From af727ea8c63faec51fe914fba0149110d8a3a26f Mon Sep 17 00:00:00 2001
From: Alexandru Foias <afoias@polymtl.ca>
Date: Thu, 19 Aug 2021 10:59:51 -0400
Subject: [PATCH 01/14] fix software logo

---
 .gitbook/assets/github-mark-120px-plus.png | Bin 0 -> 4268 bytes
 software.md                                |  26 ++++++++++-----------
 2 files changed, 13 insertions(+), 13 deletions(-)
 create mode 100644 .gitbook/assets/github-mark-120px-plus.png

diff --git a/.gitbook/assets/github-mark-120px-plus.png b/.gitbook/assets/github-mark-120px-plus.png
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diff --git a/software.md b/software.md
index 877b924d..dcb9bdd1 100644
--- a/software.md
+++ b/software.md
@@ -6,24 +6,24 @@ Below is a list of software projects created at **NeuroPoly** or at collaborativ
 
 ### Histology
 
-| Name | Description | Language | Links |
+| Logo | Name | Description | Links |
 | :--- | :--- | :--- | :--- |
-| Atlas Rat | Scripts to generate a microstructure atlas of the rat spinal cord | MATLAB | [Source Code \(GitHub\)](https://github.com/neuropoly/atlas-rat) [Documentation](https://github.com/neuropoly/atlas-rat/blob/master/README.md|Documentation) |
-| AxonSeg | Automatic segmentation of axon and myelin from microscopy data | MATLAB | [Source Code \(GitHub\)](https://github.com/neuropoly/axonseg) [Documentation](https://github.com/neuropoly/axonseg/blob/master/README.md) |
-| AxonDeepSeg | Segmentation software for microscopy data using deep learning | Python | [Source Code \(GitHub\)](https://github.com/neuropoly/axondeepseg) [Documentation](https://axondeepseg.readthedocs.io/en/latest/) |
-| AxonPacking | Simulation software for arrangements of axons in white matter | MATLAB | [Source Code \(GitHub\)](%20https://github.com/neuropoly/axonpacking) [Documentation](https://github.com/neuropoly/axonpacking/blob/master/README.md) |
-| Tract Clustering | Data-driven approach for tracts in rat histology | Python | [Source Code \(GitHub\) ](https://github.com/neuropoly/tract-clustering)[Documentation](https://github.com/neuropoly/tract-clustering/blob/master/README.md) |
+| ![](../../.gitbook/assets/github-mark-120px-plus.png) | Atlas Rat | Scripts to generate a microstructure atlas of the rat spinal cord | [Source Code \(GitHub\)](https://github.com/neuropoly/atlas-rat) [Documentation](https://github.com/neuropoly/atlas-rat/blob/master/README.md|Documentation) |
+|  | AxonSeg | Automatic segmentation of axon and myelin from microscopy data | [Source Code \(GitHub\)](https://github.com/neuropoly/axonseg) [Documentation](https://github.com/neuropoly/axonseg/blob/master/README.md) |
+|  | AxonDeepSeg | Segmentation software for microscopy data using deep learning | [Source Code \(GitHub\)](https://github.com/neuropoly/axondeepseg) [Documentation](https://axondeepseg.readthedocs.io/en/latest/) |
+|  | AxonPacking | Simulation software for arrangements of axons in white matter | [Source Code \(GitHub\)](%20https://github.com/neuropoly/axonpacking) [Documentation](https://github.com/neuropoly/axonpacking/blob/master/README.md) |
+|  | Tract Clustering | Data-driven approach for tracts in rat histology | [Source Code \(GitHub\) ](https://github.com/neuropoly/tract-clustering)[Documentation](https://github.com/neuropoly/tract-clustering/blob/master/README.md) |
 
 ### MRI
 
-| Name | Description | Language | Links |
+| Logo | Name | Description | Links |
 | :--- | :--- | :--- | :--- |
-|  ivadomed | Comprehensive and open-source repository of deep learning methods for medical data segmentation | Python | [Source Code \(GitHub\)](https://github.com/ivadomed/ivadomed) [Documentation](https://ivadomed.org/en/latest/) |
-| Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project | Python | [Source Code \(GitHub\)](https://github.com/neuropoly/multiclass-segmentation) [Documentation](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
-| qMRLab | Software for data aimulation, analysis, and visualization of qMRI data \(Magnetization Transfer, Diffusion, etc.\) | MATLAB | [Source Code \(GitHub\)](https://github.com/qMRLab/qMRLab) [Documentation](https://qmrlab.readthedocs.io/en/master/) |
-| Shimming Toolbox | Code for performing real-time shimming using external MRI shim coils | MATLAB Python | [Source Code \(GitHub\) ](https://github.com/shimming-toolbox)[Documentation](https://shimming-toolbox.org/en/latest/) |
-| Spinal Cord Toolbox | Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord | Python | [Source Code \(GitHub\)](https://github.com/neuropoly/spinalcordtoolbox) [Documentation](https://spinalcordtoolbox.com/en/latest/) |
-| Template | A framework for creating unbiased MRI templates of the spinal cord | Python | [Source Code \(GitHub\)](https://github.com/neuropoly/template) [Documentation](https://github.com/neuropoly/template/blob/master/README.md) |
+|  |  ivadomed | Comprehensive and open-source repository of deep learning methods for medical data segmentation | [Source Code \(GitHub\)](https://github.com/ivadomed/ivadomed) [Documentation](https://ivadomed.org/en/latest/) |
+|  | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project | [Source Code \(GitHub\)](https://github.com/neuropoly/multiclass-segmentation) [Documentation](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
+|  | qMRLab | Software for data aimulation, analysis, and visualization of qMRI data \(Magnetization Transfer, Diffusion, etc.\) | [Source Code \(GitHub\)](https://github.com/qMRLab/qMRLab) [Documentation](https://qmrlab.readthedocs.io/en/master/) |
+|  | Shimming Toolbox | Code for performing real-time shimming using external MRI shim coils | [Source Code \(GitHub\) ](https://github.com/shimming-toolbox)[Documentation](https://shimming-toolbox.org/en/latest/) |
+|  | Spinal Cord Toolbox | Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord | [Source Code \(GitHub\)](https://github.com/neuropoly/spinalcordtoolbox) [Documentation](https://spinalcordtoolbox.com/en/latest/) |
+|  | Template | A framework for creating unbiased MRI templates of the spinal cord | [Source Code \(GitHub\)](https://github.com/neuropoly/template) [Documentation](https://github.com/neuropoly/template/blob/master/README.md) |
 
