fly2p
Tools for analyzing two-photon (2p) imaging data collected with Vidrio Scanimage software and micromanger. Loading scanimage data relies on scanimageReader, which can be installed via 'pip install scanimage-tiff-reader'. Other dependencies are tracked using poetry.
Organization
The fly2p package contains the following submodules:
- preproc: Some file-format specific functions that extract metadata and load the imaging data. imgPreproc.py defines a data object to hold metadata and imaging data as well as basic proporcessing functions.
- viz: A collection of utility functions related to plotting flourescence traces and images.
In addition, the scripts folder contains notebooks that illustrate how to use functions in this module based on example files in sample (sample files are not currently pushed to repo).
Installation
I recommend using poetry to setup a custom conda environment. A helpful introduction can be found here.
- Clone repo, navigate into folder
- If you don't already have poetry, install poetry. You may need to close command window and open a new one.
- Create conda environment:
conda create --name fly2p python=3.8 - Activate environment:
conda activate fly2p - Make sure you are in the top folder of the cloned repo, then install dependencies:
poetry install - Setup the new environment as an ipython kernel:
conda install -c anaconda ipykernel
then
python -m ipykernel install --user --name=fly2p
Now you should be able to run the example notebooks in the scripts folder without problems.
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