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 | 1,723 | 4 days 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 | 133 | 4 days ago | A GUI-based Python framework for segmentation, tracking, cell cycle annotations and quantification of microscopy data |
| CellProfiler | 923 | 6 days ago | Open-source software helping biologists turn images into cell measurements |
| CellProfiler Analyst | 146 | 3 months ago | Open-source software for exploring and analyzing large, high-dimensional image-derived data |
| Fiji | 768 | 9 days ago | A "batteries-included" distribution of ImageJ — a popular, free scientific image processing application |
| Flika | 22 | 10 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 | 6 days ago | Simple, user-friendly tool for interactive image classification, segmentation and analysis |
| ImageJ | 572 | 12 days ago | Public domain software for processing and analyzing scientific images |
| ImageJ2 | 1,192 | about 1 month ago | A Rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging |
| ImagePy | 1,304 | 9 months ago | Open source image processing framework written in Python |
| Napari | 2,213 | 5 days ago | Fast, interactive, multi-dimensional image viewer for Python |
| OpenCV | 79,147 | 5 days ago | Open source computer vision and machine learning software library |
| PYME | 84 | 7 days ago | Open-source application suite for light microscopy acquisition, data storage, visualization, and analysis |
| Scikit-image | 6,089 | 7 days ago | Collection of algorithms for image processing |
Awesome Biological Image Analysis / Image processing and segmentation | |||
| Ark-Analysis | 76 | 14 days ago | A pipeline toolbox for analyzing multiplexed imaging data |
| AtomAI | 194 | 5 months ago | PyTorch-based package for deep/machine learning analysis of microscopy data |
| Cellpose | 1,385 | 22 days ago | A generalist algorithm for cell and nucleus segmentation |
| CellSAM | 53 | 4 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 | 424 | 3 months ago | Deep learning library for single cell analysis |
| DeepSlide | 489 | 6 months ago | A sliding window framework for classification of high resolution microscopy images |
| EBImage | 72 | about 1 month ago | Image processing toolbox for R |
| GPim | 57 | 12 months ago | Gaussian processes and Bayesian optimization for images and hyperspectral data |
| MAPS | 48 | 8 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 | 365 | 6 days ago | Tools for segmentation and tracking in microscopy build on top of SegmentAnything. Segment and track objects in microscopy images interactively |
| MorpholibJ | 101 | 23 days ago | Collection of mathematical morphology methods and plugins for ImageJ |
| PartSeg | 30 | 10 days ago | A GUI and a library for segmentation algorithms |
| Proseg | 45 | 6 days ago | : A cell segmentation method for in situ spatial transcriptomics |
| PyImSegm | 373 | almost 3 years ago | Image segmentation - general superpixel segmentation and center detection and region growing |
| Salem² | 4 | about 2 months ago | Segment Anything in Light and Electron Microscopy via Membrane Guidance |
| Squidpy | 440 | 7 days 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 | 925 | about 2 months ago | Object detection with Star-convex shapes |
| Suite2p | 358 | 5 months ago | Pipeline for processing two-photon calcium imaging data |
| SyMBac | 19 | 4 months ago | Accurate segmentation of bacterial microscope images using synthetically generated image data |
| Trainable Weka Segmentation | 112 | about 2 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 | 6 months ago | ImageJ functions and macros for working with thermal image files |
Awesome Biological Image Analysis / Neuroscience | |||
| AxonDeepSeg | 115 | 9 days ago | Segment axon and myelin from microscopy data using deep learning |
| BG-atlasAPI | 127 | 6 days ago | A lightweight Python module to interact with atlases for systems neuroscience |
| Brainreg | 123 | 9 days ago | Automated 3D brain registration with support for multiple species and atlases |
| Brainreg-napari | 15 | 11 months ago | Automated 3D brain registration in napari with support for multiple species and atlases |
| Brainrender | 547 | 9 days ago | Python package for the visualization of three dimensional neuro-anatomical data |
| CaImAn | 638 | about 1 month ago | Computational toolbox for large scale Calcium Imaging Analysis |
| Cellfinder | 181 | 7 days ago | Automated 3D cell detection and registration of whole-brain images |
| Cellfinder-napari | 24 | 11 months ago | Efficient cell detection in large images using in napari |
| CloudVolume | 134 | 13 days ago | Read and write Neuroglancer datasets programmatically |
| NeuroAnatomy Toolbox | 64 | about 1 month ago | R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons |
| Neuroglancer | 1,090 | 7 days 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 | 171 | 4 months 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 | 42 | 6 days 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 | 662 | 6 days ago | Open-source image analysis software package targeted for plant phenotyping |
| PlantSeg | 97 | 17 days 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 | 58 | 4 months ago | Deep learning segmentation of biological images with corrective annotation |
Awesome Biological Image Analysis / Fluoresence in situ hybridization | |||
| Big-fish | 57 | about 1 year ago | Python package for the analysis of smFISH images |
| DypFISH | 2 | about 1 year ago | Python library for spatial analysis of smFISH images |
| RS-FISH | 46 | 3 months ago | Fiji plugin to detect FISH spots in 2D/3D images which scales to very large images |
| Spotiflow | 61 | 9 days 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 1 year ago | ImageJ macro to calculate the modulation transfer function (MTF) based on a knife edge (or slanted edge) measurement |
| DECODE | 95 | over 1 year ago | Python and PyTorch based deep learning tool for single molecule localization microscopy |
| Empanada | 2 | over 1 year ago | Panoptic segmentation algorithms for 2D and 3D electron microscopy images |
| Em-scalebartools | 12 | 7 months ago | Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image |
| Picasso | 110 | about 2 months ago | A collection of tools for painting super-resolution images |
| SMAP | 64 | about 1 month ago | A modular super-resolution microscopy analysis platform for SMLM data |
| ThunderSTORM | 95 | about 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 | 285 | about 2 months ago | A deep learning toolbox for microscopy image restoration and analysis |
| Ijp-color | 23 | 10 months ago | Plugins for ImageJ - color space conversions and color calibration |
| Image Quality | 401 | 10 months ago | Open source software library for Image Quality Assessment (IQA) |
| LLSpy | 27 | 17 days ago | Python library to facilitate lattice light sheet data processing |
| NCS | 29 | almost 5 years ago | Noise correction algorithm for sCMOS cameras |
| Noise2Void | 408 | 8 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 | 169 | 13 days ago | User-friendly interface that allows for performing tracking, data visualization, editing results and track analysis in a convenient way |
| TrackMateR | 12 | 6 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 | 12 months ago | Software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane |
| Ultrack | 94 | 7 days ago | Versatile cell tracking method for 2D, 3D, and multichannel timelapses, overcoming segmentation challenges in complex tissues |
| Usiigaci | 193 | about 4 years ago | Stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning |
Awesome Biological Image Analysis / Pathology | |||
| FastPathology | 122 | 5 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 | 7 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 | 392 | 15 days ago | An open-source toolkit for computational pathology and machine learning |
| PAQUO | 104 | 4 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 | 11 months 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 | 9 months ago | An interactive tool for segmenting yeast cells using deep learning |
Awesome Biological Image Analysis / Other | |||
| AICSImageIO | 205 | 3 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 | 6 months ago | Collection of Fiji/ImageJ plug-ins for skeletal biology |
| CaPTk | 181 | 12 months 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 | 7 | about 2 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 month ago | Command-line tools for organizing measurements extracted from images |
| DetecDiv | 8 | 9 days ago | Comprehensive set of tools to analyze time microscopy images using deep learning methods |
| MIA | 11 | 6 days 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 | 33 | 4 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 | 2 months ago | Neural networks toolbox focused on medical image analysis |
| Nd2reader | 45 | 9 months ago | A pure-Python package that reads images produced by NIS Elements 4.0+ |
| OAD | 127 | 4 months ago | Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools |
| Pycytominer | 80 | 15 days ago | Data processing functions for profiling perturbations |
| Pyotf | 71 | 8 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 | 10 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 | 562 | 10 days ago | Google Colab to develop a free and open-source toolbox for deep-Learning in microscopy |
| ZetaStitcher | 39 | 2 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 | 73 | about 1 year ago | A curated list of awesome cytodata resources |
| Napari hub | Collection of napari plugins | ||
| OpenMicroscopy | 131 | 3 months ago | Non-comprehensive list of projects and resources related to open microscopy |
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