 ## Contributing
 

From a84b52ce35b70a4551f0317b71684d59b6878b19 Mon Sep 17 00:00:00 2001
From: Alexandru Foias <afoias@polymtl.ca>
Date: Fri, 3 Dec 2021 11:49:09 -0500
Subject: [PATCH 02/14] add logo column

---
 software.md | 41 +++++++++++++++++++----------------------
 1 file changed, 19 insertions(+), 22 deletions(-)

diff --git a/software.md b/software.md
index dcb9bdd1..0e7fb199 100644
--- a/software.md
+++ b/software.md
@@ -1,33 +1,30 @@
-# 🖥  Software
+# `🖥` Software
 
 ## Open-Source Projects
 
 Below is a list of software projects created at **NeuroPoly** or at collaborative institutions. These projects are open source and freely available.
 
-### Histology
-
-| Logo | Name | Description | Links |
-| :--- | :--- | :--- | :--- |
-| ![](../../.gitbook/assets/github-mark-120px-plus.png) | Atlas Rat | Scripts to generate a microstructure atlas of the rat spinal cord | [Source Code \(GitHub\)](https://github.com/neuropoly/atlas-rat) [Documentation](https://github.com/neuropoly/atlas-rat/blob/master/README.md|Documentation) |
-|  | AxonSeg | Automatic segmentation of axon and myelin from microscopy data | [Source Code \(GitHub\)](https://github.com/neuropoly/axonseg) [Documentation](https://github.com/neuropoly/axonseg/blob/master/README.md) |
-|  | AxonDeepSeg | Segmentation software for microscopy data using deep learning | [Source Code \(GitHub\)](https://github.com/neuropoly/axondeepseg) [Documentation](https://axondeepseg.readthedocs.io/en/latest/) |
-|  | AxonPacking | Simulation software for arrangements of axons in white matter | [Source Code \(GitHub\)](%20https://github.com/neuropoly/axonpacking) [Documentation](https://github.com/neuropoly/axonpacking/blob/master/README.md) |
-|  | Tract Clustering | Data-driven approach for tracts in rat histology | [Source Code \(GitHub\) ](https://github.com/neuropoly/tract-clustering)[Documentation](https://github.com/neuropoly/tract-clustering/blob/master/README.md) |
-
 ### MRI
 
-| Logo | Name | Description | Links |
-| :--- | :--- | :--- | :--- |
-|  |  ivadomed | Comprehensive and open-source repository of deep learning methods for medical data segmentation | [Source Code \(GitHub\)](https://github.com/ivadomed/ivadomed) [Documentation](https://ivadomed.org/en/latest/) |
-|  | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project | [Source Code \(GitHub\)](https://github.com/neuropoly/multiclass-segmentation) [Documentation](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
-|  | qMRLab | Software for data aimulation, analysis, and visualization of qMRI data \(Magnetization Transfer, Diffusion, etc.\) | [Source Code \(GitHub\)](https://github.com/qMRLab/qMRLab) [Documentation](https://qmrlab.readthedocs.io/en/master/) |
-|  | Shimming Toolbox | Code for performing real-time shimming using external MRI shim coils | [Source Code \(GitHub\) ](https://github.com/shimming-toolbox)[Documentation](https://shimming-toolbox.org/en/latest/) |
-|  | Spinal Cord Toolbox | Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord | [Source Code \(GitHub\)](https://github.com/neuropoly/spinalcordtoolbox) [Documentation](https://spinalcordtoolbox.com/en/latest/) |
-|  | Template | A framework for creating unbiased MRI templates of the spinal cord | [Source Code \(GitHub\)](https://github.com/neuropoly/template) [Documentation](https://github.com/neuropoly/template/blob/master/README.md) |
+| Logo                    | Name                    | Description                                                                                                      | Source                                                                                                                                     | Documentation                                                                                                                                                               |
+| ----------------------- | ----------------------- | ---------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ----------------------- | ivadomed                | Comprehensive and open-source repository of deep learning methods for medical data segmentation                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/ivadomed/ivadomed)                 | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://ivadomed.org/en/latest/)                                            |
+| ----------------------- | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/multiclass-segmentation) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
+| ----------------------- | qMRLab                  | Software for data aimulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.) | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/qMRLab/qMRLab)                     | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://qmrlab.readthedocs.io/en/master/)                                   |
+| ----------------------- | Shimming Toolbox        | Code for performing real-time shimming using external MRI shim coils                                             | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/shimming-toolbox)                  | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://shimming-toolbox.org/en/latest/)                                    |
+| ----------------------- | Spinal Cord Toolbox     | Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord              | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/spinalcordtoolbox)       | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://spinalcordtoolbox.com/en/latest/)                                   |
+| ----------------------- | Template                | A framework for creating unbiased MRI templates of the spinal cord                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/template)                | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/template/blob/master/README.md)                |
 
