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MoSeq2-Extract: Depth Video Rodent-Tracking Toolkit

Build Status

codecov

Welcome to moseq2, the latest version of a software package for mouse tracking in depth videos first developed by Alex Wiltschko in the Datta Lab at Harvard Medical School.

Latest version is 0.5.0


Features

Below are the commands/functionality that moseq2-extract currently affords. They are accessible via CLI or Jupyter Notebook in moseq2-app.

Usage: moseq2-extract [OPTIONS] COMMAND [ARGS]...

Options:
  --version  Show the version and exit.  [default: False]
  --help     Show this message and exit.  [default: False]

Commands:
  aggregate-results   Copies all extracted results (h5, yaml, avi) files...
  batch-extract       Batch processes all the raw depth recordings located...
  convert-raw-to-avi  Converts/Compresses a raw depth file into an avi file...
  copy-slice          Copies a segment of an input depth recording into a...
  download-flip-file  Downloads Flip-correction model that helps with...
  extract             Processes raw input depth recordings to output a...
  find-roi            Finds the ROI and background distance to subtract
                      from...
  generate-config     Generates a configuration file that holds editable...
  generate-index      Generates an index YAML file containing all extracted...

CLI Exclusive Functions

batch-extract       Batch processes all the raw depth recordings located...
convert-raw-to-avi  Converts/Compresses a raw depth file into an avi file...
copy-slice          Copies a segment of an input depth recording into a...

GUI Exclusive Function

extract_found_sessions() Extracts all found data within a given input_dir, 
 AND searches for individual session configuration parameters in the session_config.yaml

Run any command with the --help flag to display all available options and their descriptions.


Documentation

MoSeq2 uses sphinx to generate the documentation in HTML and PDF forms. To install sphinx, follow the commands below:

pip install sphinx==3.0.3 sphinx_click==2.5.0
pip install sphinx-rtd-theme
pip install rst2pdf

All documentation regarding moseq2-extract can be found in the Documentation.pdf file in the root directory, an HTML ReadTheDocs page can be generated via running the make html in the docs/ directory.

To generate a PDF version of the documentation, simply run make pdf in the docs/ directory.

For information on getting started, check out the MoSeq Roadmap.


Examples

Example find-roi Outputs

Round Arena ROI and Background

alt text

Y-Maze Arena (from Kinect v2 Camera)

alt text

Convex-shaped Bucket (\_/) (from Azure Camera)

Dilated Background and ROI respectively.

alt text alt text

Rectangular Arena (from RealSense)

ROI and Weighted Background Image respectively.

alt text

Example Extraction

alt text


Contributing

If you would like to contribute, fork the repository and issue a pull request.

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v0.7.0 for moseq2_v021

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