diff --git a/DESCRIPTION b/DESCRIPTION
index 75af02960..2ea7b373c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -6,15 +6,17 @@ Authors@R: c(
 		 role = c("aut", "cre")),
 	person("Jiaji", "George Chen", email = "jiajic@bu.edu",
 		 role = c("aut")),
-	person("Natalie", "Del Rossi", email = "natalie.delrossi@mssm.edu",
-		 role = c("aut")),
+	person("Joselyn C.", "Chávez-Fuentes", email = "joselynchavezf@gmail.com",
+		 role = c("aut"), comment = c(ORCID = "0000-0002-4974-4591")),
 	person("Guo-Cheng", "Yuan", email = "guo-cheng.yuan@mssm.edu",
 		 role = c("aut")),
     person("Matthew", "O'Brien", email = "mobrien2@bu.edu",
 		 role = c("aut")),
-	person("Joselyn C.", "Chávez-Fuentes", email = "joselynchavezf@gmail.com",
-		 role = c("aut"), comment = c(ORCID = "0000-0002-4974-4591")),
 	person("Edward", "Ruiz", email = "ecruiz@bu.edu",
+		 role = c("aut")),
+	person("Wen", "Wang", email = "wen.wang@mssm.edu",
+		 role = c("aut")),
+	person("Natalie", "Del Rossi", email = "natalie.delrossi@mssm.edu",
 		 role = c("aut"))
 	)
 Maintainer: Ruben Dries <rubendries@gmail.com>
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 728513dc7..bd729be88 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -10,7 +10,7 @@ authors:
 
 
 template:
-  bootstrap: 5
+  bootstrap: 3
   bslib:
     bg: "#FFFFFF"
     fg: "#000000"
@@ -44,8 +44,16 @@ navbar:
         href: articles/object_creation.html
       - text: Giotto Class Structure
         href: articles/structure.html
+      - text: Giotto Class Structure
+        href: articles/structure.html
+      - text: Solutions to Installation Errors
+        href: articles/errorsfaqsandtips.html
+      - text: FAQs
+        href: articles/faqs.html
       - text: Branches
         href: articles/branches.html
+      - text: How to report a bug
+        href: articles/github_issues.html
     reference:
       text: Documentation
       href: reference/index.html
@@ -87,64 +95,76 @@ navbar:
       text: Examples
       menu:
       - text: Seq-Scope
-      - text: Mouse liver
-        href: articles/seqscope_mouse_liver.html
+        menu:
+        - text: Mouse liver
+          href: articles/seqscope_mouse_liver.html
       - text: -------
       - text: Visium
-      - text: Visium Mouse Kidney
-        href: articles/visium_mouse_kidney.html
-      - text: Visium Mouse Brain
-        href: articles/visium_mouse_brain.html
-      - text: Visium Prostate Integration
-        href: articles/visium_prostate_integration.html
-      - text: CytAssist Human Lung Cancer
-        href: articles/visium_cytassist_lungcancer.html
-      - text: CytAssist Multi-omics Human Glioblastoma
-        href: articles/visium_cytassist_human_glioblastoma.html
+        menu:
+        - text: Visium Mouse Kidney
+          href: articles/visium_mouse_kidney.html
+        - text: Visium Mouse Brain
+          href: articles/visium_mouse_brain.html
+        - text: Visium Prostate Integration
+          href: articles/visium_prostate_integration.html
+        - text: CytAssist Human Lung Cancer
+          href: articles/visium_cytassist_lungcancer.html
+        - text: CytAssist Multi-omics Human Glioblastoma
+          href: articles/visium_cytassist_human_glioblastoma.html
       - text: -------
       - text: Spatial Genomics
-      - text: Mouse Kidney
-        href: articles/spatial_genomics_mouse_kidney.html
+        menu:
+        - text: Mouse Kidney
+          href: articles/spatial_genomics_mouse_kidney.html
       - text: -------
       - text: Xenium
-      - text: Xenium Human breast cancer
-        href: articles/xenium_breast_cancer.html
+        menu:
+        - text: Xenium Human breast cancer
+          href: articles/xenium_breast_cancer.html
       - text: -------
       - text: Nanostring CosMx
-      - text: Nanostring CosMx Subcellular Lung Cancer
-        href: articles/nanostring_cosmx_lung_cancer.html
+        menu:
+        - text: Nanostring CosMx Subcellular Lung Cancer
+          href: articles/nanostring_cosmx_lung_cancer.html
       - text: -------
       - text: MERFISH
-      - text: MERFISH Mouse Hypothalamic Preoptic Region
-        href: articles/merfish_mouse_hypothalamic.html
+        menu:
+        - text: MERFISH Mouse Hypothalamic Preoptic Region
+          href: articles/merfish_mouse_hypothalamic.html
       - text: -------
       - text: Vizgen
-      - text: Vizgen Mouse Brain Receptor Map
