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 12 months 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 12 months ago A GUI-based Python framework for segmentation, tracking, cell cycle annotations and quantification of microscopy data
CellProfiler 928 12 months ago Open-source software helping biologists turn images into cell measurements
CellProfiler Analyst 148 over 1 year ago Open-source software for exploring and analyzing large, high-dimensional image-derived data
Fiji 778 12 months ago A "batteries-included" distribution of ImageJ — a popular, free scientific image processing application
Flika 22 almost 2 years 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 12 months ago Simple, user-friendly tool for interactive image classification, segmentation and analysis
ImageJ 588 12 months ago Public domain software for processing and analyzing scientific images
ImageJ2 1,205 about 1 year ago A Rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging
ImagePy 1,309 almost 2 years ago Open source image processing framework written in Python
Napari 2,239 12 months ago Fast, interactive, multi-dimensional image viewer for Python
OpenCV 79,662 12 months ago Open source computer vision and machine learning software library
PYME 85 12 months ago Open-source application suite for light microscopy acquisition, data storage, visualization, and analysis
Scikit-image 6,117 12 months ago Collection of algorithms for image processing

Awesome Biological Image Analysis / Image processing and segmentation
Ark-Analysis 78 about 1 year ago A pipeline toolbox for analyzing multiplexed imaging data
AtomAI 197 over 1 year ago PyTorch-based package for deep/machine learning analysis of microscopy data
Cellpose 1,415 about 1 year ago A generalist algorithm for cell and nucleus segmentation
CellSAM 58 over 1 year ago A foundation model for cell segmentation trained on a diverse range of cells and data types
Cellshape 21 about 2 years 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 over 1 year ago Deep learning library for single cell analysis
DeepSlide 494 over 1 year ago A sliding window framework for classification of high resolution microscopy images
EBImage 71 about 1 year ago Image processing toolbox for R
GPim 57 about 2 years ago Gaussian processes and Bayesian optimization for images and hyperspectral data
MAPS 49 over 1 year 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 12 months ago Tools for segmentation and tracking in microscopy build on top of SegmentAnything. Segment and track objects in microscopy images interactively
MorpholibJ 101 12 months ago Collection of mathematical morphology methods and plugins for ImageJ
PartSeg 30 12 months ago A GUI and a library for segmentation algorithms
Proseg 46 about 1 year ago : A cell segmentation method for in situ spatial transcriptomics
PyImSegm 375 almost 4 years ago Image segmentation - general superpixel segmentation and center detection and region growing
Salem² 4 about 1 year ago Segment Anything in Light and Electron Microscopy via Membrane Guidance
Squidpy 447 12 months 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 about 1 year ago Object detection with Star-convex shapes
Suite2p 361 over 1 year ago Pipeline for processing two-photon calcium imaging data
SyMBac 19 over 1 year ago Accurate segmentation of bacterial microscope images using synthetically generated image data
Trainable Weka Segmentation 112 about 1 year 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 over 1 year ago ImageJ functions and macros for working with thermal image files

Awesome Biological Image Analysis / Neuroscience
AxonDeepSeg 115 12 months ago Segment axon and myelin from microscopy data using deep learning
BG-atlasAPI 128 12 months ago A lightweight Python module to interact with atlases for systems neuroscience
Brainreg 124 12 months ago Automated 3D brain registration with support for multiple species and atlases
Brainreg-napari 15 almost 2 years ago Automated 3D brain registration in napari with support for multiple species and atlases
Brainrender 553 12 months ago Python package for the visualization of three dimensional neuro-anatomical data
CaImAn 644 12 months ago Computational toolbox for large scale Calcium Imaging Analysis
Cellfinder 181 12 months ago Automated 3D cell detection and registration of whole-brain images
Cellfinder-napari 23 almost 2 years ago Efficient cell detection in large images using in napari
CloudVolume 135 12 months ago Read and write Neuroglancer datasets programmatically
NeuroAnatomy Toolbox 64 about 1 year ago R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons
Neuroglancer 1,109 12 months 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 12 months ago Deep learning framework for automatic and semi-automatic annotation of connectomics datasets, powered by PyTorch
RivuletPy 66 about 3 years ago Robust 3D Neuron Tracing / General 3D tree structure extraction in Python for 3D images powered by the Rivulet2 algorithm
SNT 43 12 months ago ImageJ framework for semi-automated tracing and analysis of neurons
TrailMap 45 over 5 years ago Software package to extract axonal data from cleared brains
Wholebrain 86 over 4 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 2 years 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 3 years ago A versatile, fully open-source pipeline to extract phenotypic measurements from plant images
DIRT 25 about 2 years 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 3 years ago Header-only C++11 library using OpenCV for high-throughput image-based plant phenotyping
PlantCV 671 12 months ago Open-source image analysis software package targeted for plant phenotyping
PlantSeg 101 12 months 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 4 years ago Free and open-source software developed for estimating root traits from images acquired from a flatbed scanner or camera
RootPainter 59 about 1 year ago Deep learning segmentation of biological images with corrective annotation