-## Contributing
-
-**NeuroPoly** welcomes and appreciates contributions. To get started, please check out **NeuroPoly**'s contributing guidelines: [NeuroPoly Lab: Software Contributing Guidlines](https://neuropoly.gitbook.io/neuropoly-lab/software-development/contributing).
+### Histology
 
+| Logo             | Name             | Description                                                       | Source                                                                                                                              | Documentation                                                                                                                                                                         |
+| ---------------- | ---------------- | ----------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ---------------- | Atlas Rat        | Scripts to generate a microstructure atlas of the rat spinal cord | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/atlas-rat)        | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/atlas-rat/blob/master/README.md\|Documentation)          |
+| ---------------- | AxonSeg          | Automatic segmentation of axon and myelin from microscopy data    | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonseg)          | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonseg/blob/master/README.md)                           |
+| ---------------- | AxonDeepSeg      | Segmentation software for microscopy data using deep learning     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axondeepseg)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://axondeepseg.readthedocs.io/en/latest/)                                        |
+| ---------------- | AxonPacking      | Simulation software for arrangements of axons in white matter     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonpacking)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonpacking/blob/master/README.md)                       |
+| ---------------- | Tract Clustering | Data-driven approach for tracts in rat histology                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/tract-clustering) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/tract-clustering/blob/master/README.md)                  |
 
+### Contributing
 
+**NeuroPoly** welcomes and appreciates contributions. To get started, please check out [**NeuroPoly**'s contributing guidelines](https://intranet.neuro.polymtl.ca/geek-tips/contributing).

From 2f6bd49fb4c9bd2f3c1b8d26e3bed92d1a3d1302 Mon Sep 17 00:00:00 2001
From: Alexandru Foias <afoias@polymtl.ca>
Date: Fri, 3 Dec 2021 13:45:46 -0500
Subject: [PATCH 03/14] add logos

---
 software.md | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/software.md b/software.md
index 0e7fb199..e608ff7a 100644
--- a/software.md
+++ b/software.md
@@ -8,22 +8,22 @@ Below is a list of software projects created at **NeuroPoly** or at collaborativ
 
 | Logo                    | Name                    | Description                                                                                                      | Source                                                                                                                                     | Documentation                                                                                                                                                               |
 | ----------------------- | ----------------------- | ---------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| ----------------------- | ivadomed                | Comprehensive and open-source repository of deep learning methods for medical data segmentation                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/ivadomed/ivadomed)                 | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://ivadomed.org/en/latest/)                                            |
-| ----------------------- | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/multiclass-segmentation) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
-| ----------------------- | qMRLab                  | Software for data aimulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.) | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/qMRLab/qMRLab)                     | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://qmrlab.readthedocs.io/en/master/)                                   |
-| ----------------------- | Shimming Toolbox        | Code for performing real-time shimming using external MRI shim coils                                             | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/shimming-toolbox)                  | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://shimming-toolbox.org/en/latest/)                                    |
-| ----------------------- | Spinal Cord Toolbox     | Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord              | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/spinalcordtoolbox)       | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://spinalcordtoolbox.com/en/latest/)                                   |
-| ----------------------- | Template                | A framework for creating unbiased MRI templates of the spinal cord                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/template)                | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/template/blob/master/README.md)                |
+| ![](https://raw.githubusercontent.com/ivadomed/ivadomed/master/images/ivadomed_logo.png) | ivadomed                | Comprehensive and open-source repository of deep learning methods for medical data segmentation                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/ivadomed/ivadomed)                 | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://ivadomed.org/en/latest/)                                            |
+| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/multiclass-segmentation) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
+| ![](https://raw.githubusercontent.com/qMRLab/documentation/master/logo/qMR_logo_orig.png) | qMRLab                  | Software for data aimulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.) | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/qMRLab/qMRLab)                     | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://qmrlab.readthedocs.io/en/master/)                                   |
+| ![](https://raw.githubusercontent.com/shimming-toolbox/shimming-toolbox/master/docs/source/_static/img/shimming_toolbox_logo.png) | Shimming Toolbox        | Code for performing real-time shimming using external MRI shim coils                                             | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/shimming-toolbox)                  | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://shimming-toolbox.org/en/latest/)                                    |
+| ![](https://raw.githubusercontent.com/spinalcordtoolbox/spinalcordtoolbox/master/documentation/source/_static/img/logo_sct.png) | Spinal Cord Toolbox     | Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord              | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/spinalcordtoolbox)       | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://spinalcordtoolbox.com/en/latest/)                                   |
+| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | Template                | A framework for creating unbiased MRI templates of the spinal cord                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/template)                | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/template/blob/master/README.md)                |
 