-        href: articles/vizgen_mouse_brain.html
+        menu:
+        - text: Vizgen Mouse Brain Receptor Map
+          href: articles/vizgen_mouse_brain.html
       - text: -------
       - text: seqFISH
-      - text: mini seqFISH
-        href: articles/mini_seqfish.html
-      - text: SeqFish+ Mouse Cortex Example
-        href: articles/seqfish_cortex.html
+        menu:
+        - text: mini seqFISH
+          href: articles/mini_seqfish.html
+        - text: SeqFish+ Mouse Cortex Example
+          href: articles/seqfish_cortex.html
       - text: -------
       - text: osmFISH
-      - text: osmFISH Mouse SS Cortex
-        href: articles/osmfish_mouse_ss_cortex.html
+        menu:
+        - text: osmFISH Mouse SS Cortex
+          href: articles/osmfish_mouse_ss_cortex.html
       - text: -------
       - text: Resolve Bioscience
-      - text: Resolve Bioscience Breast Cancer Subcellular
-        href: articles/resolve_biosciences.html
+        menu:
+        - text: Resolve Bioscience Breast Cancer Subcellular
+          href: articles/resolve_biosciences.html
       - text: -------
       - text: CODEX
-      - text: Codex Mouse Spleen
-        href: articles/codex_mouse_spleen.html
+        menu:
+        - text: Codex Mouse Spleen
+          href: articles/codex_mouse_spleen.html
       - text: -------
       - text: Single Cell RNA Sequencing
-      - text: Prostate
-        href: articles/singlecell_prostate_standard.html
-      - text: Prostate Integration
-        href: articles/singlecell_prostate_integration.html
+        menu:
+        - text: Prostate
+          href: articles/singlecell_prostate_standard.html
+        - text: Prostate Integration
+          href: articles/singlecell_prostate_integration.html
     news:
       text: News
       menu:
@@ -171,7 +191,10 @@ articles:
   - configuration
   - object_creation
   - structure
+  - errorsfaqsandtips
+  - faqs
   - branches
+  - github_issues
 - title: Try Giotto in the Cloud
   navbar: ~
   contents:
diff --git a/inst/pkgdown/assets/pkgdown.css b/inst/pkgdown/assets/pkgdown.css
new file mode 100644
index 000000000..61a4ed496
--- /dev/null
+++ b/inst/pkgdown/assets/pkgdown.css
@@ -0,0 +1,12 @@
+.dropdown-submenu {
+    height:200px;
+    overflow-y:scroll;
+}
+
+@media (max-width: 500px) {
+    .dropdown-menu{
+        height:200px;
+        overflow-y:scroll;
+    }
+}
+
diff --git a/vignettes/codex_mouse_spleen.Rmd b/vignettes/codex_mouse_spleen.Rmd
index 8c1c2b605..638025f41 100644
--- a/vignettes/codex_mouse_spleen.Rmd
+++ b/vignettes/codex_mouse_spleen.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Codex Mouse Spleen"
-date: 2022-09-16
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Codex Mouse Spleen}
diff --git a/vignettes/configuration.Rmd b/vignettes/configuration.Rmd
index eb74a7d1c..21b212c32 100644
--- a/vignettes/configuration.Rmd
+++ b/vignettes/configuration.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Giotto Configuration"
-date: 4/12/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Giotto Configuration}
diff --git a/vignettes/ecosystem.Rmd b/vignettes/ecosystem.Rmd
index 8ef13e4d9..154c84a76 100644
--- a/vignettes/ecosystem.Rmd
+++ b/vignettes/ecosystem.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Giotto Ecosystem"
-date: 4/12/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Giotto Ecosystem}
diff --git a/vignettes/errorsfaqsandtips.Rmd b/vignettes/errorsfaqsandtips.Rmd
new file mode 100644
index 000000000..ed484b4b7
--- /dev/null
+++ b/vignettes/errorsfaqsandtips.Rmd
@@ -0,0 +1,305 @@
+---
+title: "Solutions to Installation Errors"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Solutions to Installation Errors}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+# Errors on MacOS
+
+## Packages not Found
+
+In the event that packages are inaccessible in the default installation of the Giotto miniconda environment, one troubleshooting method is provided here.
+
+
+```{r, eval=FALSE}
+# Restart the R session, while maintaining workspace variables.
+# If using RStudio, the following command will do exactly that:
+.rs.restartR()
+# Direct reticulate to use Python within the Giotto Environment
+reticulate::use_python(default_python_path)
+# Check if packages exist again. Ensure function from above code block is defined.
+missing_packages <- pkg_check()
+retry_install <- length(missing_packages) > 0
+if(retry_install){
+
+  # Attempt to reinstall all packages.
