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
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...
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...
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.
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.
Dilated Background and ROI respectively.
ROI and Weighted Background Image respectively.
If you would like to contribute, fork the repository and issue a pull request.