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Add PyTorch🔥 documentation (#2605)
* added initial pytorch docs * Update _toc.yml * Update user_guide.md * Update architectures.md * Update labelling.md * Update labelling.md * Update codespell.yml * Update README.md * Update installation.md * Delete conda-environments/DEEPLABCUT_M1.yaml * Update DEEPLABCUT.yaml * Update installation.md * Update maDLC_UserGuide.md * Update ModelZoo.md * Update standardDeepLabCut_UserGuide.md * Update standardDeepLabCut_UserGuide.md * Update standardDeepLabCut_UserGuide.md * Update Overviewof3D.md * Update PROJECT_GUI.md * Update UseOverviewGuide.md * Update beginners-guide.md * Update intro.md * Update architectures.md * Update architectures.md * Create course.md - updating and migration from workshop materials * Update _toc.yml * Update manage-project.md * Update beginners-guide.md * Update manage-project.md * Update _toc.yml * Rename labelling.md to labeling.md * Update Training-Evaluation.md * Update video-analysis.md * Update architectures.md * Update architectures.md * Update AUTHORS * Update architectures.md * doc clean up, tested local build * Update beginners-guide.md * Update ModelZoo.md * Update ModelZoo.md * Update ModelZoo.md * Update ModelZoo.md * Update README.md - small resize on homepage * Update ModelZoo.md * Update ModelZoo.md - link update * Update AUTHORS * Update README.md - add badge for python version supported * Update installation.md * Update DEEPLABCUT.yaml - this, for now, will install from branch source (assuming the branch is named "pytorch_dlc" * Update DEEPLABCUT.yaml * Update AUTHORS * fixed typos * Update python-package.yml * Update README.md * Update beginners-guide.md * Update user_guide.md * m1 for tf only * Update README.md --------- Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> Co-authored-by: Mackenzie Mathis <mackenzie.mathis@epfl.ch>
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‎.github/workflows/codespell.yml‎

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uses: actions/checkout@v3
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- name: Codespell
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uses: codespell-project/actions-codespell@v1
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with:
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ignore_words_list: bu,BU,td,TD,ctd,CTD, Wither

‎.github/workflows/python-package.yml‎

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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-13, windows-latest]
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python-version: [3.9, "3.10"]
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python-version: ["3.10"]
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path: ~/.cache/pip

‎AUTHORS‎

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DeepLabCut (www.deeplabcut.org) was initially developed by
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Alexander & Mackenzie Mathis in collaboration with Matthias Bethge.
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Alexander & Mackenzie Mathis in collaboration with Matthias Bethge in 2017.
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It is actively developed by Alexander & Mackenzie Mathis (steering council and owners).
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DeepLabCut is an open-source tool and has benefited from suggestions and edits by many
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M Mathis, mackenzie@post.harvard.edu | https://github.com/MMathisLab
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J Lauer, jessy@deeplabcut.org | https://github.com/jeylau
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N Poulsen, neils.poulsen@epfl.ch | https://github.com/n-poulsen
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S Ye, https://github.com/yeshaokai
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S Schneider, stes@hey.com | https://github.com/stes
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S Ye, shaokai.ye@epfl.ch | https://github.com/yeshaokai
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Preprint:
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Ye, S., Filippova, A., Lauer, J., Vidal, M., Schneider, S., Qiu, T., Mathis, A., & Mathis, M.W. (2022).
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Ye, S., Filippova, A., Lauer, J., Schneider, S., Vidal, M., Qiu, T., Mathis, A., & Mathis, M.W. (2023).
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SuperAnimal pretrained pose estimation models for behavioral analysis. https://arxiv.org/abs/2203.07436
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############################################################################################################
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DeepLabCut 3.0+ additions:
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staty tuned, but includes BUCTD!
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DeepLabCut 3.0 Toolbox
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M Mathis, mackenzie@post.harvard.edu | https://github.com/MMathisLab
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A Mathis, alexander.mathis@epfl.ch | https://github.com/AlexEMG
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N Poulsen, neils.poulsen@epfl.ch | https://github.com/n-poulsen
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S Ye, shaokai.ye@epfl.ch | https://github.com/yeshaokai
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A Filippova, anastasiia.filippova@epfl.ch | https://github.com/nastya236
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Q Macé | https://github.com/QuentinJGMace
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J Lauer, jessy@deeplabcut.org | https://github.com/jeylau
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L Stoffl, lucas.stoffl@epfl.ch | https://github.com/LucZot
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We also greatly thank the 2023 DeepLabCut AI Residents who contributed:
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Anna Teruel-Sanchis | https://github.com/anna-teruel
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Riza Rae Pineda | https://github.com/rizarae-p
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Konrad Danielewski | https://github.com/KonradDanielewski
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Products:
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PyTorch backend for DeepLabCut
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Expanded SuperAnimal capabilities
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New model architectures (WIP: stay tuned, but includes BUCTD)

