Important
We are no longer actively maintaining this repository. All active work by the Allen Institute for Cell Science is located under the AllenCell organization.
| Bead Timeseries Input | Deformations Over Cells Output |
|---|---|
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A collection of tools for pre-processing, generating, and post-processing deformation related tasks.
- 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.
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[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.
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[Core] Given a list of
numpy.ndarrays(eachndarraybeing a 2d image), compute the (u, v) deformations at each (x, y) point. -
[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.
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.
This package was created with Cookiecutter. Original repository
Free software: Allen Institute Software License