awesome-biological-image-analysis

Bio imaging toolkit

A curated collection of software tools and resources for biological image analysis

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

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awesomeawesome-listbioimage-analysisbiologycellprofilerimage-analysisimage-processingimagejimagingmicroscopysegmentation

Awesome Biological Image Analysis / General image analysis software
3D Slicer 1,746 about 1 month ago Free, open source and multi-platform software package widely used for medical, biomedical, and related imaging research
BiaPy Open source ready-to-use all-in-one library that provides deep-learning workflows for a large variety of bioimage analysis tasks
BioImageXD Free, open source software package for analyzing, processing and visualizing multi-dimensional microscopy images
Cell-ACDC 138 about 1 month ago A GUI-based Python framework for segmentation, tracking, cell cycle annotations and quantification of microscopy data
CellProfiler 928 about 1 month ago Open-source software helping biologists turn images into cell measurements
CellProfiler Analyst 148 5 months ago Open-source software for exploring and analyzing large, high-dimensional image-derived data
Fiji 778 about 1 month ago A "batteries-included" distribution of ImageJ — a popular, free scientific image processing application
Flika 22 12 months ago An interactive image processing program for biologists written in Python
Icy Open community platform for bioimage informatics, providing software resources to visualize, annotate and quantify bioimaging data
Ilastik 353 about 2 months ago Simple, user-friendly tool for interactive image classification, segmentation and analysis
ImageJ 588 about 1 month ago Public domain software for processing and analyzing scientific images
ImageJ2 1,205 3 months ago A Rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging
ImagePy 1,309 11 months ago Open source image processing framework written in Python
Napari 2,239 about 1 month ago Fast, interactive, multi-dimensional image viewer for Python
OpenCV 79,662 about 1 month ago Open source computer vision and machine learning software library
PYME 85 about 1 month ago Open-source application suite for light microscopy acquisition, data storage, visualization, and analysis
Scikit-image 6,117 about 1 month ago Collection of algorithms for image processing

Awesome Biological Image Analysis / Image processing and segmentation
Ark-Analysis 78 2 months ago A pipeline toolbox for analyzing multiplexed imaging data
AtomAI 197 7 months ago PyTorch-based package for deep/machine learning analysis of microscopy data
Cellpose 1,415 about 2 months ago A generalist algorithm for cell and nucleus segmentation
CellSAM 58 6 months ago A foundation model for cell segmentation trained on a diverse range of cells and data types
Cellshape 21 about 1 year ago 3D single-cell shape analysis of cancer cells using geometric deep learning
CLIJ2 GPU-accelerated image processing library for ImageJ/Fiji, Icy, MATLAB and Java
DeepCell 431 5 months ago Deep learning library for single cell analysis
DeepSlide 494 7 months ago A sliding window framework for classification of high resolution microscopy images
EBImage 71 3 months ago Image processing toolbox for R
GPim 57 about 1 year ago Gaussian processes and Bayesian optimization for images and hyperspectral data
MAPS 49 10 months ago MAPS (Machine learning for Analysis of Proteomics in Spatial biology) is a machine learning approach facilitating rapid and precise cell type identification with human-level accuracy from spatial proteomics data
MicroSAM 372 about 1 month ago Tools for segmentation and tracking in microscopy build on top of SegmentAnything. Segment and track objects in microscopy images interactively
MorpholibJ 101 about 1 month ago Collection of mathematical morphology methods and plugins for ImageJ
PartSeg 30 about 1 month ago A GUI and a library for segmentation algorithms
Proseg 46 about 2 months ago : A cell segmentation method for in situ spatial transcriptomics
PyImSegm 375 about 3 years ago Image segmentation - general superpixel segmentation and center detection and region growing
Salem² 4 4 months ago Segment Anything in Light and Electron Microscopy via Membrane Guidance
Squidpy 447 about 1 month ago Python framework that brings together tools from omics and image analysis to enable scalable description of spatial molecular data, such as transcriptome or multivariate proteins
StarDist 944 3 months ago Object detection with Star-convex shapes
Suite2p 361 7 months ago Pipeline for processing two-photon calcium imaging data
SyMBac 19 6 months ago Accurate segmentation of bacterial microscope images using synthetically generated image data
Trainable Weka Segmentation 112 4 months ago Fiji plugin and library that combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations

Awesome Biological Image Analysis / Ecology
PAT-GEOM A software package for the analysis of animal colour pattern
ThermImageJ 46 8 months ago ImageJ functions and macros for working with thermal image files

Awesome Biological Image Analysis / Neuroscience
AxonDeepSeg 115 about 1 month ago Segment axon and myelin from microscopy data using deep learning
BG-atlasAPI 128 about 1 month ago A lightweight Python module to interact with atlases for systems neuroscience
Brainreg 124 about 2 months ago Automated 3D brain registration with support for multiple species and atlases
Brainreg-napari 15 about 1 year ago Automated 3D brain registration in napari with support for multiple species and atlases
Brainrender 553 about 1 month ago Python package for the visualization of three dimensional neuro-anatomical data
CaImAn 644 about 1 month ago Computational toolbox for large scale Calcium Imaging Analysis
Cellfinder 181 about 2 months ago Automated 3D cell detection and registration of whole-brain images
Cellfinder-napari 23 about 1 year ago Efficient cell detection in large images using in napari
CloudVolume 135 about 1 month ago Read and write Neuroglancer datasets programmatically
NeuroAnatomy Toolbox 64 3 months ago R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons
Neuroglancer 1,109 about 1 month ago WebGL-based viewer for volumetric data
NeuronJ An ImageJ plugin for neurite tracing and analysis
Panda Pipeline for Analyzing braiN Diffusion imAges: A MATLAB toolbox for pipeline processing of diffusion MRI images
PyTorch Connectomics 172 about 1 month ago Deep learning framework for automatic and semi-automatic annotation of connectomics datasets, powered by PyTorch
RivuletPy 66 about 2 years ago Robust 3D Neuron Tracing / General 3D tree structure extraction in Python for 3D images powered by the Rivulet2 algorithm
SNT 43 about 1 month ago ImageJ framework for semi-automated tracing and analysis of neurons
TrailMap 45 over 4 years ago Software package to extract axonal data from cleared brains
Wholebrain 86 over 3 years ago Automated cell detection and registration of whole-brain images with plot of cell counts per region and Hemishpere
ZVQ - Zebrafish Vascular Quantification 10 over 1 year ago Image analysis pipeline to perform 3D quantification of the total or regional zebrafish brain vasculature using the image analysis software Fiji

Awesome Biological Image Analysis / Plant science
Aradeepopsis 41 about 2 years ago A versatile, fully open-source pipeline to extract phenotypic measurements from plant images
DIRT 25 about 1 year ago Digital Imaging of Root Traits: Extract trait measurements from images of monocot and dicot roots
LeafByte Free and open source mobile app for measuring herbivory quickly and accurately
PaCeQuant An ImageJ-based tool which provides a fully automatic image analysis workflow for PC shape quantification
PhenotyperCV 4 over 2 years ago Header-only C++11 library using OpenCV for high-throughput image-based plant phenotyping
PlantCV 671 about 1 month ago Open-source image analysis software package targeted for plant phenotyping
PlantSeg 101 about 1 month ago Tool for cell instance aware segmentation in densely packed 3D volumetric images
RhizoTrak Open source tool for flexible and efficient manual annotation of complex time-series minirhizotron images
Rhizovision Explorer 14 over 3 years ago Free and open-source software developed for estimating root traits from images acquired from a flatbed scanner or camera
RootPainter 59 2 months ago Deep learning segmentation of biological images with corrective annotation

Awesome Biological Image Analysis / Fluoresence in situ hybridization
Big-fish 58 about 1 year ago Python package for the analysis of smFISH images
DypFISH 2 over 1 year ago Python library for spatial analysis of smFISH images
RS-FISH 48 about 2 months ago Fiji plugin to detect FISH spots in 2D/3D images which scales to very large images
Spotiflow 64 about 1 month ago A deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method developed for spatial transcriptomics workflows
TissUUmaps Visualizer of NGS data, plot millions of points and interact, gate, export. ISS rounds and base visualization