‎README.md‎

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</p>
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<p align="center">
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<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1665060917309-V0YVY2UKVLKSS6O18XDI/MousereachGIF.gif?format=1000w?format=250w" height="150">
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<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1665060917309-V0YVY2UKVLKSS6O18XDI/MousereachGIF.gif?format=1000w?format=180w" height="150">
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<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/daed7f16-527f-4150-8bdd-cbb20e267451/cheetah-ezgif.com-video-to-gif-converter.gif?format=250w" height="150">
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<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/daed7f16-527f-4150-8bdd-cbb20e267451/cheetah-ezgif.com-video-to-gif-converter.gif?format=180w" height="150">
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<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1534797521117-EIEUED03C68241QZ4KCK/ke17ZwdGBToddI8pDm48kAx9qLOWpcHWRGxWsJQSczRZw-zPPgdn4jUwVcJE1ZvWQUxwkmyExglNqGp0IvTJZUJFbgE-7XRK3dMEBRBhUpwdr4GYy30vFzf31Oe7KAPZKkqgaiEgc5jBNdhZmDPlzxdkDSclo6ofuXZm6YCEhUo/MATHIS_2018_fly.gif?format=250w" height="150">
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<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1534797521117-EIEUED03C68241QZ4KCK/ke17ZwdGBToddI8pDm48kAx9qLOWpcHWRGxWsJQSczRZw-zPPgdn4jUwVcJE1ZvWQUxwkmyExglNqGp0IvTJZUJFbgE-7XRK3dMEBRBhUpwdr4GYy30vFzf31Oe7KAPZKkqgaiEgc5jBNdhZmDPlzxdkDSclo6ofuXZm6YCEhUo/MATHIS_2018_fly.gif?format=180w" height="150">
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<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1619609897110-TKSTWKEM6HTGXID9D489/ke17ZwdGBToddI8pDm48kAvjv6tW_eojYQmNU0ncbllZw-zPPgdn4jUwVcJE1ZvWEtT5uBSRWt4vQZAgTJucoTqqXjS3CfNDSuuf31e0tVHBSTXHtjUKlhRtWJ1Vo6l1B2bxJtByvWSjL6Vz3amc5yb8BodarTVrzIWCp72ioWw/triMouseDLC.gif?format=250w" height="150">
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<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1619609897110-TKSTWKEM6HTGXID9D489/ke17ZwdGBToddI8pDm48kAvjv6tW_eojYQmNU0ncbllZw-zPPgdn4jUwVcJE1ZvWEtT5uBSRWt4vQZAgTJucoTqqXjS3CfNDSuuf31e0tVHBSTXHtjUKlhRtWJ1Vo6l1B2bxJtByvWSjL6Vz3amc5yb8BodarTVrzIWCp72ioWw/triMouseDLC.gif?format=180w" height="150">
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[👩🏾‍💻👨‍💻 DeepLabCut AI Residency](https://www.deeplabcutairesidency.org/)
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![Vesion](https://img.shields.io/badge/python_version-3.10-purple)
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[![Downloads](https://pepy.tech/badge/deeplabcut)](https://pepy.tech/project/deeplabcut)
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[![Downloads](https://pepy.tech/badge/deeplabcut/month)](https://pepy.tech/project/deeplabcut)
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[![PyPI version](https://badge.fury.io/py/deeplabcut.svg)](https://badge.fury.io/py/deeplabcut)
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# [Installation: how to install DeepLabCut](https://deeplabcut.github.io/DeepLabCut/docs/installation.html)
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Very quick start: `pip install "deeplabcut[gui,tf]"` that includes all functions plus GUIs, or `pip install deeplabcut[tf]` (headless version with PyTorch and TensorFlow).
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* We recommend using our conda file, see [here](https://github.com/DeepLabCut/DeepLabCut/blob/main/conda-environments/README.md) or the new [`deeplabcut-docker` package](https://github.com/DeepLabCut/DeepLabCut/tree/main/docker). Please note that currently we support Python 3.9 (see conda files for guidance).
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Please click the link above for all the information you need to get started! Please note that currently we support only Python 3.10+ (see conda files for guidance).
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Developers Stable Release:
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- Very quick start: You need to have TensorFlow installed (up to v2.10 supported across platforms) `pip install "deeplabcut[gui,tf]"` that includes all functions plus GUIs, or `pip install deeplabcut[tf]` (headless version with PyTorch and TensorFlow).
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Developers Alpha Release:
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- We also have an alpha release of PyTorch DeepLabCut available! [Please see here for instructions and information](https://github.com/DeepLabCut/DeepLabCut/blob/pytorch_docs/docs/pytorch/user_guide.md).
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We recommend using our conda file, see [here](https://github.com/DeepLabCut/DeepLabCut/blob/main/conda-environments/README.md) or the new [`deeplabcut-docker` package](https://github.com/DeepLabCut/DeepLabCut/tree/main/docker).
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# [Documentation: The DeepLabCut Process](https://deeplabcut.github.io/DeepLabCut)
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- For all versions, please see [here](https://github.com/DeepLabCut/DeepLabCut/releases).
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VERSION 3.0: A whole new experience with PyTorch🔥. While the high-level API remains the same, the backend and developer friendliness have greatly improved, along with performance gains!
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VERSION 2.3: Model Zoo SuperAnimals, and a whole new GUI experience.
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# News (and in the news):
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:purple_heart: We released a major update, moving from 2.x --> 3.x with the backend change to PyTorch
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:purple_heart: The DeepLabCut Model Zoo launches SuperAnimals, see more [here](http://www.mackenziemathislab.org/dlc-modelzoo/).
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:purple_heart: **DeepLabCut supports multi-animal pose estimation!** maDLC is out of beta/rc mode and beta is deprecated, thanks to the testers out there for feedback! Your labeled data will be backwards compatible, but not all other steps. Please see the [new `2.2+` releases](https://github.com/DeepLabCut/DeepLabCut/releases) for what's new & how to install it, please see our new [paper, Lauer et al 2022](https://www.nature.com/articles/s41592-022-01443-0), and the [new docs]( https://deeplabcut.github.io/DeepLabCut) on how to use it!
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:purple_heart: We have a **real-time** package available! http://DLClive.deeplabcut.org
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- June 2024: Our second DLC paper ['Using DeepLabCut for 3D markerless pose estimation across species and behaviors'](https://www.nature.com/articles/s41596-019-0176-0) in Nature Protocols has surpassed 1,000 Google Scholar citations!
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- May 2024: DeepLabCut was featured in Nature: ['DeepLabCut: the motion-tracking tool that went viral'](https://www.nature.com/articles/d41586-024-01474-x)
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- January 2024: Our original paper ['DeepLabCut: markerless pose estimation of user-defined body parts with deep learning'](https://www.nature.com/articles/s41593-018-0209-y) in Nature Neuroscience has surpassed 3,000 Google Scholar citations!
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- October 2023: DeepLabCut celebrates a milestone with 4,000 🌟 in Github!

