diff --git a/_toc.yml b/_toc.yml index 6bb51801f..495a9110c 100644 --- a/_toc.yml +++ b/_toc.yml @@ -2,125 +2,111 @@ format: jb-book root: README parts: -- caption: Getting Started - chapters: - - file: docs/UseOverviewGuide - - file: docs/course - -- caption: Installation - chapters: - - file: docs/installation - - file: docs/recipes/installTips - - file: docs/docker - -- caption: Main User Guides - chapters: - - file: docs/standardDeepLabCut_UserGuide - - file: docs/maDLC_UserGuide - - file: docs/Overviewof3D - - file: docs/HelperFunctions - -- caption: Graphical User Interfaces (GUIs) - chapters: - - file: docs/gui/PROJECT_GUI - - file: docs/gui/napari_GUI - sections: - - file: docs/gui/napari/basic_usage - - file: docs/gui/napari/advanced_usage - -- caption: DLC3 PyTorch Specific Docs - chapters: - - file: docs/pytorch/user_guide.md - - file: docs/pytorch/pytorch_config.md - - file: docs/pytorch/architectures.md - -- caption: Quick Start Tutorials - chapters: - - file: docs/quick-start/single_animal_quick_guide - - file: docs/quick-start/tutorial_maDLC - -- caption: "🚀 Beginner's Guide to DeepLabCut" - chapters: - - file: docs/beginner-guides/beginners-guide - - file: docs/beginner-guides/manage-project - - file: docs/beginner-guides/labeling - - file: docs/beginner-guides/Training-Evaluation - - file: docs/beginner-guides/video-analysis - -- caption: "🚀 Main Demo Notebooks" - chapters: - - file: examples/COLAB/COLAB_DEMO_SuperAnimal - - file: examples/COLAB/COLAB_DEMO_mouse_openfield - - file: examples/COLAB/COLAB_3miceDemo - - file: examples/COLAB/COLAB_HumanPose_with_RTMPose - -- caption: "🚀 Notebooks For Your Data" - chapters: - - file: examples/COLAB/COLAB_YOURDATA_SuperAnimal - - file: examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis - - file: examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis - -- caption: "🚀 Special Feature Demos" - chapters: - - file: examples/COLAB/COLAB_transformer_reID - - file: examples/COLAB/COLAB_BUCTD_and_CTD_tracking - - file: examples/JUPYTER/Demo_3D_DeepLabCut - - file: examples/COLAB/COLAB_DLC_ModelZoo - -- caption: "🧑‍🍳 Cookbook (detailed helper guides)" - chapters: - - file: docs/convert_maDLC - - file: docs/recipes/OtherData - - file: docs/recipes/io - - file: docs/recipes/nn - - file: docs/recipes/post - - file: docs/recipes/BatchProcessing - - file: docs/recipes/DLCMethods - - file: docs/recipes/ClusteringNapari - - file: docs/recipes/OpenVINO - - file: docs/recipes/flip_and_rotate - - file: docs/recipes/pose_cfg_file_breakdown - - file: docs/recipes/publishing_notebooks_into_the_DLC_main_cookbook - -- caption: Hardware Tips - chapters: - - file: docs/recipes/TechHardware - -- caption: DeepLabCut-Live! - chapters: - - file: docs/dlc-live/deeplabcutlive - - file: docs/dlc-live/dlc-live-gui/index - sections: - - file: docs/dlc-live/dlc-live-gui/quickstart/install - - file: docs/dlc-live/dlc-live-gui/user_guide/overview - - file: docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/camera_support + - caption: Getting started + chapters: + - file: docs/UseOverviewGuide + - file: docs/installation sections: - - file: docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/opencv_backend - - file: docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/basler_backend - - file: docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/aravis_backend - - file: docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/gentl_backend - - file: docs/dlc-live/dlc-live-gui/user_guide/misc/misc_landing + # - file: docs/recipes/installTips + - file: docs/docker + - file: docs/quick-start/index sections: - - file: docs/dlc-live/dlc-live-gui/user_guide/misc/modelzoo_downloads - - file: docs/dlc-live/dlc-live-gui/user_guide/misc/timestamp_format - -- caption: "🦄 DeepLabCut Model Zoo" - chapters: - - file: docs/ModelZoo - - file: docs/recipes/UsingModelZooPupil - -- caption: DeepLabCut Benchmarking - chapters: - - file: docs/benchmark - - file: docs/pytorch/Benchmarking_shuffle_guide - -- caption: "Mission & Contribute" - chapters: - - file: docs/MISSION_AND_VALUES - - file: docs/roadmap - - file: docs/Governance - - file: CONTRIBUTING - -- caption: Citations for DeepLabCut - chapters: - - file: docs/citation + - file: docs/quick-start/single_animal_quick_guide + - file: docs/quick-start/tutorial_maDLC + + - caption: Main workflows overview + chapters: + - file: docs/standardDeepLabCut_UserGuide + - file: docs/maDLC_UserGuide + - file: docs/Overviewof3D + + - caption: GUI workflow + chapters: + - file: docs/gui/PROJECT_GUI + - file: docs/beginner-guides/beginners-guide + sections: + - file: docs/beginner-guides/manage-project + - file: docs/beginner-guides/labeling + - file: docs/beginner-guides/Training-Evaluation + - file: docs/beginner-guides/video-analysis + - file: docs/gui/napari_GUI + sections: + - file: docs/gui/napari/basic_usage + - file: docs/gui/napari/advanced_usage + - file: docs/dlc-live/dlc-live-gui/index + sections: + - file: docs/dlc-live/dlc-live-gui/quickstart/install + - file: docs/dlc-live/dlc-live-gui/user_guide/overview + - file: docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/camera_support + sections: + - file: docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/opencv_backend + - file: docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/basler_backend + - file: docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/aravis_backend + - file: docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/gentl_backend + - file: docs/dlc-live/dlc-live-gui/user_guide/misc/misc_landing + sections: + - file: docs/dlc-live/dlc-live-gui/user_guide/misc/modelzoo_downloads + - file: docs/dlc-live/dlc-live-gui/user_guide/misc/timestamp_format + + + - caption: Notebooks & Demos + chapters: + - file: docs/notebooks/main_demos + sections: + - file: examples/COLAB/COLAB_DEMO_SuperAnimal + - file: examples/COLAB/COLAB_DEMO_mouse_openfield + - file: examples/COLAB/COLAB_3miceDemo + - file: examples/COLAB/COLAB_HumanPose_with_RTMPose + - file: docs/notebooks/your_data + sections: + - file: examples/COLAB/COLAB_YOURDATA_SuperAnimal + - file: examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis + - file: examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis + - file: docs/notebooks/extra + sections: + - file: examples/COLAB/COLAB_transformer_reID + - file: examples/COLAB/COLAB_BUCTD_and_CTD_tracking + - file: examples/JUPYTER/Demo_3D_DeepLabCut + - file: examples/COLAB/COLAB_DLC_ModelZoo + + - caption: Advanced, Performance & Live + chapters: + - file: docs/ModelZoo + sections: + - file: docs/recipes/UsingModelZooPupil + - file: docs/dlc-live/deeplabcutlive + - file: docs/pytorch/index + sections: + - file: docs/pytorch/user_guide.md + - file: docs/pytorch/pytorch_config.md + - file: docs/pytorch/architectures.md + - file: docs/pytorch/Benchmarking_shuffle_guide + - file: docs/benchmark + - file: docs/recipes/TechHardware + + - caption: Additional guides (Recipes) + chapters: + - file: docs/recipes/index + sections: + - file: docs/HelperFunctions + - file: docs/convert_maDLC + - file: docs/recipes/OtherData + - file: docs/recipes/io + - file: docs/recipes/nn + - file: docs/recipes/post + - file: docs/recipes/BatchProcessing + - file: docs/recipes/DLCMethods + - file: docs/recipes/ClusteringNapari + - file: docs/recipes/OpenVINO + - file: docs/recipes/flip_and_rotate + - file: docs/recipes/pose_cfg_file_breakdown + - file: docs/recipes/publishing_notebooks_into_the_DLC_main_cookbook + # - file: docs/course + + - caption: Project & Community + chapters: + - file: docs/MISSION_AND_VALUES + - file: docs/roadmap + - file: docs/Governance + - file: CONTRIBUTING + - file: docs/citation diff --git a/docs/gui/index.md b/docs/gui/index.md new