 ### Histology
 
 | Logo             | Name             | Description                                                       | Source                                                                                                                              | Documentation                                                                                                                                                                         |
 | ---------------- | ---------------- | ----------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| ---------------- | Atlas Rat        | Scripts to generate a microstructure atlas of the rat spinal cord | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/atlas-rat)        | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/atlas-rat/blob/master/README.md\|Documentation)          |
-| ---------------- | AxonSeg          | Automatic segmentation of axon and myelin from microscopy data    | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonseg)          | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonseg/blob/master/README.md)                           |
-| ---------------- | AxonDeepSeg      | Segmentation software for microscopy data using deep learning     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axondeepseg)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://axondeepseg.readthedocs.io/en/latest/)                                        |
-| ---------------- | AxonPacking      | Simulation software for arrangements of axons in white matter     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonpacking)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonpacking/blob/master/README.md)                       |
-| ---------------- | Tract Clustering | Data-driven approach for tracts in rat histology                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/tract-clustering) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/tract-clustering/blob/master/README.md)                  |
+| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | Atlas Rat        | Scripts to generate a microstructure atlas of the rat spinal cord | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/atlas-rat)        | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/atlas-rat/blob/master/README.md)          |
+| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | AxonSeg          | Automatic segmentation of axon and myelin from microscopy data    | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonseg)          | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonseg/blob/master/README.md)                           |
+| ![](https://raw.githubusercontent.com/neuropoly/axondeepseg/master/docs/source/_static/logo_ads-alpha.png) | AxonDeepSeg      | Segmentation software for microscopy data using deep learning     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axondeepseg)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://axondeepseg.readthedocs.io/en/latest/)                                        |
+| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | AxonPacking      | Simulation software for arrangements of axons in white matter     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonpacking)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonpacking/blob/master/README.md)                       |
+| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | Tract Clustering | Data-driven approach for tracts in rat histology                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/tract-clustering) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/tract-clustering/blob/master/README.md)                  |
 
 ### Contributing
 

From de4cadaf05d503200d866ceee949d210802dafdf Mon Sep 17 00:00:00 2001
From: Alexandru Foias <afoias@polymtl.ca>
Date: Fri, 3 Dec 2021 14:12:22 -0500
Subject: [PATCH 04/14] force fixed height

---
 software.md | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/software.md b/software.md
index e608ff7a..8df7400d 100644
--- a/software.md
+++ b/software.md
@@ -8,22 +8,22 @@ Below is a list of software projects created at **NeuroPoly** or at collaborativ
 
 | Logo                    | Name                    | Description                                                                                                      | Source                                                                                                                                     | Documentation                                                                                                                                                               |
 | ----------------------- | ----------------------- | ---------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| ![](https://raw.githubusercontent.com/ivadomed/ivadomed/master/images/ivadomed_logo.png) | ivadomed                | Comprehensive and open-source repository of deep learning methods for medical data segmentation                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/ivadomed/ivadomed)                 | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://ivadomed.org/en/latest/)                                            |
-| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/multiclass-segmentation) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
-| ![](https://raw.githubusercontent.com/qMRLab/documentation/master/logo/qMR_logo_orig.png) | qMRLab                  | Software for data aimulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.) | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/qMRLab/qMRLab)                     | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://qmrlab.readthedocs.io/en/master/)                                   |
-| ![](https://raw.githubusercontent.com/shimming-toolbox/shimming-toolbox/master/docs/source/_static/img/shimming_toolbox_logo.png) | Shimming Toolbox        | Code for performing real-time shimming using external MRI shim coils                                             | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/shimming-toolbox)                  | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://shimming-toolbox.org/en/latest/)                                    |
-| ![](https://raw.githubusercontent.com/spinalcordtoolbox/spinalcordtoolbox/master/documentation/source/_static/img/logo_sct.png) | Spinal Cord Toolbox     | Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord              | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/spinalcordtoolbox)       | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://spinalcordtoolbox.com/en/latest/)                                   |
-| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | Template                | A framework for creating unbiased MRI templates of the spinal cord                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/template)                | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/template/blob/master/README.md)                |
+| <img src="https://raw.githubusercontent.com/ivadomed/ivadomed/master/images/ivadomed_logo.png"  height="50" /> | ivadomed                | Comprehensive and open-source repository of deep learning methods for medical data segmentation                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/ivadomed/ivadomed)                 | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://ivadomed.org/en/latest/)                                            |
+|  | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/multiclass-segmentation) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
+| <img src="https://raw.githubusercontent.com/qMRLab/documentation/master/logo/qMR_logo_orig.png" height="100" /> | qMRLab                  | Software for data aimulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.) | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/qMRLab/qMRLab)                     | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://qmrlab.readthedocs.io/en/master/)                                   |
+| <img src="https://raw.githubusercontent.com/shimming-toolbox/shimming-toolbox/master/docs/source/_static/img/shimming_toolbox_logo.png"  height="100" /> | Shimming Toolbox        | Code for performing real-time shimming using external MRI shim coils                                             | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/shimming-toolbox)                  | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://shimming-toolbox.org/en/latest/)                                    |
+| <img src="https://raw.githubusercontent.com/spinalcordtoolbox/spinalcordtoolbox/master/documentation/source/_static/img/logo_sct.png" height="100" /> | Spinal Cord Toolbox     | Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord              | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/spinalcordtoolbox)       | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://spinalcordtoolbox.com/en/latest/)                                   |
+|  | Template                | A framework for creating unbiased MRI templates of the spinal cord                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/template)                | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/template/blob/master/README.md)                |
 