‎_toc.yml‎

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- caption: Getting Started
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chapters:
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- file: docs/course
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- caption: Installation
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- caption: Graphical User Interfaces (GUIs)
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- file: docs/gui/PROJECT_GUI
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- file: docs/gui/napari_GUI
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- caption: DLC3 PyTorch Specific Docs
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chapters:
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- file: docs/pytorch/user_guide.md
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- file: docs/pytorch/pytorch_config.md
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- file: docs/pytorch/architectures.md
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- file: docs/tutorial_maDLC
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- file: docs/quick-start/single_animal_quick_guide
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- file: docs/quick-start/tutorial_maDLC
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- caption: Beginner's Guide to DeepLabCut
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chapters:
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- file: docs/beginner-guides/beginners-guide
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- file: docs/beginner-guides/manage-project
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- file: docs/beginner-guides/labeling
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- file: docs/beginner-guides/Training-Evaluation
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- file: docs/beginner-guides/video-analysis
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- caption: Cookbook (detailed helper guides)
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- caption: Beginner's Guide to DeepLabCut in the GUI
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‎conda-environments/DEEPLABCUT.yaml‎

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# DEEPLABCUT.yaml
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#DeepLabCut2.0 Toolbox (deeplabcut.org)
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#DeepLabCut Toolbox (deeplabcut.org)
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#© A. & M.W. Mathis Labs
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#https://github.com/DeepLabCut/DeepLabCut
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#Please see AUTHORS for contributors.
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#https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
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#https://github.com/DeepLabCut/DeepLabCut/blob/main/AUTHORS
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#Licensed under GNU Lesser General Public License v3.0
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- "git+https://github.com/DeepLabCut/DeepLabCut.git@pytorch_dlc#egg=deeplabcut[gui,modelzoo,wandb]"

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