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URL: http://github.com/DeepLabCut/DeepLabCut/pull/3042

ss" /> Added high-level diagrams by ivanmilevtues · Pull Request #3042 · DeepLabCut/DeepLabCut · GitHub
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Added high-level diagrams#3042

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Added high-level diagrams#3042
ivanmilevtues wants to merge 1 commit intoDeepLabCut:mainfrom
CodeBoarding:main

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@ivanmilevtues ivanmilevtues commented Jul 4, 2025

I’ve generated a first diagram-based documentation for DeepLabCut to help new users—especially scientists—get up to speed more quickly with the codebase. You can see a preview here: https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/DeepLabCut/on_boarding.md

The diagrams aim to show the core components of the project and how they interact with each other. As many users are more interested in understanding the high-level flow (rather than reading through all the source code), this should help them navigate the codebase more easily. From the diagrams, one can click into a specific component of interest and explore it in detail—enabling focused exploration while still seeing how everything fits together.

This can be especially useful for:

  • Modifying the pipeline for custom applications
  • Teaching DeepLabCut in academic settings
  • Quickly understanding what each module does without needing to trace function calls

We’ve also released a free GitHub Action that automatically keeps the diagrams updated, so they stay in sync with code changes.

Would love to get your feedback! And happy to chat about how we can support onboarding and collaboration for scientist-developers using DeepLabCut.

@MMathisLab MMathisLab requested review from MMathisLab and Copilot July 5, 2025 06:39
Copilot AI reviewed Jul 5, 2025
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Pull Request Overview

This PR introduces a set of mermaid-based, high-level architecture diagrams and accompanying component documentation under the .codeboarding directory to help scientists and new users quickly understand and navigate the DeepLabCut codebase.

  • Added a top-level onboarding document with an overall system flow diagram and clickable links to component details.
  • Created component-specific diagrams and detailed descriptions for each of the five core subsystems.
  • Included styling badges and FAQ links to integrate with CodeBoarding’s generated documentation workflow.

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 6 comments.

Show a summary per file
File Description
.codeboarding/on_boarding.md Added overall DeepLabCut architecture diagram and component links
.codeboarding/User_Interface.md Added UI subsystem diagram and detailed component descriptions
.codeboarding/Project_Data_Workflow_Management.md Added project and data workflow management diagram and details
.codeboarding/Core_Deep_Learning_Engine.md Added core deep learning engine diagram and descriptions
.codeboarding/Advanced_Analysis_Post_processing.md Added advanced analysis & post-processing diagram and descriptions
.codeboarding/System_Utilities_Benchmarking.md Added system utilities & benchmarking diagram and details

.codeboarding/on_boarding.md
Comment on lines +35 to +43
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//User_Interface.md" "Details"

click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Project_Data_Workflow_Management.md" "Details"

click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Core_Deep_Learning_Engine.md" "Details"

click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Advanced_Analysis_Post_processing.md" "Details"

click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//System_Utilities_Benchmarking.md" "Details"
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There’s an extra slash in the URL path (.codeboarding//User_Interface.md), which may break the link. Please remove the duplicate slash.

Suggested change
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//User_Interface.md" "Details"
click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Project_Data_Workflow_Management.md" "Details"
click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Core_Deep_Learning_Engine.md" "Details"
click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Advanced_Analysis_Post_processing.md" "Details"
click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//System_Utilities_Benchmarking.md" "Details"
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/User_Interface.md" "Details"
click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Project_Data_Workflow_Management.md" "Details"
click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Core_Deep_Learning_Engine.md" "Details"
click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Advanced_Analysis_Post_processing.md" "Details"
click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/System_Utilities_Benchmarking.md" "Details"

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.codeboarding/on_boarding.md
Comment on lines +35 to +43
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//User_Interface.md" "Details"

click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Project_Data_Workflow_Management.md" "Details"

click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Core_Deep_Learning_Engine.md" "Details"

click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Advanced_Analysis_Post_processing.md" "Details"

click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//System_Utilities_Benchmarking.md" "Details"
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There’s an extra slash in the URL path (.codeboarding//Project_Data_Workflow_Management.md), which may break the link. Please remove the duplicate slash.