+  pkgs_w_versions <- c('pandas==1.5.1',
+                       'networkx==2.8.8',
+                       'python-igraph==0.10.2',
+                       'leidenalg==0.9.0',
+                       'python-louvain==0.16',
+                       'python.app==1.4',
+                       'scikit-learn==1.1.3')
+
+  python_version = "3.10.2"
+
+  py_pkgs = c('pandas','networkx',
+              'igraph', 'leidenalg',
+              'python-louvain','scikit-learn','python.app')
+
+  if(Sys.info()[['sysname']] != "Darwin"){
+    pkgs_w_versions = pkgs_w_versions[!grepl(pattern = 'python.app', x = pkgs_w_versions)]
+    py_pkgs = py_pkgs[!grepl(pattern = 'python.app', x = py_pkgs)]
+  }
+
+  env_location <- reticulate::py_discover_config()$pythonhome
+  partial_path_to_conda <- paste0(reticulate::miniconda_path(),'/envs/giotto_env')
+
+  py_lou = pkgs_w_versions[grepl(pattern = 'python-louvain',x = pkgs_w_versions)]
+  pip_packages = c("smfishhmrf", py_lou)
+  pkgs_w_versions = pkgs_w_versions[!grepl(pattern = 'python-louvain',x = pkgs_w_versions)]
+
+  if(.Platform[['OS.type']] == 'unix') {
+
+    conda_full_path = paste0(partial_conda_path,'/','bin/conda')
+
+    # Remove all previous installations
+    reticulate::conda_remove(envname = env_location,
+                             packages = py_pkgs,
+                             conda = conda_full_path)
+
+    # Reinstall
+    reticulate::conda_install(packages = pkgs_w_versions,
+                              envname = env_location,
+                              method = 'conda',
+                              conda = conda_full_path,
+                              python_version = python_version)
+
+    # Reinstall with pip
+    reticulate::conda_install(packages = pip_packages,
+                              envname = env_location,
+                              method = 'conda',
+                              conda = conda_full_path,
+                              pip = TRUE,
+                              python_version = python_version)
+  }
+  else if(.Platform[['OS.type']] == 'windows'){
+    conda_full_path = paste0(partial_conda_path,'/','condabin/conda.bat')
+
+    # Remove all previous installations
+    reticulate::conda_remove(envname = env_location,
+                             packages = py_pkgs,
+                             conda = conda_full_path)
+
+    # Reinstall
+    reticulate::conda_install(packages = pkgs_w_versions,
+                              envname = env_location,
+                              method = 'conda',
+                              conda = conda_full_path,
+                              python_version = python_version,
+                              channel = c('conda-forge', 'vtraag'))
+
+    # Reinstall with pip
+    reticulate::conda_install(packages = pip_packages,
+                              envname = env_location,
+                              method = 'conda',
+                              conda = conda_full_path,
+                              pip = TRUE,
+                              python_version = python_version)
+
+  }
+}
+```
+
+
+# Errors on Windows
+
+## Windows 11 OpenSSL Error 
+
+*Please note that this troubleshooting workflow is for a Windows 11 64-bit machine.*
+
+Unfortunately, it is known that installing miniconda on Windows 11 can sometimes result in an [OpenSSL error](https://github.com/drieslab/Giotto/issues/425#issuecomment-1320499840).
+
+It should be noted that Conda developers are aware of this, and that this particular issue does not have to do with the configuration of the Giotto package. One workaround for this error is described below and on the conda repository, [here](https://github.com/conda/conda/issues/8273#issue-409800067).
+
+First, open a terminal and navigate to the folder in which miniconda lives on the machine. To find this, press the Windows Key and search for "Anaconda Prompt". If anaconda3 is installed on the machine, there may be multiple options for this terminal; choose the Anaconda Prompt with "R-MINI~1" in parenthesis.
+
+Output from the following commands will be provided as a comparative guide. Once the terminal is open, identify the Conda environments on the machine by running the following:
+
+
+```{r, eval=FALSE}
+(base) PS > conda info --envs
+
+# conda environments:
+#
+# base                  *  C:\Users\matto\AppData\Local\R-MINI~1
+# giotto_env               C:\Users\matto\AppData\Local\R-MINI~1\envs\giotto_env
+#                          C:\Users\matto\AppData\Local\r-miniconda\envs\giotto_env
+#                          C:\Users\matto\anaconda3
+```
+
+
+Change your current directory to the R-MINI\~1 subdirectory. Then, navigate to the Library/bin/ subdirectory within. Use the dir command to search bin for two groups of files. These files will be moved to a different directory, and should fix the issue. There may be more than two files per group here, and that is okay. All of the files with these names will be moved, regardless of the extension.
+
+
+```{r, eval=FALSE}
+(base) PS > cd C:\Users\matto\AppData\Local\R-MINI~1
+(base) PS > cd .\Library\bin
+(base) PS > dir libssl-1_1-x64.*
+
+#    Directory: C:\Users\matto\AppData\Local\r-miniconda\Library\bin
+
+
+#  Mode                 LastWriteTime         Length Name
+#  ----                 -------------         ------ ----
+#  -a----         11/4/2022  11:06 AM         686080 libssl-1_1-x64.dll
+#  -a----         11/4/2022  11:06 AM        2338816 libssl-1_1-x64.pdbo
+
+(base) PS > dir libcrypto-1_1-x64.*
+
+#    Directory: C:\Users\matto\AppData\Local\r-miniconda\Library\bin
+
+
+#  Mode                 LastWriteTime         Length Name
+#  ----                 -------------         ------ ----
+#  -a----         11/4/2022  11:06 AM        3416064 libcrypto-1_1-x64.dll
+#  -a----         11/4/2022  11:06 AM       10219520 libcrypto-1_1-x64.pdb
+```
+
+
+Once these files are located, they may be moved to R-MINI\~1/DLLs/, the proper directory for the search path.
+
+
+```{r, eval=FALSE}
+(base) PS > pwd
+
+# Path
+# ----
+# C:\Users\matth\AppData\Local\r-miniconda\Library\bin
+
+(base) PS > mv libssl-1_1-x64.* ..\..\DLLs\
+(base) PS > mv libcrypto-1_1-x64.* ..\..\DLLs\
+```
+
+
+Finally, change to the DLLs directory within R-MINI\~1 and verify that the files now exist there.
