{"id":19091992,"url":"https://github.com/allencellmodeling/aics-deformation","last_synced_at":"2025-07-09T14:05:52.116Z","repository":{"id":91697637,"uuid":"170911470","full_name":"AllenCellModeling/aics-deformation","owner":"AllenCellModeling","description":"Tools to use when working on deformation projects.","archived":false,"fork":false,"pushed_at":"2019-07-16T19:25:23.000Z","size":133206,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-06-29T18:03:40.767Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/AllenCellModeling.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.rst","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-02-15T18:38:44.000Z","updated_at":"2020-11-26T12:49:48.000Z","dependencies_parsed_at":null,"dependency_job_id":"055d6649-2ba6-4bb0-904c-105b288f3469","html_url":"https://github.com/AllenCellModeling/aics-deformation","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/AllenCellModeling/aics-deformation","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Faics-deformation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Faics-deformation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Faics-deformation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Faics-deformation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenCellModeling","download_url":"https://codeload.github.com/AllenCellModeling/aics-deformation/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Faics-deformation/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264473866,"owners_count":23613958,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-09T03:17:45.954Z","updated_at":"2025-07-09T14:05:52.093Z","avatar_url":"https://github.com/AllenCellModeling.png","language":"Python","readme":"# AICS Deformation\n\n[![build status](https://travis-ci.org/AllenCellModeling/aics-deformation.svg?branch=master)](https://travis-ci.org/AllenCellModeling/aics-deformation)\n[![codecov](https://codecov.io/gh/AllenCellModeling/aics-deformation/branch/master/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/aics-deformation)\n\n\n\n\n\n| **Bead Timeseries Input** | **Deformations Over Cells Output** |\n|---------------------------|------------------------------------|\n| \u003cimg src=\"resources/beads.gif\" width=\"400px\"\u003e | \u003cimg src=\"resources/defs.gif\" width=\"400px\"\u003e |\n\nA collection of tools for pre-processing, generating, and post-processing deformation related tasks.\n\n---\n\n## Features\n* AICSDeformation object that wraps openPIV to make deformation generation quick and easy.\n* Simple interface for deformation parameter searching.\n* Pre-process and post-process cleaning, formatting, and visualization tools.\n\n## Overview\n1. **[Optional]** Pre-process a CZI time-lapse movie of cells grown on matrix containing beads into (1) a stack of bead\nslices and (2) a stack of max-projections. This component also applies Ransac to remove camera jitter from the\ntime-lapse.\n\n2. **[Core]** Given a list of `numpy.ndarrays` (each `ndarray` being a 2d image), compute the (u, v) deformations at each\n(x, y) point.\n\n3. **[Optional]** Post-process the deformation data into a heatmap image and overlay the cell max-projection onto it.\nComposite these frames into an mpg movie.\n\n## Installation\nPyPi installation not available at this time, please install using git.\n\n`pip install git+https://github.com/AllenCellModeling/aics-deformation.git`\n\n***Note:*** For the Core components `Numpy` and `Cython` are required to be installed before attempting to install this\npackage. For the optional components it is required to install `openCV`. Some of these pre-install requirements suggest\nsource builds. To make life easier it is recommended to use a conda environment and using `conda install -c conda-forge\nopenpiv numpy opencv`.\n\n\n### Credits\nThis package was created with Cookiecutter. [Original repository](https://github.com/audreyr/cookiecutter)\n\n\n***Free software: Allen Institute Software License***\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fallencellmodeling%2Faics-deformation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fallencellmodeling%2Faics-deformation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fallencellmodeling%2Faics-deformation/lists"}