Repository Index

Image analysis and comparison

3D visualization and mesh analysis for science and engineering

• vtk
• python
• visualization
• 3d

PyGraphistry is a Python library to quickly load, shape, embed, and explore big graphs with the GPU-accelerated Graphistry visual graph analyzer

• graph
• visualization
• gpu
• graphistry

A python module for scientific analysis of 3D data based on VTK and Numpy

• 3d-graphics
• vtk
• 3d
• mesh

cuGraph - RAPIDS Graph Analytics Library

• rapids
• nvidia
• gpu
• cuda

Leptonica is an open source library containing software that is broadly useful for image processing and image analysis applications. The official github repository for Leptonica is: danbloomberg/leptonica. See leptonica.org for more documentation.

An open-source application for biological image analysis

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

• calcium-imaging
• deconvolution
• source-extraction
• motion-correction

cell detection in calcium imaging recordings

• imaging
• neuroscience
• data-analysis

a generic C++ library for image analysis

Open source math and physics engine that executes MATLAB-syntax code. Features a modern compiler, automatic GPU acceleration for large calculations, and support for math on geometry / FEA calculations.

• matlab
• rust
• jit-compiler
• linear-algebra

TrackMate is your buddy for your everyday tracking.

• image-analysis
• single-particle-tracking
• fiji-plugin

Allocators, I/O streams, math, geometry, image and audio processing for D

• utility-library
• dlang
• linear-algebra
• computational-geometry

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

• python
• microscopy
• scripting
• automation

Collection of mathematical morphology methods and plugins for ImageJ

• image-processing
• image-analysis
• imagej
• fiji

:art: Image processing toolbox for R

• r
• bioinformatics
• image-processing
• image-analysis

HistoClean is a tool for the preprocessing and augmentation of images used in deep learning models. This easy to use application brings together the most popular image processing packages from across the python universe, meaning no more looking at documentation! HistoClean provides real time feedback to augmentations and preprocessing options. This allows users to evaluate their steps before implementation.

• image-processing
• images
• image-analysis
• deep-learning

Plugins for bone image analysis

• fiji-plugin
• image-analysis
• image-processing
• imagej-plugins

Lattice light-sheet post-processing utility.

• microscopy
• light-sheet
• image-processing
• image-analysis

Imagej macro to calculate the MTF based on a knife edge measurement

• imagej-macro
• electron-microscopy
• image-analysis
• x-ray-imaging

Modular image and object analysis workflows for ImageJ/Fiji

• fiji-plugin
• modular
• imagej
• image-processing

A Python package to analyze matrix fiber orientation and intensity around cells as a proxy for cellular forces. Also measures alignment relative to X/Y axes, points and lines, with optional masks, a Python API and browser tools for analysis and group comparisons.

• imaging
• microscopy
• contractility
• collagen

🔬Python package for high-throughput single-cell imaging analysis.

• microscopy-image-analysis
• single-cell-analysis

Python library for statistical analysis of mRNA and protein distributions in fluorescent microscopy images