Python implementation of the Light Beads Microscopy (LBM) computational pipeline.

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  • Author: Flynn OConnell
  • Tags Pipeline , Numpy , Microscopy , ScanImage , multiROI , tiff
  • Requires: Python >=3.9
  • Provides-Extra: all , docs , gui , io , notebook
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Project description

LBM-CaImAn-Python

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Python implementation of the Light Beads Microscopy (LBM) computational pipeline.

For the MATLAB implementation, see here

Pipeline Steps:

  1. Extraction
    • De-interleave zT
    • Scan Phase-Correlation
  2. Registration
    • Template creation
    • Rigid registration
    • Piecewise-rigid registration
  3. 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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Maintainers
Avatar for FlynnOConnell from gravatar.com FlynnOConnell Avatar for rchhmiscope from gravatar.com rchhmiscope

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Project links
Meta
  • Author: Flynn OConnell
  • Tags Pipeline , Numpy , Microscopy , ScanImage , multiROI , tiff
  • Requires: Python >=3.9
  • Provides-Extra: all , docs , gui , io , notebook
Classifiers

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0.7.0

0.2.0

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