From 6e8a11bb5cf5d6d7a95287e3589aaa636531ff49 Mon Sep 17 00:00:00 2001 From: Jasmine Shao Date: Fri, 4 Oct 2024 11:08:57 -0400 Subject: [PATCH 1/5] add annotation naming scheme --- docs/upload.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/docs/upload.md b/docs/upload.md index b13d8e0..d7c69fb 100644 --- a/docs/upload.md +++ b/docs/upload.md @@ -139,6 +139,20 @@ This directory contains microscopy data files [as described in detail in the BID In this example the data include images (`.tif`) and metadata (`.json`) from multiple brain sections. For each section there is a blockface photo (`_photo`) and a histological stain (`_stain`). Sections from Ken1 and Ken2 were either processed with a Nissl stain and imaged under brightfield microscopy (`_BF`), or processed for the fluorescent tracer Lucifer Yellow (`LY`) and imaged under darkfield microscopy (`_DF`). Additional sections from Ken2 were processed for the fluorescent tracer Fluoro-Ruby (`FR`) and imaged under darkfield microscopy (`_DF`). + +#### high-res histology annotation +All datasets used for annotations use the same naming scheme as the rawdata. + +All annotation files use the following naming scheme: +dataset name + _suffix +when annotaing discrete segmentations, use _dseg as the suffix. + +When there are multiple annotators working on the same dataset, each annotation file is distinguish by adding a _desc-[label] entity before the suffix, where [label] is replaced by the annotator's initials. + +For example, an annotator with an initial JS would name the anotation file as sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg + + + ### samples.tsv This text file is [described in detail in the BIDS specification](https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files.html#samples-file). For Ken1, the `samples.tsv` would look like this: @@ -150,6 +164,7 @@ sub-Ken1 sample-slice0009 tissue sub-Ken1 sample-slice0010 tissue ``` + ## Upload your data Upload the data from your local machine to lincbrain.org: From f2da6e1f5d181f40d68fd1d7c378ac83bda5f4cf Mon Sep 17 00:00:00 2001 From: Jasmine Shao Date: Tue, 8 Oct 2024 10:10:30 -0400 Subject: [PATCH 2/5] fix spelling --- docs/upload.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/upload.md b/docs/upload.md index d7c69fb..f30d5b4 100644 --- a/docs/upload.md +++ b/docs/upload.md @@ -145,11 +145,11 @@ All datasets used for annotations use the same naming scheme as the rawdata. All annotation files use the following naming scheme: dataset name + _suffix -when annotaing discrete segmentations, use _dseg as the suffix. +when annotating discrete segmentations, use _dseg as the suffix. When there are multiple annotators working on the same dataset, each annotation file is distinguish by adding a _desc-[label] entity before the suffix, where [label] is replaced by the annotator's initials. -For example, an annotator with an initial JS would name the anotation file as sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg +For example, an annotator with an initial JS would name the annotation file as sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg From 6eb0fa090f5ea6b3acc544265a4e7289fa733b34 Mon Sep 17 00:00:00 2001 From: Jasmine Shao Date: Mon, 28 Oct 2024 11:43:53 -0400 Subject: [PATCH 3/5] incorporate suggestions --- docs/upload.md | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/docs/upload.md b/docs/upload.md index f30d5b4..554a30c 100644 --- a/docs/upload.md +++ b/docs/upload.md @@ -141,15 +141,20 @@ In this example the data include images (`.tif`) and metadata (`.json`) from mul #### high-res histology annotation -All datasets used for annotations use the same naming scheme as the rawdata. - All annotation files use the following naming scheme: -dataset name + _suffix -when annotating discrete segmentations, use _dseg as the suffix. +` + _desc-[label] + _suffix.ome.zarr` +where `[label]` is replaced by the annotator's initials and `_suffix` indicates the type of segementations being annoated. Specifically, when annotating discrete segmentations, use `_dseg` as the suffix (see the [BIDS spec on discrete segementations](https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#discrete-segmentations)). -When there are multiple annotators working on the same dataset, each annotation file is distinguish by adding a _desc-[label] entity before the suffix, where [label] is replaced by the annotator's initials. +For example, an