[38;5;12m                                                                       [39m[38;2;255;187;0m[1m[4mAwesome Biological Image Analysis [0m[38;5;14m[1m[4m![0m[38;2;255;187;0m[1m[4mAwesome[0m[38;5;14m[1m[4m (https://awesome.re/badge.svg)[0m[38;2;255;187;0m[1m[4m (https://awesome.re)[0m


[38;5;12m  [39m
[48;5;235m[38;5;249m[49m[39m
[38;5;12m [39m
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[38;5;11m[1m▐[0m[38;5;12m [39m[38;5;12mTools and resources for biological image analysis.[39m

[38;5;12mBiological image analysis aims to increase our understanding of biology through the use of various computational techniques and approaches to obtain valuable information from images.[39m

[38;2;255;187;0m[4mContents[0m
[38;5;12m- [39m[38;5;14m[1mGeneral image analysis software[0m[38;5;12m (#general-image-analysis-software)[39m
[38;5;12m- [39m[38;5;14m[1mImage processing and segmentation[0m[38;5;12m (#image-processing-and-segmentation)[39m
[38;5;12m- [39m[38;5;14m[1mEcology[0m[38;5;12m (#ecology)[39m
[38;5;12m- [39m[38;5;14m[1mNeuroscience[0m[38;5;12m (#neuroscience)[39m
[38;5;12m- [39m[38;5;14m[1mPlant science[0m[38;5;12m (#plant-science)[39m
[38;5;12m- [39m[38;5;14m[1mFluoresence in situ hybridization[0m[38;5;12m (#fluoresence-in-situ-hybridization)[39m
[38;5;12m- [39m[38;5;14m[1mElectron and super resolution microscopy[0m[38;5;12m (#electron-and-super-resolution-microscopy)[39m
[38;5;12m- [39m[38;5;14m[1mImage restoration and quality assessment[0m[38;5;12m (#image-restoration-and-quality-assessment)[39m
[38;5;12m- [39m[38;5;14m[1mCell migration and particle tracking[0m[38;5;12m (#cell-migration-and-particle-tracking)[39m
[38;5;12m- [39m[38;5;14m[1mPathology[0m[38;5;12m (#pathology)[39m
[38;5;12m- [39m[38;5;14m[1mMycology[0m[38;5;12m (#mycology)[39m
[38;5;12m- [39m[38;5;14m[1mMicrobiology[0m[38;5;12m (#microbiology)[39m
[38;5;12m- [39m[38;5;14m[1mYeast imaging[0m[38;5;12m (#yeast-imaging)[39m
[38;5;12m- [39m[38;5;14m[1mOther[0m[38;5;12m (#other)[39m
[38;5;12m- [39m[38;5;14m[1mPublications[0m[38;5;12m (#publications)[39m

