twoppp: two-photon data processing pipeline

This package allows to process simulataneously recorded two-photon imaging data and behavioural data.

Most of the sub-modules and functions are already documented. More docstrings are forthcoming!

This includes:

• two-photon processing:
  • converting from .raw to .tif
  • motion correction using center of mass and optical flow registration
    • both local and preparing for on cluster computation
  • denoising using DeppInterpolation
  • DF/F computation
  • ROI extraction
• behavioural data processing:
  • running DeepFly3D and postprocessing it
  • optical flow ball tracking processing
  • fictrac data handling
  • olfactory stimulation data processing
• combined behavioural and two-photon data processing:
  • synchronisation of the two (or three) modalities
  • creating pandas dataframes with synchronised data from behavioural and neural data
  • making videos

The "examples" folder showcases example usecases of each of the sub-modules.

If you want to run the entire processing pipeline in one go, look at the run_processing_pipeline_local.py script.

Installation instructions:

1. Create conda environment and install required packages according to their respective install instructions:
   • conda create -n twoppp37 python=3.7
   • conda activate twoppp37
   • conda install jupyter
   • DeepFly3D: https://github.com/NeLy-EPFL/DeepFly3D
   • deepinterpolation: https://github.com/NeLy-EPFL/deepinterpolation/tree/adapttoR57C10
     • this might throw an error like: "ERROR: pip's dependency resolver does not currently take into account all the packages that are installed." ... for incompatibilities of numpy and scipy version, but this can be ignored.
   • conda install pandas
   • conda install numpy
   • utils2p: https://github.com/NeLy-EPFL/utils2p
   • ofco: https://github.com/NeLy-EPFL/ofco
     • this might again throw a dependency error about numpy and scipy, but it can be ignored.
   • utils_video: https://github.com/NeLy-EPFL/utils_video
   • df3dPostProcessing: https://github.com/NeLy-EPFL/df3dPostProcessing
   • pip install behavelet
   • try whether the pandas instruction works:
     • type python -c "import pandas as pd; print(pd.__version__)"
     • If this returns just the version number, your're fine. If this returns an ImportError, this means that some of the installs messed up with the pandas/numpy dependencies. Fix the problem as follows:
     • pip uninstall pandas
     • pip uninstall numpy
     • conda install pandas
2. Finally, we can install the twoppp package:
   • clone repository: git clone https://github.com/NeLy-EPFL/twoppp
   • change directory: cd twoppp
   • install using pip: pip install -e .