deploy: e2f0d58

README.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>

_sources/data/README.md

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 # <span>💾</span> Data
 
+## Dataset curation
+
 For the details of how we structure datasets at the lab, see:
 
 ```{toctree}
 :maxdepth: 1
 dataset-curation
 ```
 
+## Dataset storage
+
+MRI, microscopy and other research data are stored in the following servers:
+
+```{toctree}
+:maxdepth: 1
+git-datasets
+duke
+```
+
+And [here](https://docs.google.com/spreadsheets/d/1yjcA8Z0COn4OZxusIDHjStH2DpeXvscsj-aWE2X-_sg) is a useful list of MRI data to use for various projects.
+
+
+## Dataset management (admin)
+
 For instructions on how to do various admin tasks on our data server, see:
 
 ```{toctree}
 :maxdepth: 1
 admin-guide
 ```
 
-MRI, microscopy and other research data are stored in the following servers:
+## Deep learning models
+
+If you train deep learning models, here's how to organize them:
 
 ```{toctree}
 :maxdepth: 1
-git-datasets
-duke
-django
+deeplearning-models
 ```
-
-[Here](https://docs.google.com/spreadsheets/d/1yjcA8Z0COn4OZxusIDHjStH2DpeXvscsj-aWE2X-_sg) is a useful list of MRI data to use for various projects.

_sources/data/deeplearning-models.md

@@ -0,0 +1,34 @@
+# Deep Learning Models
+
+## Naming models
+
+Each model is saved in its own repository under the [ivadomed](https://github.com/ivadomed) organization. The convention for naming repositories is the following:
+
+~~~
+model_task_animal_pathology_region_contrast_architecture
+
+Should be small letters only.
+
+Fields:
+- task = {seg, label, find}, default=seg
+- animal = {human, dog, cat, rat, mouse, ...}, default=human
+- pathology = {ms, sci}
+- region = {sc, gm, csf, brainstem, axon, myelin, ...}, default=sc
+- contrast = {t1, t2, t2star, dwi, sem, tem, oi, ...}, default=None
+- architecture = {unet2d, unet3d, filmCharley, hemisAndreanne}, default=unet2d
+
+Examples: 
+
+model_seg_monkey_sc_t1_unet3d
+
+# multi-channel, multi-class
+model_seg_sc-gm_t1-t2_unet3d
+~~~
+
+## Packaging models
+
+Models to be used by 3rd party software (e.g. [SCT](https://spinalcordtoolbox.com/)) should be uploaded as 'assets' to a release of the repository. The steps are:
+- Create a release of the repository. The tag and title of the release should be `rYYYYMMDD`, example: `r20211223`.
+- Put the model and JSON file inside a folder that has the name of the model.
+- Zip the folder and upload it as an asset in the release
+- Publish the release.

agenda-and-calendar.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>

bibliography/README.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>

bibliography/deep-learning.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>

bibliography/histology.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>

bibliography/index.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>

bibliography/lab-theses.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>

bibliography/mri-analysis.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>

bibliography/mri.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>

bibliography/shared-paperpile-folder.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>

bibliography/spinal-cord-injury.html

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 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../data/dataset-curation.html">Dataset curation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="../data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="../data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/admin-guide.html">Dataset admin guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../data/deeplearning-models.html">Deep Learning Models</a></li>
 </ul>
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../mri-scanning/README.html"><span>🧲</span> MRI Scanning</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>