+
+
+```{r, eval=FALSE}
+(base) PS > cd C:\Users\matth\AppData\Local\r-miniconda\DLLs\
+(base) PS > dir libssl-1_1-x64.*
+
+#     Directory: C:\Users\matth\AppData\Local\r-miniconda\DLLs
+
+
+#  Mode                 LastWriteTime         Length Name
+#  ----                 -------------         ------ ----
+#  -a----         11/4/2022  11:07 AM         686080 libssl-1_1-x64.dll
+#  -a----         11/4/2022  11:07 AM        2338816 libssl-1_1-x64.pdb
+
+(base) PS > dir libcrypto-1_1-x64.*
+
+#    Directory: C:\Users\matto\AppData\Local\r-miniconda\DLLs
+
+
+#  Mode                 LastWriteTime         Length Name
+#  ----                 -------------         ------ ----
+#  -a----         11/4/2022  11:07 AM        3416064 libcrypto-1_1-x64.dll
+#  -a----         11/4/2022  11:07 AM       10219520 libcrypto-1_1-x64.pdb
+```
+
+
+Now that these files have moved, this error should disappear. Activate the Giotto environment, and run python within it to test a package import. The OpenSSL error should no longer occur.
+
+
+```{r, eval=FALSE}
+(base) PS > conda info --envs
+
+# conda environments:
+#
+# base                  *  C:\Users\matto\AppData\Local\R-MINI~1
+# giotto_env               C:\Users\matto\AppData\Local\R-MINI~1\envs\giotto_env
+#                          C:\Users\matto\AppData\Local\r-miniconda\envs\giotto_env
+#                          C:\Users\matto\anaconda3
+
+(base) PS > conda activate giotto_env
+(giotto_env) PS > cd C:\Users\matto\AppData\Local\R-MINI~1\envs\giotto_env
+(giotto_env) PS > python
+Python 3.10.2 | packaged by conda-forge | (main, Mar  8 2022, 15:47:33) [MSC v.1929 64 bit (AMD64)] on win32
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import pandas, networkx, igraph, leidenalg, community, sklearn
+>>>
+```
+
+
+# UnsatisfiableError
+
+This error results from conflicts within the anaconda and miniconda environment. This error presents itself when conflicting versions of conda live on the same machine; conda environments can only be so isolated from each other. To begin the troubleshooting workflow, open a terminal (macOS, Linux) or an Anaconda Prompt (Windows), and identify the environments on the machine. If anaconda3 is installed on the Windows machine, there may be multiple options for this terminal; choose the Anaconda Prompt with "anaconda3" in parenthesis.
+
+**NOTE:** The following commands will be shown as if within an Anaconda Prompt to emphasize the difference for Windows users; for these purposes, the only difference between terminals is the appearance of the message (i.e., (active_env) PS \>) preceding the textual entry. No output will be shown here as differences in OS, environments, and versions will vary.
+
+First, identify the environments on the machine:
+
+
+```{r, eval=FALSE}
+(base) PS > conda info --envs
+```
+
+
+To proceed, any r-miniconda associated environments will be deleted, and the base environment will be updated. If **any** environment is frequently used for other analyses and a python version update is undesirable, it may be preserved by cloning the environment. The original environment, however, will be removed or updated, so ensure that files and workflows associated with this environment are redirected to the new, cloned environment. Ensure the path of the cloned environment is not associated with r-miniconda.
+
+**It is recommended that conda is updated within any cloned environment (see below).**
+
+
+```{r, eval=FALSE}
+(base) PS > conda create --name my_base_clone --clone base
+```
+
+
+Verify that the clone exists to the proper specifications before proceeding by comparing packages and python versions:
+
+
+```{r, eval=FALSE}
+(base) PS > conda info --envs
+(base) PS > conda activate my_base_clone
+(my_base_clone) PS > conda update conda
+(my_base_clone) PS > python -V
+(my_base_clone) PS > conda list
+(my_base_clone) PS > conda activate base
+(base) PS > python -V
+(base) PS > conda list 
+```
+
+
+Ensure the base environment is activated. If the r-miniconda environments are still on the machine, remove them. Specify the r-miniconda environments other than giotto_env, as these will be unique to the machine. This may be done at the command line:
+
+
+```{r, eval=FALSE}
+(base) PS > conda env remove --name giotto_env
+(base) PS > conda env remove /path/to/r-miniconda/
+```
+
+
+Alternatively, in R, reticulate can uninstall miniconda and remove the associated environments:
+
+
+```{r, eval=FALSE}
+reticulate::miniconda_uninstall()
+```
+
+
+It is advisable to remove any and all environments which are outdated and/or no longer used.
+
+Recall that by default, Giotto installs a miniconda environment with python v3.10.2 for interfacing with R. Older versions of conda in the base environment cannot handle a python version that high in a different environment. Therefore, the recommended troubleshooting method is to update conda and python within the base environment at a minimum. Updating to python v3.8.5 at a minimum is recommended. It is advisable to update conda and python within *each* environment on the machine if feasible.
+
+
+```{r, eval=FALSE}
+(base) PS > conda update conda
+(base) PS > conda update python==3.8.5
+```
+
+
+Finally, close the terminal and open the RStudio, VSCode, or an alternative IDE. Running the following should ensure successful installation:
+
+
+```{r, eval=FALSE}
+library(Giotto)
+installGiottoEnvironment(force_environment = TRUE, force_miniconda = TRUE)
+```
+
+
+If the issue persists, please post an issue on the [GitHub](https://github.com/drieslab/Giotto/issues).