Suggested change
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//User_Interface.md" "Details"
click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Project_Data_Workflow_Management.md" "Details"
click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Core_Deep_Learning_Engine.md" "Details"
click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Advanced_Analysis_Post_processing.md" "Details"
click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//System_Utilities_Benchmarking.md" "Details"
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/User_Interface.md" "Details"
click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Project_Data_Workflow_Management.md" "Details"
click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Core_Deep_Learning_Engine.md" "Details"
click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Advanced_Analysis_Post_processing.md" "Details"
click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/System_Utilities_Benchmarking.md" "Details"

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.codeboarding/on_boarding.md
Comment on lines +35 to +43
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//User_Interface.md" "Details"

click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Project_Data_Workflow_Management.md" "Details"

click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Core_Deep_Learning_Engine.md" "Details"

click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Advanced_Analysis_Post_processing.md" "Details"

click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//System_Utilities_Benchmarking.md" "Details"
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There’s an extra slash in the URL path (.codeboarding//Core_Deep_Learning_Engine.md), which may break the link. Please remove the duplicate slash.

Suggested change
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//User_Interface.md" "Details"
click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Project_Data_Workflow_Management.md" "Details"
click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Core_Deep_Learning_Engine.md" "Details"
click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Advanced_Analysis_Post_processing.md" "Details"
click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//System_Utilities_Benchmarking.md" "Details"
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/User_Interface.md" "Details"
click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Project_Data_Workflow_Management.md" "Details"
click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Core_Deep_Learning_Engine.md" "Details"
click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Advanced_Analysis_Post_processing.md" "Details"
click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/System_Utilities_Benchmarking.md" "Details"

Copilot uses AI. Check for mistakes.
.codeboarding/on_boarding.md

click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Core_Deep_Learning_Engine.md" "Details"

click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Advanced_Analysis_Post_processing.md" "Details"
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There’s an extra slash in the URL path (.codeboarding//Advanced_Analysis_Post_processing.md), which may break the link. Please remove the duplicate slash.

Suggested change
click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Advanced_Analysis_Post_processing.md" "Details"
click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Advanced_Analysis_Post_processing.md" "Details"

Copilot uses AI. Check for mistakes.
.codeboarding/on_boarding.md
Comment on lines +35 to +43
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//User_Interface.md" "Details"

click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Project_Data_Workflow_Management.md" "Details"

click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Core_Deep_Learning_Engine.md" "Details"

click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Advanced_Analysis_Post_processing.md" "Details"

click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//System_Utilities_Benchmarking.md" "Details"
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There’s an extra slash in the URL path (.codeboarding//System_Utilities_Benchmarking.md), which may break the link. Please remove the duplicate slash.

Suggested change
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//User_Interface.md" "Details"
click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Project_Data_Workflow_Management.md" "Details"
click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Core_Deep_Learning_Engine.md" "Details"
click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Advanced_Analysis_Post_processing.md" "Details"
click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//System_Utilities_Benchmarking.md" "Details"
click User_Interface href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/User_Interface.md" "Details"
click Project_Data_Workflow_Management href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Project_Data_Workflow_Management.md" "Details"
click Core_Deep_Learning_Engine href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Core_Deep_Learning_Engine.md" "Details"
click Advanced_Analysis_Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Advanced_Analysis_Post_processing.md" "Details"
click System_Utilities_Benchmarking href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/System_Utilities_Benchmarking.md" "Details"

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.codeboarding/Advanced_Analysis_Post_processing.md

Pose_Estimation_3D -- "uses" --> Post_processing

click Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Post_processing.md" "Details"
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There’s an extra slash in the URL path (.codeboarding//Post_processing.md), which may break the link. Please remove the duplicate slash.

Suggested change
click Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding//Post_processing.md" "Details"
click Post_processing href "https://github.com/DeepLabCut/DeepLabCut/blob/main/.codeboarding/Post_processing.md" "Details"

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ivanmilevtues commented Aug 3, 2025

Hey, a quick update on our side, this week we released our diagram generaiton engine as an open-source project! If you are interested to see more on how the generation works you can do so at https://github.com/CodeBoarding/CodeBoarding

@C-Achard C-Achard self-assigned this Feb 13, 2026
@C-Achard C-Achard added documentation documentation updates/comments enhancement New feature or request labels Feb 13, 2026
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