DeepLabCut · C-Achard · May 5, 2026 · May 6, 2026 · May 6, 2026 · May 6, 2026
diff --git 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
@@ -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
@@ -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
@@ -0,0 +1 @@
+# Additional features notebooks
diff --git a/docs/notebooks/main_demos.md 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
@@ -0,0 +1 @@
+# Notebooks for your data
diff --git a/docs/pytorch/index.md 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
@@ -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
@@ -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
@@ -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
@@ -0,0 +1 @@
+# The DeepLabCut Cookbook
diff --git 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).
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,6 +8,8 @@ deeplabcut: @@
       recommendation: keep
     ---
+    (file:multi-animal-quick-start)=
     # Multi-animal pose estimation with DeepLabCut: A 5-minute tutorial
     ## GUI:
@@ Expand Down @@