+
diff --git a/vignettes/faqs.Rmd b/vignettes/faqs.Rmd
new file mode 100644
index 000000000..3f78be4d0
--- /dev/null
+++ b/vignettes/faqs.Rmd
@@ -0,0 +1,70 @@
+---
+title: "Frequently Asked Questions"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Frequently Asked Questions}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+# Installation
+
+- [How do I install an R package for the first time?](https://drieslab.github.io/Giotto/articles/installation.html)
+
+- [Can I install Python components manually?](https://drieslab.github.io/Giotto/articles/configuration.html)
+
+# Data Availability
+
+- Where can I find seqFISH+ and other ready-to-use datasets?
+
+Checkout our [GiottoData](https://github.com/drieslab/GiottoData) extension package to find already preprocessed datasets and Giotto mini Objects.
+
+-  Where else can I find more spatial datasets?
+
+Checkout the following for more spatial-omics data:
+
+ - [Aquila](https://aquila.cheunglab.org/view)
+ - Tencent\'s [SODB](https://gene.ai.tencent.com/SpatialOmics/)
+ - [PySODB](https://pysodb.readthedocs.io/en/latest/), a python interface for the SODB
+
+- How can I automatically download tutorial datasets?
+
+Use `getSpatialDataset()` from GiottoData:
+
+```{r, eval=FALSE}
+# Ensure Giotto Suite is installed
+if(!"Giotto" %in% installed.packages()) {
+  devtools::install_github("drieslab/Giotto@suite")
+}
+
+library(Giotto)
+
+# Ensure Giotto Data is installed
+if(!"GiottoData" %in% installed.packages()) {
+  devtools::install_github("drieslab/GiottoData")
+}
+
+library(GiottoData)
+
+
+# choose your directory
+my_working_dir = getwd()
+
+# merFISH example:
+
+# standard download data to working directory
+getSpatialDataset(dataset = 'merfish_preoptic', 
+                  directory = my_working_dir)
+
+# use wget to  download data to working directory (much faster)
+getSpatialDataset(dataset = 'merfish_preoptic', 
+                  directory = my_working_dir, 
+                  method = 'wget')
+
+# avoid certification issues with wget
+getSpatialDataset(dataset = 'merfish_preoptic', 
+                  directory = my_working_dir, 
+                  method = 'wget', 
+                  extra = '--no-check-certificate')
+```
+
diff --git a/vignettes/github_issues.Rmd b/vignettes/github_issues.Rmd
new file mode 100644
index 000000000..775718d94
--- /dev/null
+++ b/vignettes/github_issues.Rmd
@@ -0,0 +1,212 @@
+---
+title: "How to Submit a GitHub Issue"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{How to Submit a GitHub Issue}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+Please read through the information below before submitting your issue to our GitHub page. The link to report an issue can be found at the bottom of the page.
+
+## GitHub Issues Guidelines
+
+### Some Useful Commands
+
+It is helpful if you provide any relevant information about the software and Giotto object you are using. See below for some tips to get this information.
+
+- What version of R are you using?
+
+```{r, eval=FALSE}
+R.version.string
+```
+
+```{r, eval=FALSE}
+R version 4.0.4 (2021-02-15)
+```
+
+- What version of Giotto are you using?
+
+```{r, eval=FALSE}
+packageVersion("Giotto")
+```
+
+```{r, eval=FALSE}
+2.0.0.9044
+```
+
+- Are you using the Giotto environment or your own python path?
+
+```{r, eval=FALSE}
+# Check Giotto environment
+Giotto:::checkGiottoEnvironment()
+```
+
+```{r, eval=FALSE}
+giotto environment found at 
+/Users/natalie_dr/Library/r-miniconda/envs/giotto_env/bin/pythonw 
+```
+
+- Show sequential processing steps/commands in the Giotto object
+
+```{r, eval=FALSE}
+Giotto:::showProcessingSteps(my_giotto_object)
+```
+
+```{r, eval=FALSE}
+Processing steps: 
+0_normalize 
+```
+
+- Show the structure of the Giotto object
+
+```{r, eval=FALSE}
+str(my_giotto_object, max.level = 3)
+```
+
+```{r, eval=FALSE}
+Formal class 'giotto' [package "Giotto"] with 20 slots
+..@ expression         :List of 1
+.. ..$ rna:List of 3
+..@ expression_feat    : chr "rna"
+..@ spatial_locs       :List of 1
+.. ..$ raw:Classes ‘data.table’ and 'data.frame':   73655 obs. of  4 variables:
+.. .. ..- attr(*, ".internal.selfref")=<externalptr> 
+..@ spatial_info       : NULL
+..@ cell_metadata      :List of 1
+.. ..$ rna:Classes ‘data.table’ and 'data.frame':   73655 obs. of  1 variable:
+.. .. ..- attr(*, ".internal.selfref")=<externalptr> 
+..@ feat_metadata      :List of 1
+.. ..$ rna:Classes ‘data.table’ and 'data.frame':   161 obs. of  1 variable:
+.. .. ..- attr(*, ".internal.selfref")=<externalptr> 
+..@ feat_info          : NULL
+..@ cell_ID            : chr [1:73655] "cell_1" "cell_2" "cell_3" "cell_4" ...