annotator with an initial JS annotating discrete segments would name the annotation file as `sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg.ome.zarr` -For example, an annotator with an initial JS would name the annotation file as sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg +A `.tsv` file could be included to map the IDs (integer values) of the discrete segmentations to the custome labels, where `` is replaced by the name of the annotation file. It contains a lookup table with the following columns (see the [BIDS spec on custome TSV](https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#common-image-derived-labels)): +``` +index name +1 Single Fiber +2 Light Bundle +3 Moderate Bundle +... +``` From c6243f094e2ca58c5c69477bff12d6ba40386f3b Mon Sep 17 00:00:00 2001 From: Jasmine Shao Date: Mon, 28 Oct 2024 11:47:35 -0400 Subject: [PATCH 4/5] fix spelling --- docs/upload.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/upload.md b/docs/upload.md index 554a30c..5b886e3 100644 --- a/docs/upload.md +++ b/docs/upload.md @@ -143,11 +143,11 @@ In this example the data include images (`.tif`) and metadata (`.json`) from mul #### high-res histology annotation All annotation files use the following naming scheme: ` + _desc-[label] + _suffix.ome.zarr` -where `[label]` is replaced by the annotator's initials and `_suffix` indicates the type of segementations being annoated. Specifically, when annotating discrete segmentations, use `_dseg` as the suffix (see the [BIDS spec on discrete segementations](https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#discrete-segmentations)). +where `[label]` is replaced by the annotator's initials and `_suffix` indicates the type of segmentations being annotated. Specifically, when annotating discrete segmentations, use `_dseg` as the suffix (see the [BIDS spec on discrete segmentations](https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#discrete-segmentations)). For example, an annotator with an initial JS annotating discrete segments would name the annotation file as `sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg.ome.zarr` -A `.tsv` file could be included to map the IDs (integer values) of the discrete segmentations to the custome labels, where `` is replaced by the name of the annotation file. It contains a lookup table with the following columns (see the [BIDS spec on custome TSV](https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#common-image-derived-labels)): +A `.tsv` file could be included to map the IDs (integer values) of the discrete segmentations to the custom labels, where `` is replaced by the name of the annotation file. It contains a lookup table with the following columns (see the [BIDS spec on custom TSV](https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#common-image-derived-labels)): ``` index name 1 Single Fiber From c5b332275b5aaf6e7a0c2e4f9082f8d6312dfea8 Mon Sep 17 00:00:00 2001 From: Jasmine Shao <124855181+jssyq@users.noreply.github.com> Date: Tue, 29 Oct 2024 11:48:51 -0400 Subject: [PATCH 5/5] Update docs/upload.md Co-authored-by: Kabilar Gunalan --- docs/upload.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/upload.md b/docs/upload.md index 5b886e3..3060ce2 100644 --- a/docs/upload.md +++ b/docs/upload.md @@ -145,7 +145,7 @@ All annotation files use the following naming scheme: ` + _desc-[label] + _suffix.ome.zarr` where `[label]` is replaced by the annotator's initials and `_suffix` indicates the type of segmentations being annotated. Specifically, when annotating discrete segmentations, use `_dseg` as the suffix (see the [BIDS spec on discrete segmentations](https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#discrete-segmentations)). -For example, an annotator with an initial JS annotating discrete segments would name the annotation file as `sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg.ome.zarr` +For example, an annotator with an initial JS annotating discrete segments would name the annotation file as `000003_sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg.ome.zarr` A `.tsv` file could be included to map the IDs (integer values) of the discrete segmentations to the custom labels, where `` is replaced by the name of the annotation file. It contains a lookup table with the following columns (see the [BIDS spec on custom TSV](https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#common-image-derived-labels)): ```