 ### Histology
 
 | Logo             | Name             | Description                                                       | Source                                                                                                                              | Documentation                                                                                                                                                                         |
 | ---------------- | ---------------- | ----------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | Atlas Rat        | Scripts to generate a microstructure atlas of the rat spinal cord | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/atlas-rat)        | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/atlas-rat/blob/master/README.md)          |
-| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | AxonSeg          | Automatic segmentation of axon and myelin from microscopy data    | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonseg)          | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonseg/blob/master/README.md)                           |
-| ![](https://raw.githubusercontent.com/neuropoly/axondeepseg/master/docs/source/_static/logo_ads-alpha.png) | AxonDeepSeg      | Segmentation software for microscopy data using deep learning     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axondeepseg)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://axondeepseg.readthedocs.io/en/latest/)                                        |
-| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | AxonPacking      | Simulation software for arrangements of axons in white matter     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonpacking)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonpacking/blob/master/README.md)                       |
-| ![](https://avatars.githubusercontent.com/u/7755716?s=200&v=4) | Tract Clustering | Data-driven approach for tracts in rat histology                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/tract-clustering) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/tract-clustering/blob/master/README.md)                  |
+|  | Atlas Rat        | Scripts to generate a microstructure atlas of the rat spinal cord | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/atlas-rat)        | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/atlas-rat/blob/master/README.md)          |
+|  | AxonSeg          | Automatic segmentation of axon and myelin from microscopy data    | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonseg)          | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonseg/blob/master/README.md)                           |
+| <img src="https://raw.githubusercontent.com/neuropoly/axondeepseg/master/docs/source/_static/logo_ads-alpha.png" height="100" /> | AxonDeepSeg      | Segmentation software for microscopy data using deep learning     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axondeepseg)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://axondeepseg.readthedocs.io/en/latest/)                                        |
+|  | AxonPacking      | Simulation software for arrangements of axons in white matter     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonpacking)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonpacking/blob/master/README.md)                       |
+|  | Tract Clustering | Data-driven approach for tracts in rat histology                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/tract-clustering) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/tract-clustering/blob/master/README.md)                  |
 
 ### Contributing
 

From ef311af570c9d2255626eb2e8b75a7c5379147ab Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Sat, 4 Dec 2021 16:34:40 -0500
Subject: [PATCH 05/14] Implemented gallery view for software

---
 .gitignore  |  2 ++
 Makefile    |  4 +++
 conf.py     | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 gallery.yml | 20 ++++++++++++
 setup.py    |  3 +-
 software.md | 30 +++++++++--------
 6 files changed, 138 insertions(+), 15 deletions(-)
 create mode 100644 gallery.yml

diff --git a/.gitignore b/.gitignore
index 4e434a90..ebcf7b27 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,5 @@ _build/
 
 .DS_Store
 Thumbs.db
+
+gallery.txt
diff --git a/Makefile b/Makefile
index d4bb2cbb..9bf70d34 100644
--- a/Makefile
+++ b/Makefile
@@ -17,4 +17,8 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
+	# @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+# live:
+#   sphinx-autobuild . _build/html/ --ignore */contributing.md --ignore */gallery.txt --ignore */team_panels_code.txt
\ No newline at end of file
diff --git a/conf.py b/conf.py
index f3554fcf..82587edd 100644
--- a/conf.py
+++ b/conf.py
@@ -34,6 +34,7 @@
 extensions = [
         'myst_parser', # there's also myst_nb, which supports embedding Jupyter notebooks, but is heavier.
         'sphinx_panels',
+        'sphinx_design',
 ]
 
 myst_heading_anchors = 4 # enable #section links: https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#syntax-header-anchors
@@ -103,3 +104,96 @@
                                   "README.html")): # don't create dangling symlinks;
                                                    # it annoyes Github Pages.
                 os.symlink("README.html", z)
+
+
+
+
+# -- Custom scripts ----------------------------------------------------------
+
+import os
+from pathlib import Path
+import random
+import requests
+from subprocess import run
+from textwrap import dedent
+from urllib.parse import urlparse
+from ghapi.all import GhApi
+import pandas as pd
+
+import yaml
+
+from sphinx.application import Sphinx
+from sphinx.util import logging
+
+LOGGER = logging.getLogger("conf")
+
+def build_gallery(app: Sphinx):
+    # Build the gallery file
+    LOGGER.info("building gallery...")
+    grid_items = []
+    projects = yaml.safe_load((Path(app.srcdir) / "gallery.yml").read_text())
+    random.shuffle(projects)
+    for item in projects:
+        if not item.get("image"):
+            item["image"] = "https://jupyterbook.org/_images/logo-square.svg"
+
+        repo_text = ""
+        star_text = ""
+
+        if item["repository"]:
+            repo_text = f'{{bdg-link-secondary}}`repo <{item["repository"]}>`'
+
+            try:
+                url = urlparse(item["repository"])
+                if url.netloc == "github.com":
+                    _, org, repo = url.path.rstrip("/").split("/")
+                    star_text = f"[![GitHub Repo stars](https://img.shields.io/github/stars/{org}/{repo}?style=social)]({item['repository']})"
+            except Exception as error:
+                pass
+
+        grid_items.append(
+            f"""\
+        `````{{grid-item-card}} {" ".join(item["name"].split())}
+        :text-align: center
+        <img src="{item["image"]}" alt="logo" loading="lazy" style="max-width: 100%; max-height: 200px; margin-top: 1rem;" />
+        +++
+        ````{{grid}} 2 2 2 2
+        :margin: 0 0 0 0
+        :padding: 0 0 0 0
+        :gutter: 1
+        ```{{grid-item}}
+        :child-direction: row
+        :child-align: start
+        :class: sd-fs-5
+        {{bdg-link-secondary}}`website <{item["website"]}>`
+        {repo_text}
+        ```
+        ```{{grid-item}}
+        :child-direction: row
+        :child-align: end
+        {star_text}
+        ```
+        ````
+        `````
+        """
+        )
+    grid_items = "\n".join(grid_items)
+
+# :column: text-center col-6 col-lg-4
+# :card: +my-2
+# :img-top-cls: w-75 m-auto p-2
+# :body: d-none
+
+    panels = f"""
+``````{{grid}} 1 2 3 3
+:gutter: 1 1 2 2
+:class-container: full-width
+{dedent(grid_items)}
+``````
+    """
+    (Path(app.srcdir) / "gallery.txt").write_text(panels)
+
+
+def setup(app: Sphinx):
+    app.add_css_file("_static/theme.css")
+    app.connect("builder-inited", build_gallery)
diff --git a/gallery.yml b/gallery.yml
new file mode 100644
index 00000000..0bcba76d
--- /dev/null
+++ b/gallery.yml
@@ -0,0 +1,20 @@
+- name: Spinal Cord Toolbox
+  website: https://spinalcordtoolbox.com/
+  repository: https://github.com/spinalcordtoolbox/spinalcordtoolbox
+  image: https://raw.githubusercontent.com/spinalcordtoolbox/spinalcordtoolbox/master/documentation/source/_static/img/logo_sct.png
+- name: ivadomed
+  website: https://ivadomed.org
+  repository: https://github.com/ivadomed/ivadomed
+  image: https://raw.githubusercontent.com/ivadomed/ivadomed/master/images/ivadomed_logo.png
+- name: qmMRLab
+  website: https://qmrlab.readthedocs.io
+  repository: https://github.com/qMRLab/qMRLab
+  image: https://raw.githubusercontent.com/qMRLab/documentation/master/logo/qMR_logo_orig.png
+- name: Shimming Toolbox
+  website: https://shimming-toolbox.org
+  repository: https://github.com/shimming-toolbox
+  image: https://raw.githubusercontent.com/shimming-toolbox/shimming-toolbox/master/docs/source/_static/img/shimming_toolbox_logo.png
+- name: AxonDeepSeg
+  website: https://axondeepseg.readthedocs.io/
+  repository: https://github.com/neuropoly/axondeepseg
+  image: https://raw.githubusercontent.com/neuropoly/axondeepseg/master/docs/source/_static/logo_ads-alpha.png
diff --git a/setup.py b/setup.py
index 2dec8a9e..c3a287f3 100644
--- a/setup.py
+++ b/setup.py
@@ -20,7 +20,8 @@
             "myst-parser",
             "sphinx-book-theme",
             "sphinx-panels",
-            # pinned because of this bug https://github.com/pydata/pydata-sphinx-theme/pull/509
+            "sphinx-design~=0.0.11",
+# pinned because of this bug https://github.com/pydata/pydata-sphinx-theme/pull/509
             # and that the patched sphinx-book-theme isn't out yet: https://github.com/executablebooks/sphinx-book-theme/issues/428#issuecomment-966021270
             "sphinx~=4.2.0", # TODO: unpin when the next sphinx-book-theme is released
         ],
diff --git a/software.md b/software.md
index 8df7400d..1a0e21b3 100644
--- a/software.md
+++ b/software.md
@@ -4,26 +4,28 @@
 