+..@ feat_ID            :List of 1
+.. ..$ rna: chr [1:161] "Ace2" "Adora2a" "Aldh1l1" "Amigo2" ...
+..@ spatial_network    : NULL
+..@ spatial_grid       : NULL
+..@ spatial_enrichment : NULL
+..@ dimension_reduction: NULL
+..@ nn_network         : NULL
+..@ images             : NULL
+..@ parameters         :List of 1
+.. ..$ 0_normalize: Named chr [1:13] "my_giotto_object" "standard" "TRUE" "6000" ...
+.. .. ..- attr(*, "names")= chr [1:13] "gobject" "norm_methods" "library_size_norm" "scalefactor" ...
+..@ instructions       :List of 11
+.. ..$ python_path: chr "/Users/natalie_dr/Library/r-miniconda/envs/giotto_env/bin/pythonw"
+.. ..$ show_plot  : logi TRUE
+.. ..$ return_plot: logi TRUE
+.. ..$ save_plot  : logi FALSE
+.. ..$ save_dir   : chr "/Users/natalie_dr/Desktop/my_giotto/giotto_user_help"
+.. ..$ plot_format: chr "png"
+.. ..$ dpi        : num 300
+.. ..$ units      : chr "in"
+.. ..$ height     : num 9
+.. ..$ width      : num 9
+.. ..$ is_docker  : logi FALSE
+..@ offset_file        : NULL
+..@ OS_platform        : chr "unix"
+..@ join_info          : NULL
+```
+
+### Warning Messages
+
+- Deprecation warning
+
+```{r, eval=FALSE}
+my_giotto_object <- createGiottoObject(raw_exprs = "path/to/expression/data",
+                                   spatial_locs = "path/to/spatial/data")
+```
+
+```{r, eval=FALSE}
+Warning message:
+In createGiottoObject(raw_exprs = "/Users/username/path/to/data",  :
+    raw_exprs argument is deprecated, use expression argument in the future 
+```
+
+**Solution** The code has still run and your object has been created, but in the future use the following command:
+
+```{r, eval=FALSE}
+my_giotto_object <- createGiottoObject(expression = "path/to/expression/data",
+                                   spatial_locs = "path/to/spatial/data")
+```
+
+### Errors
+
+- Is this an error from Giotto?
+
+```{r, eval=FALSE}
+Error in adjustGiottoMatrix(gobject = my_giotto_object, expression_values = c("normalized"): covariate column name(s) were not found in the cell metadata 
+```
+
+**Solution** In this case, you would need to check your cell metadata (`my_giotto_object@cell_metadata`) and make appropriate adjustments.
+
+- Is this an error from an external package?
+
+```{r, eval=FALSE}
+Error in methods::as(as.matrix(x[, -1]), "Matrix") : 
+no method or default for coercing "matrix" to "Matrix"
+```
+
+**Solution** Ensure that the Matrix library is loaded:
+
+```{r, eval=FALSE}
+library(Matrix)
+```
+
+## Some steps before posting an issue
+
+- Google (or whichever search engine you prefer) the error
+- Look up the documentation for the package the error came from
+
+### Required information to provide
+
+- What code/data did you use? (copy-pasted or an example is helpful)
+- What did you expect your result to be?
+- What was your result?
+- If your result was an error message, please see the category on error messages to determine whether the source was Giotto or an external package.
+
+### How to create a reproducible example
+
+For us to be able to help you at the best of our ability, it\'s helpful if you can provide a reproducible example. This just means that anyone who reads your GitHub issue should be able to accurately reproduce your error.
+
+For more information on minimal reproducible examples check out [this link](https://stackoverflow.com/help/minimal-reproducible-example).
+
+And to see what other people recommend, please check out [this forum](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example).
+
+### Example of a Good GitHub issue
+
+- Provide a code example
+- Please use the GitHub "insert code" function or wrap your code like so:
+
+```{r, eval=FALSE}
+`x <- "hello world"
+
+print(x)`
+```
+
+*If applicable, provide a screenshot of the issue*
+
+I am having trouble adjusting my Giotto matix. I have inputted the
+following code:
+
+```{r, eval=FALSE}
+my_giotto_object <- adjustGiottoMatrix(gobject = my_giotto_object, 
+                                       expression_values = c('normalized'),
+                                       covariate_columns = c('nr_genes',
+                                                             'total_expr'))
+```
+
+I expected that my matrix would be appropriately adjusted, but I got the following error:
+
+```{r, eval=FALSE}
+Error in adjustGiottoMatrix(gobject = my_giotto_object, expression_values = c("normalized"): covariate column name(s) were not found in the cell metadata 
+```
+
+For more context, I am running R version 4.04 and Giotto version 2.0.0.9044. I can send you the data I used if necessary.
+
+### Example of a Bad GitHub issue
+
+I am having trouble adjusting my Giotto matrix. My error says that the covariate column name(s) were not found in the cell meta data. What do I do?
