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.
-
[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.
-
[Core] Given a list of
numpy.ndarrays
(eachndarray
being 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