 Below is a list of software projects created at **NeuroPoly** or at collaborative institutions. These projects are open source and freely available.
 
-### MRI
+```{include} gallery.txt
+```
 
-| Logo                    | Name                    | Description                                                                                                      | Source                                                                                                                                     | Documentation                                                                                                                                                               |
-| ----------------------- | ----------------------- | ---------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| <img src="https://raw.githubusercontent.com/ivadomed/ivadomed/master/images/ivadomed_logo.png"  height="50" /> | ivadomed                | Comprehensive and open-source repository of deep learning methods for medical data segmentation                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/ivadomed/ivadomed)                 | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://ivadomed.org/en/latest/)                                            |
-|  | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/multiclass-segmentation) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
-| <img src="https://raw.githubusercontent.com/qMRLab/documentation/master/logo/qMR_logo_orig.png" height="100" /> | qMRLab                  | Software for data aimulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.) | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/qMRLab/qMRLab)                     | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://qmrlab.readthedocs.io/en/master/)                                   |
-| <img src="https://raw.githubusercontent.com/shimming-toolbox/shimming-toolbox/master/docs/source/_static/img/shimming_toolbox_logo.png"  height="100" /> | Shimming Toolbox        | Code for performing real-time shimming using external MRI shim coils                                             | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/shimming-toolbox)                  | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://shimming-toolbox.org/en/latest/)                                    |
-| <img src="https://raw.githubusercontent.com/spinalcordtoolbox/spinalcordtoolbox/master/documentation/source/_static/img/logo_sct.png" height="100" /> | Spinal Cord Toolbox     | Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord              | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/spinalcordtoolbox)       | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://spinalcordtoolbox.com/en/latest/)                                   |
-|  | Template                | A framework for creating unbiased MRI templates of the spinal cord                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/template)                | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/template/blob/master/README.md)                |
+<!-- Deprecated software:
 
-### Histology
+|  | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/multiclass-segmentation) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
 
-| Logo             | Name             | Description                                                       | Source                                                                                                                              | Documentation                                                                                                                                                                         |
-| ---------------- | ---------------- | ----------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-|  | Atlas Rat        | Scripts to generate a microstructure atlas of the rat spinal cord | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/atlas-rat)        | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/atlas-rat/blob/master/README.md)          |
 |  | AxonSeg          | Automatic segmentation of axon and myelin from microscopy data    | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonseg)          | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonseg/blob/master/README.md)                           |
-| <img src="https://raw.githubusercontent.com/neuropoly/axondeepseg/master/docs/source/_static/logo_ads-alpha.png" height="100" /> | AxonDeepSeg      | Segmentation software for microscopy data using deep learning     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axondeepseg)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://axondeepseg.readthedocs.io/en/latest/)                                        |
+
+
 |  | AxonPacking      | Simulation software for arrangements of axons in white matter     | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonpacking)      | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonpacking/blob/master/README.md)                       |
+-->
+
+<!-- Data / Atlas to add in another section
+
+|  | Template                | A framework for creating unbiased MRI templates of the spinal cord                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/template)                | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/template/blob/master/README.md)                |
+
+|  | Atlas Rat        | Scripts to generate a microstructure atlas of the rat spinal cord | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/atlas-rat)        | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/atlas-rat/blob/master/README.md)          |
+
 |  | Tract Clustering | Data-driven approach for tracts in rat histology                  | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/tract-clustering) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/tract-clustering/blob/master/README.md)                  |
+-->
+
 
