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AllenCellModeling/aics-deformation

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We are no longer actively maintaining this repository. All active work by the Allen Institute for Cell Science is located under the AllenCell organization.

AICS Deformation

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Bead Timeseries Input Deformations Over Cells Output

A collection of tools for pre-processing, generating, and post-processing deformation related tasks.


Features

  • AICSDeformation object that wraps openPIV to make deformation generation quick and easy.
  • Simple interface for deformation parameter searching.
  • Pre-process and post-process cleaning, formatting, and visualization tools.

Overview

  1. [Optional] Pre-process a CZI time-lapse movie of cells grown on matrix containing beads into (1) a stack of bead slices and (2) a stack of max-projections. This component also applies Ransac to remove camera jitter from the time-lapse.

  2. [Core] Given a list of numpy.ndarrays (each ndarray being a 2d image), compute the (u, v) deformations at each (x, y) point.

  3. [Optional] Post-process the deformation data into a heatmap image and overlay the cell max-projection onto it. Composite these frames into an mpg movie.

Installation

PyPi installation not available at this time, please install using git.

pip install git+https://github.com/AllenCellModeling/aics-deformation.git

Note: For the Core components Numpy and Cython are required to be installed before attempting to install this package. For the optional components it is required to install openCV. Some of these pre-install requirements suggest source builds. To make life easier it is recommended to use a conda environment and using conda install -c conda-forge openpiv numpy opencv.

Credits

This package was created with Cookiecutter. Original repository

Free software: Allen Institute Software License

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Tools to use when working on deformation projects.

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