vrAnalysis

Tools for processing and analyzing data from behavior and imaging experiments. The package contains processing methods for data that is specific to the experiments I'm doing, but can be rewritten to work with any experimental system, there's a few places where user-specific functions need to be re-written (which are discussed in the documentation).

The experimental backbone is Rigbox, which uses an experiment management program called "Timeline". Behavioral processing is designed to work with experiments operated by the vrControl package in conjunction with timeline. These are virtual reality experiments where subjects (mice) run on a virtual linear track to collect rewards. The imaging processing is designed to work with the standard output of suite2p.

Finally, the package assumes Alyx database structure. This means that the data should be organized in a directory first by mouse, then by date, then by session ID. These files should be contained in a directory, which you can set in the files module with the local_data_path method.

Installation

1. Clone the repository:

git clone https://github.com/landoskape/vrAnalysis
cd vrAnalysis

2. Create a conda environment (Python >= 3.9) and install in development mode:

conda create -n vrAnalysis python>=3.9
conda activate vrAnalysis
pip install -e .

3. Optional: Install extra dependencies:

pip install -e .[registration]  # for deconvolution and registration
pip install -e .[gui]           # for GUI tools
pip install -e .[all]           # includes everything

4. Install PyTorch separately following the official instructions. Not necessary for most components of the package (more so the "dimilibi" stuff).

5. Configure paths: Set your data directory in vrAnalysis/files.py and database paths in vrAnalysis/database.py.

For detailed setup instructions including database configuration and preprocessing workflows, see the installation guide and registration workflow.

Documentation

This is not professional software, but it's hopefully useful to people (especially maybe 1 other person in cortex lab). So anyway I made a "proper" documentation system which you can find here.

Some old documentation that is all outdated but still a tiny bit useful is here:

1. Standard Workflows
2. Components
   • Database
   • Red Cell Curation Interface
   • Analyzing Data