 ### Contributing
 

From 508f2ed6d4d6afe6b6dcc6057f552408353a7f11 Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Sat, 4 Dec 2021 16:39:15 -0500
Subject: [PATCH 06/14] Removed temporary changes in Makefile

---
 Makefile | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/Makefile b/Makefile
index 9bf70d34..d4bb2cbb 100644
--- a/Makefile
+++ b/Makefile
@@ -17,8 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	# @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-# live:
-#   sphinx-autobuild . _build/html/ --ignore */contributing.md --ignore */gallery.txt --ignore */team_panels_code.txt
\ No newline at end of file

From f0a218e97abd39787295ae40fe482658860355fe Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Sat, 4 Dec 2021 16:47:34 -0500
Subject: [PATCH 07/14] Fixed typo

---
 gallery.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gallery.yml b/gallery.yml
index 0bcba76d..7b6bd2df 100644
--- a/gallery.yml
+++ b/gallery.yml
@@ -6,7 +6,7 @@
   website: https://ivadomed.org
   repository: https://github.com/ivadomed/ivadomed
   image: https://raw.githubusercontent.com/ivadomed/ivadomed/master/images/ivadomed_logo.png
-- name: qmMRLab
+- name: qMRLab
   website: https://qmrlab.readthedocs.io
   repository: https://github.com/qMRLab/qMRLab
   image: https://raw.githubusercontent.com/qMRLab/documentation/master/logo/qMR_logo_orig.png

From 176ebe57d49e93a0e5e362eaf85b2f26e02475a4 Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Sat, 4 Dec 2021 17:47:44 -0500
Subject: [PATCH 08/14] Removed empty lines

https://github.com/neuropoly/neuro.polymtl.ca/pull/19#discussion_r762472783
---
 conf.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/conf.py b/conf.py
index 82587edd..a65d23c1 100644
--- a/conf.py
+++ b/conf.py
@@ -106,8 +106,6 @@
                 os.symlink("README.html", z)
 
 
-
-
 # -- Custom scripts ----------------------------------------------------------
 
 import os

From 72c5bf10bca96bead31321c70a1cb66377267708 Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Sat, 4 Dec 2021 17:51:06 -0500
Subject: [PATCH 09/14] fixed comment

---
 setup.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/setup.py b/setup.py
index c3a287f3..4299a35d 100644
--- a/setup.py
+++ b/setup.py
@@ -20,9 +20,7 @@
             "myst-parser",
             "sphinx-book-theme",
             "sphinx-panels",
-            "sphinx-design~=0.0.11",
-# pinned because of this bug https://github.com/pydata/pydata-sphinx-theme/pull/509
-            # and that the patched sphinx-book-theme isn't out yet: https://github.com/executablebooks/sphinx-book-theme/issues/428#issuecomment-966021270
+            "sphinx-design~=0.0.11", # pinned because of this bug https://github.com/pydata/pydata-sphinx-theme/pull/50# and that the patched sphinx-book-theme isn't out yet: https://github.com/executablebooks/sphinx-book-theme/issues/428#issuecomment-966021270
             "sphinx~=4.2.0", # TODO: unpin when the next sphinx-book-theme is released
         ],
     },

From c3e6c8c409a122de911d45f80b6b248865ef05ae Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Sat, 4 Dec 2021 17:52:41 -0500
Subject: [PATCH 10/14] No more randomization of projects

h/t https://github.com/neuropoly/neuro.polymtl.ca/pull/19#pullrequestreview-823305103
---
 conf.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf.py b/conf.py
index a65d23c1..5cdb4817 100644
--- a/conf.py
+++ b/conf.py
@@ -130,7 +130,6 @@ def build_gallery(app: Sphinx):
     LOGGER.info("building gallery...")
     grid_items = []
     projects = yaml.safe_load((Path(app.srcdir) / "gallery.yml").read_text())
-    random.shuffle(projects)
     for item in projects:
         if not item.get("image"):
             item["image"] = "https://jupyterbook.org/_images/logo-square.svg"

From 667b9e38913381f039f961c55377a4957daccb85 Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Sat, 11 Dec 2021 13:45:51 -0500
Subject: [PATCH 11/14] Added software descriptions

