trialexp

Package to analyze PyControl and PyPhotometry experiments by trials, and integrate with other data such as DeepLabCut or spikes data

• Free software: MIT license
• Documentation: https://trialexp.readthedocs.io.

Features

• TODO

Install

• Make sure you have conda installed
• download https://github.com/juliencarponcy/trialexp
• or, if you have git installed:

git clone https://github.com/juliencarponcy/trialexp

• Navigate into the root folder

cd trialexp

• Create environment called trialexp (you can change the name of the environment by modifying the trialexp.yaml file

conda env create -f trialexp.yaml

Usage

• Activate notebooks by command line using:

conda activate trialexp

• Do this in the virtual environment to make modules in the repo available:

pip install -e .

• Edit config files

  • for execution: `workflow/conf/config.yaml

  • for development:

    • .env setting the directory for snakehelper to switch to automatically (i.e. project root folder)
    • workflow/settings.py setting the debug session folder during development

• Launch Jupyter

jupyter-notebook

In the `/notebooks` folder, you can then open the different templates notebooks, create your own notebook or copy and edit the different workflow notebooks.

• You can alternatively open the different workflow notebooks in a code editor which support jupyter notebooks.
• Or you can create a new python script or notebook and import trialexp modules
• Copy extern_scriptssessionTemplate_nxp.m to the Cell explorer folder calc_CellMetrics

Credits

This package is an extension on the work of Thomas Akam for:

• PyControl (Open source, Python based, behavioural experiment control)

  • https://pycontrol.readthedocs.io
  • https://github.com/pyControl/code

• PyPhotometry (Open source, Python based, fiber photometry data acquisition)

  • https://github.com/pyPhotometry/code
  • https://pyphotometry.readthedocs.io

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

• Cookiecutter: https://github.com/audreyr/cookiecutter
• audreyr/cookiecutter-pypackage: https://github.com/audreyr/cookiecutter-pypackage