+
+Report An Issue <https://github.com/drieslab/Giotto/issues>
diff --git a/vignettes/image_alignment.Rmd b/vignettes/image_alignment.Rmd
index 23fc4e40f..a12ab97fb 100644
--- a/vignettes/image_alignment.Rmd
+++ b/vignettes/image_alignment.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Image Alignment"
-date: 4/14/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Image Alignment}
diff --git a/vignettes/installation.Rmd b/vignettes/installation.Rmd
index 09ce57fca..79718bc57 100644
--- a/vignettes/installation.Rmd
+++ b/vignettes/installation.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Installation"
-date: 4/12/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Installation}
@@ -30,7 +29,7 @@ if(!"devtools" %in% installed.packages()) {
   install.packages("devtools")
 }
 
-devtools::install_github("drieslab/Giotto@suite")
+devtools::install_github("drieslab/Giotto@suite_modular")
 ```
 
 
@@ -45,9 +44,9 @@ installGiottoEnvironment()
 
 # 3. Try Giotto in the cloud
 
-You can also run analyses in Giotto on Terra.bio. Take a look on the [Terra tutorial](https://giottosuite.readthedocs.io/en/latest/subsections/trygiotto/terra.html#terra/).
+You can also run analyses in Giotto on Terra.bio. Take a look on the [Terra tutorial]https://drieslab.github.io/Giotto/articles/terra.html).
 
-Encountering errors? Checkout out the [Troubleshooting page](../errorsfaqsandtips.html) for help. Alternatively, post to an issue to the Giotto GitHub page [here](https://github.com/drieslab/Giotto). Please include the version numbers of R, Giotto, and the OS in use at the time of the issue.
+Encountering errors? Checkout out the [Troubleshooting page](https://drieslab.github.io/Giotto/articles/errorsfaqsandtips.html) for help. Alternatively, post to an issue to the Giotto GitHub page [here](https://github.com/drieslab/Giotto). Please include the version numbers of R, Giotto, and the OS in use at the time of the issue.
 
 # 4. Session Info
 
diff --git a/vignettes/interactive_selection.Rmd b/vignettes/interactive_selection.Rmd
index 64cf6f35d..095bdb17c 100644
--- a/vignettes/interactive_selection.Rmd
+++ b/vignettes/interactive_selection.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Interactive selection"
-date: 2022-11-17
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Interactive selection}
diff --git a/vignettes/interoperability_anndata.Rmd b/vignettes/interoperability_anndata.Rmd
index b815c7b25..3a455d072 100644
--- a/vignettes/interoperability_anndata.Rmd
+++ b/vignettes/interoperability_anndata.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Interoperability: AnnData"
-date: 4/14/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Interoperability: AnnData}
diff --git a/vignettes/merfish_mouse_hypothalamic.Rmd b/vignettes/merfish_mouse_hypothalamic.Rmd
index 3dda9836f..b4f3d66ef 100644
--- a/vignettes/merfish_mouse_hypothalamic.Rmd
+++ b/vignettes/merfish_mouse_hypothalamic.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "MERFISH Mouse Hypothalamic Preoptic Region"
-date: 2022-09-16
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{MERFISH Mouse Hypothalamic Preoptic Region}
diff --git a/vignettes/mini_seqfish.Rmd b/vignettes/mini_seqfish.Rmd
index dbe4c5416..de4af1689 100644
--- a/vignettes/mini_seqfish.Rmd
+++ b/vignettes/mini_seqfish.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "mini seqFISH"
-date: 2022-09-16
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{mini seqFISH}
diff --git a/vignettes/nanostring_cosmx_lung_cancer.Rmd b/vignettes/nanostring_cosmx_lung_cancer.Rmd
index aa6ebcc75..7b4137672 100644
--- a/vignettes/nanostring_cosmx_lung_cancer.Rmd
+++ b/vignettes/nanostring_cosmx_lung_cancer.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Nanostring CosMx Subcellular Lung Cancer"
-date: 2022-11-30
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Nanostring CosMx Subcellular Lung Cancer}
diff --git a/vignettes/object_creation.Rmd b/vignettes/object_creation.Rmd
index 20bafb502..c1111dc23 100644
--- a/vignettes/object_creation.Rmd
+++ b/vignettes/object_creation.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Giotto Object Creation"
-date: 2023-07-26
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Giotto Object Creation}
diff --git a/vignettes/osmfish_mouse_ss_cortex.Rmd b/vignettes/osmfish_mouse_ss_cortex.Rmd
index 939dc9579..7eab5e5a9 100644
--- a/vignettes/osmfish_mouse_ss_cortex.Rmd
+++ b/vignettes/osmfish_mouse_ss_cortex.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "osmFISH Mouse SS Cortex"
-date: 2022-09-16
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{osmFISH Mouse SS Cortex}
diff --git a/vignettes/saving_object.Rmd b/vignettes/saving_object.Rmd
index 6c0457813..107e2916d 100644
--- a/vignettes/saving_object.Rmd
+++ b/vignettes/saving_object.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Saving your analysis"
-date: 4/14/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Saving your analysis}
diff --git a/vignettes/saving_plots.Rmd b/vignettes/saving_plots.Rmd
index 018ed287a..fb2c63d3f 100644
--- a/vignettes/saving_plots.Rmd
+++ b/vignettes/saving_plots.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Saving Plots"
-date: 4/14/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Saving Plots}
diff --git a/vignettes/seqfish_cortex.Rmd b/vignettes/seqfish_cortex.Rmd
