https://github.com/allencellmodeling/aics-deformation

Tools to use when working on deformation projects.
https://github.com/allencellmodeling/aics-deformation

Last synced: 4 months ago
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Tools to use when working on deformation projects.

• Host: GitHub
• URL: https://github.com/allencellmodeling/aics-deformation
• Owner: AllenCellModeling
• License: other
• Created: 2019-02-15T18:38:44.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2019-07-16T19:25:23.000Z (almost 6 years ago)
• Last Synced: 2025-01-02T23:14:21.883Z (5 months ago)
• Language: Python
• Size: 127 MB
• Stars: 1
• Watchers: 5
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE

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README

        
# AICS Deformation

[![build status](https://travis-ci.org/AllenCellModeling/aics-deformation.svg?branch=master)](https://travis-ci.org/AllenCellModeling/aics-deformation)

[![codecov](https://codecov.io/gh/AllenCellModeling/aics-deformation/branch/master/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/aics-deformation)

| **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](https://github.com/audreyr/cookiecutter)

***Free software: Allen Institute Software License***