---
 gallery.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gallery.yml b/gallery.yml
index 7b6bd2df..1ce78830 100644
--- a/gallery.yml
+++ b/gallery.yml
@@ -1,20 +1,20 @@
-- name: Spinal Cord Toolbox
+- name: Comprehensive library of analysis tools for multi-parametric MRI of the spinal cord
   website: https://spinalcordtoolbox.com/
   repository: https://github.com/spinalcordtoolbox/spinalcordtoolbox
   image: https://raw.githubusercontent.com/spinalcordtoolbox/spinalcordtoolbox/master/documentation/source/_static/img/logo_sct.png
-- name: ivadomed
+- name: Integrated framework for medical image analysis with deep learning
   website: https://ivadomed.org
   repository: https://github.com/ivadomed/ivadomed
   image: https://raw.githubusercontent.com/ivadomed/ivadomed/master/images/ivadomed_logo.png
-- name: qMRLab
+- name: Simulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.)
   website: https://qmrlab.readthedocs.io
   repository: https://github.com/qMRLab/qMRLab
   image: https://raw.githubusercontent.com/qMRLab/documentation/master/logo/qMR_logo_orig.png
-- name: Shimming Toolbox
+- name: Software tools to perform advanced static and real-time shimming experiments with MRI.
   website: https://shimming-toolbox.org
   repository: https://github.com/shimming-toolbox
   image: https://raw.githubusercontent.com/shimming-toolbox/shimming-toolbox/master/docs/source/_static/img/shimming_toolbox_logo.png
-- name: AxonDeepSeg
+- name: Segmentation of axon and myelin on microscopy data.
   website: https://axondeepseg.readthedocs.io/
   repository: https://github.com/neuropoly/axondeepseg
   image: https://raw.githubusercontent.com/neuropoly/axondeepseg/master/docs/source/_static/logo_ads-alpha.png

From 494892b1a6804ea77e3dff9462e8fe2752095749 Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Sat, 11 Dec 2021 14:14:27 -0500
Subject: [PATCH 12/14] Moved software description below the logo

---
 conf.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/conf.py b/conf.py
index 5cdb4817..08fb8739 100644
--- a/conf.py
+++ b/conf.py
@@ -150,10 +150,11 @@ def build_gallery(app: Sphinx):
 
         grid_items.append(
             f"""\
-        `````{{grid-item-card}} {" ".join(item["name"].split())}
+        `````{{grid-item-card}}
         :text-align: center
-        <img src="{item["image"]}" alt="logo" loading="lazy" style="max-width: 100%; max-height: 200px; margin-top: 1rem;" />
+        <img src="{item["image"]}" alt="logo" loading="lazy" style="max-width: 100%; max-height: 100px; margin: auto" />
         +++
+        {" ".join(item["name"].split())}
         ````{{grid}} 2 2 2 2
         :margin: 0 0 0 0
         :padding: 0 0 0 0

From 993d3d11bf8f95c0410c46c4ed1249940f22212d Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Sat, 11 Dec 2021 14:29:35 -0500
Subject: [PATCH 13/14] Fixed URL to shimming toolbox repo

---
 gallery.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gallery.yml b/gallery.yml
index 1ce78830..fd50cc56 100644
--- a/gallery.yml
+++ b/gallery.yml
@@ -12,7 +12,7 @@
   image: https://raw.githubusercontent.com/qMRLab/documentation/master/logo/qMR_logo_orig.png
 - name: Software tools to perform advanced static and real-time shimming experiments with MRI.
   website: https://shimming-toolbox.org
-  repository: https://github.com/shimming-toolbox
+  repository: https://github.com/shimming-toolbox/shimming-toolbox
   image: https://raw.githubusercontent.com/shimming-toolbox/shimming-toolbox/master/docs/source/_static/img/shimming_toolbox_logo.png
 - name: Segmentation of axon and myelin on microscopy data.
   website: https://axondeepseg.readthedocs.io/

From ab7b846abf3f727ae158383332c0fec821d477ae Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Sun, 12 Dec 2021 12:04:13 -0500
Subject: [PATCH 14/14] Changed gallery for gallery_software

anticipating there will be more galleries in the future
---
 conf.py                             |  4 ++--
 gallery.yml => gallery_software.yml |  0
 software.md                         | 13 +++++++++----
 3 files changed, 11 insertions(+), 6 deletions(-)
 rename gallery.yml => gallery_software.yml (100%)

diff --git a/conf.py b/conf.py
index 08fb8739..2117ba72 100644
--- a/conf.py
+++ b/conf.py
@@ -129,7 +129,7 @@ def build_gallery(app: Sphinx):
     # Build the gallery file
     LOGGER.info("building gallery...")
     grid_items = []
-    projects = yaml.safe_load((Path(app.srcdir) / "gallery.yml").read_text())
+    projects = yaml.safe_load((Path(app.srcdir) / "gallery_software.yml").read_text())
     for item in projects:
         if not item.get("image"):
             item["image"] = "https://jupyterbook.org/_images/logo-square.svg"
@@ -189,7 +189,7 @@ def build_gallery(app: Sphinx):
 {dedent(grid_items)}
 ``````
     """
-    (Path(app.srcdir) / "gallery.txt").write_text(panels)
+    (Path(app.srcdir) / "gallery_software.txt").write_text(panels)
 
 
 def setup(app: Sphinx):
diff --git a/gallery.yml b/gallery_software.yml
similarity index 100%
rename from gallery.yml
rename to gallery_software.yml
diff --git a/software.md b/software.md
index 1a0e21b3..4c34abc5 100644
--- a/software.md
+++ b/software.md
@@ -1,12 +1,17 @@
 # `🖥` Software
 
-## Open-Source Projects
-
 Below is a list of software projects created at **NeuroPoly** or at collaborative institutions. These projects are open source and freely available.
 
-```{include} gallery.txt
+## Image analysis
+
+```{include} gallery_software.txt
 ```
 
+<!-- ## Pipeline and template
+
+TODO: Add this section
+This section contains projects  -->
+
 <!-- Deprecated software:
 
 |  | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project                                               | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/multiclass-segmentation) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) |
@@ -27,6 +32,6 @@ Below is a list of software projects created at **NeuroPoly** or at collaborativ
 -->
 
 
-### Contributing
+## Contributing
 
 **NeuroPoly** welcomes and appreciates contributions. To get started, please check out [**NeuroPoly**'s contributing guidelines](https://intranet.neuro.polymtl.ca/geek-tips/contributing).