index efa3929ac..4434cac6f 100644
--- a/vignettes/seqfish_cortex.Rmd
+++ b/vignettes/seqfish_cortex.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "SeqFish+ Mouse Cortex Example"
-date: 2022-09-16
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{SeqFish+ Mouse Cortex Example}
diff --git a/vignettes/seqscope_mouse_liver.rmd b/vignettes/seqscope_mouse_liver.rmd
index 520661ec0..6d523a465 100644
--- a/vignettes/seqscope_mouse_liver.rmd
+++ b/vignettes/seqscope_mouse_liver.rmd
@@ -1,6 +1,5 @@
 ---
 title: "Seq-Scope Mouse liver"
-date: 2022-11-15
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Seq-Scope Mouse liver}
diff --git a/vignettes/singlecell_prostate_integration.Rmd b/vignettes/singlecell_prostate_integration.Rmd
index c2cbc2eb7..cc828f7c1 100644
--- a/vignettes/singlecell_prostate_integration.Rmd
+++ b/vignettes/singlecell_prostate_integration.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Integration of single cell datasets"
-date: 2022-09-16
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Integration of single cell datasets}
diff --git a/vignettes/spatial_genomics_mouse_kidney.Rmd b/vignettes/spatial_genomics_mouse_kidney.Rmd
index 684c9472c..c2b752a01 100644
--- a/vignettes/spatial_genomics_mouse_kidney.Rmd
+++ b/vignettes/spatial_genomics_mouse_kidney.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Spatial Genomics Mouse Kidney"
-date: 8/9/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Spatial Genomics Mouse Kidney}
diff --git a/vignettes/spatial_transformations.Rmd b/vignettes/spatial_transformations.Rmd
index dd085626e..74e8f5f9e 100644
--- a/vignettes/spatial_transformations.Rmd
+++ b/vignettes/spatial_transformations.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Spatial Transformations"
-date: 7/28/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Spatial Transformations}
diff --git a/vignettes/structure.Rmd b/vignettes/structure.Rmd
index c7e833344..7aee15f88 100644
--- a/vignettes/structure.Rmd
+++ b/vignettes/structure.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "An introduction to the Giotto Suite classes"
-date: 2023-07-26
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{An introduction to the Giotto Suite classes}
diff --git a/vignettes/visium_cytassist_human_glioblastoma.Rmd b/vignettes/visium_cytassist_human_glioblastoma.Rmd
index 3863bb9bb..f7a423809 100644
--- a/vignettes/visium_cytassist_human_glioblastoma.Rmd
+++ b/vignettes/visium_cytassist_human_glioblastoma.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Visium CytAssist Multi-omics Human Glioblastoma"
-date: 9/7/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Visium CytAssist Multi-omics Human Glioblastoma}
diff --git a/vignettes/visium_cytassist_lungcancer.Rmd b/vignettes/visium_cytassist_lungcancer.Rmd
index 0dab4b186..a96185f16 100644
--- a/vignettes/visium_cytassist_lungcancer.Rmd
+++ b/vignettes/visium_cytassist_lungcancer.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Visium CytAssist Human Lung Cancer"
-date: 2022-11-23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Visium CytAssist Human Lung Cancer}
diff --git a/vignettes/visium_mouse_brain.Rmd b/vignettes/visium_mouse_brain.Rmd
index 2b5ccd910..2da1cc2fd 100644
--- a/vignettes/visium_mouse_brain.Rmd
+++ b/vignettes/visium_mouse_brain.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Visium Mouse Brain"
-date: 2022-09-16
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Visium Mouse Brain}
diff --git a/vignettes/visium_mouse_kidney.Rmd b/vignettes/visium_mouse_kidney.Rmd
index d693c5b84..7520bd5ae 100644
--- a/vignettes/visium_mouse_kidney.Rmd
+++ b/vignettes/visium_mouse_kidney.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Visium Mouse Kidney"
-date: 2021-08-30
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Visium Mouse Kidney}
diff --git a/vignettes/visium_prostate_integration.Rmd b/vignettes/visium_prostate_integration.Rmd
index 40c9a44da..e365c165e 100644
--- a/vignettes/visium_prostate_integration.Rmd
+++ b/vignettes/visium_prostate_integration.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Visium Prostate Integration"
-date: 5/5/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Visium Prostate Integration}
diff --git a/vignettes/visualizations.Rmd b/vignettes/visualizations.Rmd
index 39642443f..596b92453 100644
--- a/vignettes/visualizations.Rmd
+++ b/vignettes/visualizations.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Visualizations"
-date: 4/14/23
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Visualizations}
diff --git a/vignettes/vizgen_mouse_brain.Rmd b/vignettes/vizgen_mouse_brain.Rmd
index ed8ef462d..cabf8bc6a 100644
--- a/vignettes/vizgen_mouse_brain.Rmd
+++ b/vignettes/vizgen_mouse_brain.Rmd
@@ -1,6 +1,5 @@
 ---
 title: "Vizgen Mouse Brain Receptor Map"
-date: 2021-09-29
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Vizgen Mouse Brain Receptor Map}
diff --git a/vignettes/xenium_breast_cancer.rmd b/vignettes/xenium_breast_cancer.rmd
index e4f73619d..463d157b3 100644
--- a/vignettes/xenium_breast_cancer.rmd
+++ b/vignettes/xenium_breast_cancer.rmd
@@ -1,6 +1,5 @@
 ---
 title: "Xenium Human Breast Cancer Pre-Release"
-date: 2022-11-18
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Xenium Human Breast Cancer Pre-Release}