Awesome Biological Image Analysis / Electron and super resolution microscopy
ASI_MTF 17 almost 2 years ago ImageJ macro to calculate the modulation transfer function (MTF) based on a knife edge (or slanted edge) measurement
DECODE 96 over 1 year ago Python and PyTorch based deep learning tool for single molecule localization microscopy
Empanada 2 almost 2 years ago Panoptic segmentation algorithms for 2D and 3D electron microscopy images
Em-scalebartools 12 9 months ago Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image
Picasso 110 about 1 month ago A collection of tools for painting super-resolution images
SMAP 66 about 1 month ago A modular super-resolution microscopy analysis platform for SMLM data
ThunderSTORM 95 over 6 years ago A comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging

Awesome Biological Image Analysis / Image restoration and quality assessment
CSBDeep 287 3 months ago A deep learning toolbox for microscopy image restoration and analysis
Ijp-color 23 about 1 year ago Plugins for ImageJ - color space conversions and color calibration
Image Quality 402 12 months ago Open source software library for Image Quality Assessment (IQA)
LLSpy 27 about 2 months ago Python library to facilitate lattice light sheet data processing
NCS 29 about 5 years ago Noise correction algorithm for sCMOS cameras
Noise2Void 414 10 months ago Learning denoising from single noisy images

Awesome Biological Image Analysis / Cell migration and particle tracking
CellMigration 7 over 3 years ago Analysis of 2D cell migration in Igor
TrackMate 173 about 1 month ago User-friendly interface that allows for performing tracking, data visualization, editing results and track analysis in a convenient way
TrackMateR 12 7 months ago R package to analyze cell migration and particle tracking experiments using outputs from TrackMate
Trackpy Fast and Flexible Particle-Tracking Toolkit
TracX MATLAB generic toolbox for cell tracking from various microscopy image modalities such as Bright-field (BF), phase contrast (PhC) or fluorescence (FL) with an automated track quality assessment in absence of a ground truth
TraJClassifier Fiji plugin that loads trajectories from TrackMate, characterizes them using TraJ and classifiies them into normal diffusion, subdiffusion, confined diffusion and directed/active motion by a random forest approach (through Renjin)
QuimP 7 about 1 year ago Software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane
Ultrack 98 about 1 month ago Versatile cell tracking method for 2D, 3D, and multichannel timelapses, overcoming segmentation challenges in complex tissues
Usiigaci 193 over 4 years ago Stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

Awesome Biological Image Analysis / Pathology
FastPathology 123 7 months ago Open-source software for deep learning-based digital pathology
HistoClean 27 almost 3 years ago Tool for the preprocessing and augmentation of images used in deep learning models
Minerva 50 8 months ago Image viewer designed specifically to make it easy for non-expert users to interact with complex tissue images
Orbit A versatile image analysis software for biological image-based quantification using machine learning, especially for whole slide imaging
PathML 398 2 months ago An open-source toolkit for computational pathology and machine learning
PAQUO 106 6 months ago A library for interacting with QuPath from Python
QuPath Open source software for digital pathology image analysis

Awesome Biological Image Analysis / Mycology
DeepMushroom 69 almost 5 years ago Image classification of fungus using ResNet
Fungal Feature Tracker (FFT) 13 over 2 years ago Tool to quantitatively characterize morphology and growth of filamentous fungi

Awesome Biological Image Analysis / Microbiology
BactMap 4 about 1 year ago A command-line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs into various plots
BacStalk Interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial species
BiofilmQ Advanced biofilm analysis tool for quantifying the properties of cells inside large 3-dimensional biofilm communities in space and time