Awesome Biological Image Analysis / Fluoresence in situ hybridization
Big-fish 58 about 2 years ago Python package for the analysis of smFISH images
DypFISH 2 about 2 years ago Python library for spatial analysis of smFISH images
RS-FISH 48 12 months ago Fiji plugin to detect FISH spots in 2D/3D images which scales to very large images
Spotiflow 64 12 months 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 over 2 years ago ImageJ macro to calculate the modulation transfer function (MTF) based on a knife edge (or slanted edge) measurement
DECODE 96 over 2 years ago Python and PyTorch based deep learning tool for single molecule localization microscopy
Empanada 2 almost 3 years ago Panoptic segmentation algorithms for 2D and 3D electron microscopy images
Em-scalebartools 12 over 1 year ago Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image
Picasso 110 12 months ago A collection of tools for painting super-resolution images
SMAP 66 12 months ago A modular super-resolution microscopy analysis platform for SMLM data
ThunderSTORM 95 about 7 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 about 1 year ago A deep learning toolbox for microscopy image restoration and analysis
Ijp-color 23 almost 2 years ago Plugins for ImageJ - color space conversions and color calibration
Image Quality 402 almost 2 years ago Open source software library for Image Quality Assessment (IQA)
LLSpy 27 12 months ago Python library to facilitate lattice light sheet data processing
NCS 29 almost 6 years ago Noise correction algorithm for sCMOS cameras
Noise2Void 414 over 1 year ago Learning denoising from single noisy images

Awesome Biological Image Analysis / Cell migration and particle tracking
CellMigration 7 over 4 years ago Analysis of 2D cell migration in Igor
TrackMate 173 12 months ago User-friendly interface that allows for performing tracking, data visualization, editing results and track analysis in a convenient way
TrackMateR 12 over 1 year 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 2 years ago Software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane
Ultrack 98 12 months ago Versatile cell tracking method for 2D, 3D, and multichannel timelapses, overcoming segmentation challenges in complex tissues
Usiigaci 193 about 5 years ago Stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

Awesome Biological Image Analysis / Pathology
FastPathology 123 over 1 year ago Open-source software for deep learning-based digital pathology
HistoClean 27 almost 4 years ago Tool for the preprocessing and augmentation of images used in deep learning models
Minerva 50 over 1 year 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 about 1 year ago An open-source toolkit for computational pathology and machine learning
PAQUO 106 over 1 year 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 6 years ago Image classification of fungus using ResNet
Fungal Feature Tracker (FFT) 13 over 3 years ago Tool to quantitatively characterize morphology and growth of filamentous fungi

Awesome Biological Image Analysis / Microbiology
BactMap 4 about 2 years 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 almost 2 years 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 over 1 year ago An interactive tool for segmenting yeast cells using deep learning

Awesome Biological Image Analysis / Other
AICSImageIO 207 over 1 year 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 12 months ago Collection of Fiji/ImageJ plug-ins for skeletal biology
CaPTk 182 almost 2 years ago Cancer Imaging Phenomics Toolkit: A software platform to perform image analysis and predictive modeling tasks
ColiCoords 26 over 4 years ago Python project for analysis of fluorescence microscopy data from rodlike cells
CompactionAnalyzer 8 12 months 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 about 1 year ago Command-line tools for organizing measurements extracted from images
DetecDiv 8 about 1 year ago Comprehensive set of tools to analyze time microscopy images using deep learning methods
MIA 11 12 months 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 over 1 year ago Multiple file format reading directly into napari using pure Python
NEFI2 34 over 4 years ago Python tool created to extract networks from images
Neurite 340 12 months ago Neural networks toolbox focused on medical image analysis
Nd2reader 45 almost 2 years ago A pure-Python package that reads images produced by NIS Elements 4.0+
OAD 129 12 months ago Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools
Pycytominer 82 12 months ago Data processing functions for profiling perturbations
Pyotf 71 over 1 year 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 almost 2 years 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 2 years ago Multi-lingual medical image registration library
Vaa3D Open-source software for 3D/4D/5D image visualization and analysis
XitoSBML 7 about 4 years ago ImageJ plugin which creates a Spatial SBML model from segmented images
Z-stack Depth Color Code 22 almost 5 years ago ImageJ/Fiji plugin to colorcode Z-stacks/hyperstacks
ZeroCostDL4Mic 568 12 months ago Google Colab to develop a free and open-source toolbox for deep-Learning in microscopy
ZetaStitcher 40 about 1 year 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 2 years ago A curated list of awesome cytodata resources
Napari hub Collection of napari plugins
OpenMicroscopy 135 over 1 year ago Non-comprehensive list of projects and resources related to open microscopy

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