(value){
                     return {
-                        'text': includeKey ? (key.replaceAll("_","\\_") + ': ' + value.replaceAll("_","\\_")) : value.replaceAll("_","\\_"),
+                        'text': includeKey ? (value[0].replaceAll("_","\\_") + ': ' + value[1].replaceAll("_","\\_")) : value[1].replaceAll("_","\\_"),
                         'size': labelSize,
                         'position': labelPosition,
                         'color': labelColor,

From 6457eccf1e4d937566100ebeeed5ca484709cfb3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dornier?= <remy.dornier@epfl.ch>
Date: Fri, 1 Dec 2023 13:12:29 +0100
Subject: [PATCH 79/79] Update tips

---
 omero_figure/templates/figure/index.html | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/omero_figure/templates/figure/index.html b/omero_figure/templates/figure/index.html
index 4cc25126b..4dec7e29e 100644
--- a/omero_figure/templates/figure/index.html
+++ b/omero_figure/templates/figure/index.html
@@ -520,8 +520,14 @@ <h4 class="modal-title">Label Formatting</h4>
                     <h4>Markdown formatting</h4>
                     <p>
                         You can use "Markdown" syntax to add formatting to plain text. For example,
-                        **this text will be bold** and this *word* will be italic. NB: Links are not
-                        supported for panel labels.
+                        **this text will be bold** and this *word* will be italic. 
+                    </p>
+                    <p>
+                        NB: Links are not supported for panel labels.
+                    </p>
+                    <p>
+                        NB: You can escape a certain character to not be interpreted as Markdown by adding \ in front of the 
+                        character. Ex: "my_string_" is interpreted as "my<i>string</i>" but "my\_string\_" is now interpreted as "my_string_"
                     </p>
 
                     <table class="table">
@@ -531,21 +537,21 @@ <h4>Markdown formatting</h4>
                             <th>...this text</th></tr>
                         <tr>
                             <th>BOLD</th>
-                            <td>Use 2 stars for **bold**.</td>
-                            <td>Use 2 stars for <strong>bold</strong>.</td>
+                            <td>**bold** or __bold__</td>
+                            <td><strong>bold</strong> or <strong>bold</strong></td>
                         </tr>
                         <tr>
                             <th>ITALIC</th>
-                            <td>Use 1 star for *italic*.</td>
-                            <td>Use 1 star for <i>italic</i>.</td>
+                            <td>*italic* or _italic_</td>
+                            <td><i>italic</i> or <i>italic</i></td>
                         </tr>
                         <tr>
                             <th>LINKS</th>
-                            <td>Add links with [Link text](http://link_url.com)</td>
-                            <td>Add links with <a href="#">Link text</a></td>
+                            <td>[Link text](http://link_url.com)</td>
+                            <td><a href="#">Link text</a></td>
                         </tr>
                        <!--  <tr><td>You need to use 2 line breaks between paragraphs</td><td></td></tr> -->
-                    </table>
+                    </table>                    
                     <h4>Dynamic properties</h4>
                     <p>
                         The drop-down menu in the 'Add Labels' form allows you to create labels based on Image metadata.