Awesome Biological Image Analysis / Yeast imaging
BABY An image processing pipeline for accurate single-cell growth estimation of budding cells from bright-field stacks
htsimaging 5 about 1 year ago Python package for high-throughput single-cell imaging analysis
YeastMate Neural network-assisted segmentation of mating and budding events in S. cerevisiae
YeaZ 27 11 months ago An interactive tool for segmenting yeast cells using deep learning

Awesome Biological Image Analysis / Other
AICSImageIO 207 5 months ago Image reading, metadata conversion, and image writing for nicroscopy images in Python
Biobeam Open source software package that is designed to provide fast methods for in-silico optical experiments with an emphasize on image formation in biological tissues
BoneJ 20 about 1 month ago Collection of Fiji/ImageJ plug-ins for skeletal biology
CaPTk 182 about 1 year ago Cancer Imaging Phenomics Toolkit: A software platform to perform image analysis and predictive modeling tasks
ColiCoords 26 over 3 years ago Python project for analysis of fluorescence microscopy data from rodlike cells
CompactionAnalyzer 8 about 1 month ago Python package to quantify the tissue compaction (as a measure of the contractile strength) generated by cells or multicellular spheroids that are embedded in fiber materials
Cytominer-database 10 3 months ago Command-line tools for organizing measurements extracted from images
DetecDiv 8 about 2 months ago Comprehensive set of tools to analyze time microscopy images using deep learning methods
MIA 11 about 1 month ago Fiji plugin which provides a modular framework for assembling image and object analysis workflows
MorphoGraphX Open source application for the visualization and analysis of 4D biological datasets
Napari-aicsimageio 34 6 months ago Multiple file format reading directly into napari using pure Python
NEFI2 34 over 3 years ago Python tool created to extract networks from images
Neurite 340 about 1 month ago Neural networks toolbox focused on medical image analysis
Nd2reader 45 11 months ago A pure-Python package that reads images produced by NIS Elements 4.0+
OAD 129 about 1 month ago Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools
Pycytominer 82 about 1 month ago Data processing functions for profiling perturbations
Pyotf 71 9 months ago A simulation software package for modelling optical transfer functions (OTF)/point spread functions (PSF) of optical microscopes written in Python
PyScratch Open source tool that autonomously performs quantitative analysis of in vitro scratch assays
Quanfima 28 12 months ago Quantitative Analysis of Fibrous Materials: A collection of useful functions for morphological analysis and visualization of 2D/3D data from various areas of material science
SimpleElastix 513 over 1 year ago Multi-lingual medical image registration library
Vaa3D Open-source software for 3D/4D/5D image visualization and analysis
XitoSBML 7 about 3 years ago ImageJ plugin which creates a Spatial SBML model from segmented images
Z-stack Depth Color Code 22 almost 4 years ago ImageJ/Fiji plugin to colorcode Z-stacks/hyperstacks
ZeroCostDL4Mic 568 about 1 month ago Google Colab to develop a free and open-source toolbox for deep-Learning in microscopy
ZetaStitcher 40 4 months ago Tool designed to stitch large volumetric images such as those produced by light-sheet fluorescence microscopes

Awesome Biological Image Analysis / Publications
A Hitchhiker's guide through the bio-image analysis software universe An article presenting a curated guide and glossary of bio-image analysis terms and tools
Biological imaging software tools The steps of biological image analysis and the appropriate tools for each step
Data-analysis strategies for image-based cell profiling In-detail explanations of image analysis pipelines
Large-scale image-based screening and profiling of cellular phenotypes A workflow for phenotype extraction from high throughput imaging experiments
Workflow and metrics for image quality control in large-scale high-content screens Approaches for quality control in high-content imaging screens

Awesome Biological Image Analysis / Footnotes / Similar lists and repositories
BIII Repository of bioimage analysis tools
Bio-image Analysis Notebooks Notebooks for bioimage analysis in Python
Bioimaging Guide Microscopy for beginners reference guide
Cytodata 77 about 1 year ago A curated list of awesome cytodata resources
Napari hub Collection of napari plugins
OpenMicroscopy 135 5 months ago Non-comprehensive list of projects and resources related to open microscopy

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