Python implementation of the Light Beads Microscopy (LBM) computational pipeline.
Project description
LBM-CaImAn-Python
Python implementation of the Light Beads Microscopy (LBM) computational pipeline.
For the MATLAB implementation, see here
Pipeline Steps:
- Extraction
- De-interleave zT
- Scan Phase-Correlation
- Registration
- Template creation
- Rigid registration
- Piecewise-rigid registration
- Segmentation
- Iterative CNMF segmentation
- Deconvolution
- Refinement
Requirements
- caiman
- numpy
- scipy
See the `environment.yml` file at the root of this project for a complete list of package dependencies.
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