CaImaging

Installation

Some important points:

• We'll use conda to create an environment, but first:

• Make sure you're only using conda forge channel for FMI computers, if you're not sure do this:

  • conda config --add channels conda-forge
  • conda config --set channel_priority strict
  • conda config --remove channels defaults
  • conda config --show channels (only the conda-forge should appear)

• Create the environment: Use python3.11 for the suitable Suite2p version. Otherwise the script will have problems due to the differences in Suite2p code.

  • conda create -n CaImaging python=3.11
  • conda activate CaImaging

• Install the following packages

  • suite2p: > pip install suite2p
  • For VS Code interactive kernel, ipykernel: conda install ipykernel -c conda-forge
  • For interactive ROI selection: pyqt: conda install pyqt=5 -c conda-forge
  • other packages as necessary (once you run the code you'll see it), one example conda install conda-forge::scikit-image
  • For server computer Windows to fix
    • Fixing the shm.dll error: conda install mkl intel-openmp --force-reinstall -c conda-forge

Running

Folder organization

• Folders can be organized using folder_processor.py

Motion correction

• Motion correction can be done using the script: batch_pre_process.py