twoppp: two-photon data processing pipeline

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

The standard interface to automatically run the entire pipeline or subsets of it on multiple flies is documented here:

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
  • running Sleap for 2D pose estimation and processing it
  • optical flow ball tracking processing
  • fictrac data handling
  • wheel speed calculation
  • olfactory stimulation data processing
  • optogenetic stimulus 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.

The new (2022) interface to automatically run the entire pipeline or subsets of it on multiple flies is documented here:

Installation instructions:

conda (preferred)

Create conda environment and install twoppp package

• conda create -n twoppp37 python=3.7
• conda activate twoppp37
• pip install numpy
• clone repository: git clone https://github.com/NeLy-EPFL/twoppp
• change directory: cd twoppp
• install using pip: pip install -e .
• fix numpy installation: pip install numpy --upgrade (ignore the warning message about numpy incompatibility)

pure pip

• pip install numpy
• pip install -e .
• pip install numpy --upgrade