file mode 100644 index 000000000..7219999f9 --- /dev/null +++ b/docs/gui/index.md @@ -0,0 +1,10 @@ +# GUIde + +```{toctree} +--- +maxdepth: 2 +caption: GUI Workflows & Beginner Guides +--- + docs/gui/PROJECT_GUI + docs/gui/napari_GUI +``` diff --git a/docs/maDLC_UserGuide.md b/docs/maDLC_UserGuide.md index 99641a59b..5ca4fc31e 100644 --- a/docs/maDLC_UserGuide.md +++ b/docs/maDLC_UserGuide.md @@ -11,7 +11,7 @@ deeplabcut: (multi-animal-userguide)= -# DeepLabCut for Multi-Animal Projects +# Multi-animal projects This document should serve as the user guide for maDLC, and it is here to support the scientific advances presented in [Lauer et al. 2022](https://doi.org/10.1038/s41592-022-01443-0). diff --git a/docs/notebooks/extra.md b/docs/notebooks/extra.md new file mode 100644 index 000000000..127406c58 --- /dev/null +++ b/docs/notebooks/extra.md @@ -0,0 +1 @@ +# Additional features notebooks diff --git a/docs/notebooks/main_demos.md b/docs/notebooks/main_demos.md new file mode 100644 index 000000000..789d47b33 --- /dev/null +++ b/docs/notebooks/main_demos.md @@ -0,0 +1 @@ +# Demo notebooks diff --git a/docs/notebooks/your_data.md b/docs/notebooks/your_data.md new file mode 100644 index 000000000..3ec1e2fc5 --- /dev/null +++ b/docs/notebooks/your_data.md @@ -0,0 +1 @@ +# Notebooks for your data diff --git a/docs/pytorch/index.md b/docs/pytorch/index.md new file mode 100644 index 000000000..efc258222 --- /dev/null +++ b/docs/pytorch/index.md @@ -0,0 +1 @@ +# PyTorch backend guide diff --git a/docs/quick-start/index.md b/docs/quick-start/index.md new file mode 100644 index 000000000..f05057b8a --- /dev/null +++ b/docs/quick-start/index.md @@ -0,0 +1,15 @@ +--- +deeplabcut: + ignore: false + visibility: online + status: viable + recommendation: keep + last_metadata_updated: '2026-05-12' + last_verified: '2026-05-12' + verified_for: 3.0.0rc14 +--- + +# Quick start guides + +- Single animal: {ref}`file:single-animal-quick-start` +- Multi-animal: {ref}`file:multi-animal-quick-start` diff --git a/docs/quick-start/single_animal_quick_guide.md b/docs/quick-start/single_animal_quick_guide.md index 96af3d092..16b68873c 100644 --- a/docs/quick-start/single_animal_quick_guide.md +++ b/docs/quick-start/single_animal_quick_guide.md @@ -9,6 +9,8 @@ deeplabcut: notes: This is a bit stuck between minimal guide and quick start, as the lack of explanations makes it more into a catalogue of commands (which is an API docs responsibility), and a proper quick start guide that gives users a proper sense of the workflow. This should either be expanded greatly or simply archived. For simplicity, I recommend archiving. --- +(file:single-animal-quick-start)= + # QUICK GUIDE to single Animal Training: **The main steps to take you from project creation to analyzed videos:** diff --git a/docs/quick-start/tutorial_maDLC.md b/docs/quick-start/tutorial_maDLC.md index 000b6d0c0..e33fe44bc 100644 --- a/docs/quick-start/tutorial_maDLC.md +++ b/docs/quick-start/tutorial_maDLC.md @@ -8,6 +8,8 @@ deeplabcut: recommendation: keep --- +(file:multi-animal-quick-start)= + # Multi-animal pose estimation with DeepLabCut: A 5-minute tutorial ## GUI: diff --git a/docs/recipes/index.md b/docs/recipes/index.md new file mode 100644 index 000000000..195e8987f --- /dev/null +++ b/docs/recipes/index.md @@ -0,0 +1 @@ +# The DeepLabCut Cookbook diff --git a/docs/standardDeepLabCut_UserGuide.md b/docs/standardDeepLabCut_UserGuide.md index 8d6847c5f..914d85d08 100644 --- a/docs/standardDeepLabCut_UserGuide.md +++ b/docs/standardDeepLabCut_UserGuide.md @@ -11,7 +11,7 @@ deeplabcut: (single-animal-userguide)= -# DeepLabCut User Guide (for single animal projects) +# Single animal projects This document covers single/standard DeepLabCut use. If you have a complicated multi-animal scenario (i.e., they look the same), then please see our [maDLC user guide](multi-animal-userguide).