[38;2;255;187;0m[4mGeneral image analysis software[0m
[38;5;12m- [39m[38;5;14m[1m3D Slicer[0m[38;5;12m (https://github.com/Slicer/Slicer) - Free, open source and multi-platform software package widely used for medical, biomedical, and related imaging research.[39m
[38;5;12m- [39m[38;5;14m[1mBiaPy[0m[38;5;12m (https://biapyx.github.io/) - Open source ready-to-use all-in-one library that provides deep-learning workflows for a large variety of bioimage analysis tasks.[39m
[38;5;12m- [39m[38;5;14m[1mBioImageXD[0m[38;5;12m (https://bioimagexd.net) - Free, open source software package for analyzing, processing and visualizing multi-dimensional microscopy images.[39m
[38;5;12m- [39m[38;5;14m[1mCell-ACDC[0m[38;5;12m (https://github.com/SchmollerLab/Cell_ACDC) - A GUI-based Python framework for segmentation, tracking, cell cycle annotations and quantification of microscopy data.[39m
[38;5;12m- [39m[38;5;14m[1mCellProfiler[0m[38;5;12m (https://github.com/CellProfiler/CellProfiler) - Open-source software helping biologists turn images into cell measurements.[39m
[38;5;12m- [39m[38;5;14m[1mCellProfiler Analyst[0m[38;5;12m (https://github.com/CellProfiler/CellProfiler-Analyst) - Open-source software for exploring and analyzing large, high-dimensional image-derived data.[39m
[38;5;12m- [39m[38;5;14m[1mFiji[0m[38;5;12m (https://github.com/fiji/fiji) - A "batteries-included" distribution of ImageJ — a popular, free scientific image processing application.[39m
[38;5;12m- [39m[38;5;14m[1mFlika[0m[38;5;12m (https://github.com/flika-org/flika) - An interactive image processing program for biologists written in Python.[39m
[38;5;12m- [39m[38;5;14m[1mIcy[0m[38;5;12m (https://github.com/Icy-imaging) - Open community platform for bioimage informatics, providing software resources to visualize, annotate and quantify bioimaging data.[39m
[38;5;12m- [39m[38;5;14m[1mIlastik[0m[38;5;12m (https://github.com/ilastik/ilastik) - Simple, user-friendly tool for interactive image classification, segmentation and analysis.[39m
[38;5;12m- [39m[38;5;14m[1mImageJ[0m[38;5;12m (https://github.com/imagej/ImageJ) - Public domain software for processing and analyzing scientific images.[39m
[38;5;12m- [39m[38;5;14m[1mImageJ2[0m[38;5;12m (https://github.com/imagej/imagej2) - A Rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging.[39m
[38;5;12m- [39m[38;5;14m[1mImagePy[0m[38;5;12m (https://github.com/Image-Py/imagepy) - Open source image processing framework written in Python.[39m
[38;5;12m- [39m[38;5;14m[1mNapari[0m[38;5;12m (https://github.com/napari/napari) - Fast, interactive, multi-dimensional image viewer for Python.[39m
[38;5;12m- [39m[38;5;14m[1mOpenCV[0m[38;5;12m (https://github.com/opencv/opencv) - Open source computer vision and machine learning software library.[39m
[38;5;12m- [39m[38;5;14m[1mPYME[0m[38;5;12m (https://github.com/python-microscopy/python-microscopy) - Open-source application suite for light microscopy acquisition, data storage, visualization, and analysis.[39m
[38;5;12m- [39m[38;5;14m[1mScikit-image[0m[38;5;12m (https://github.com/scikit-image/scikit-image) - Collection of algorithms for image processing.[39m


[38;2;255;187;0m[4mImage processing and segmentation[0m
[38;5;12m- [39m[38;5;14m[1mArk-Analysis[0m[38;5;12m (https://github.com/angelolab/ark-analysis) - A pipeline toolbox for analyzing multiplexed imaging data.[39m
[38;5;12m- [39m[38;5;14m[1mAtomAI[0m[38;5;12m (https://github.com/pycroscopy/atomai) - PyTorch-based package for deep/machine learning analysis of microscopy data.[39m
[38;5;12m- [39m[38;5;14m[1mCellpose[0m[38;5;12m (https://github.com/MouseLand/cellpose) - A generalist algorithm for cell and nucleus segmentation.[39m
[38;5;12m- [39m[38;5;14m[1mCellshape[0m[38;5;12m (https://github.com/Sentinal4D/cellshape) - 3D single-cell shape analysis of cancer cells using geometric deep learning.[39m
[38;5;12m- [39m[38;5;14m[1mCLIJ2[0m[38;5;12m (https://clij.github.io/) - GPU-accelerated image processing library for ImageJ/Fiji, Icy, MATLAB and Java.[39m
[38;5;12m- [39m[38;5;14m[1mDeepCell[0m[38;5;12m (https://github.com/vanvalenlab/deepcell-tf) - Deep learning library for single cell analysis.[39m
[38;5;12m- [39m[38;5;14m[1mDeepSlide[0m[38;5;12m (https://github.com/BMIRDS/deepslide) - A sliding window framework for classification of high resolution microscopy images.[39m
[38;5;12m- [39m[38;5;14m[1mEBImage[0m[38;5;12m (https://github.com/aoles/EBImage) - Image processing toolbox for R.[39m
[38;5;12m- [39m[38;5;14m[1mGPim[0m[38;5;12m (https://github.com/ziatdinovmax/GPim) - Gaussian processes and Bayesian optimization for images and hyperspectral data.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mMAPS[0m[38;5;12m [39m[38;5;12m(https://github.com/mahmoodlab/MAPS)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mMAPS[39m[38;5;12m [39m[38;5;12m(Machine[39m[38;5;12m [39m[38;5;12mlearning[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mAnalysis[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mProteomics[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mSpatial[39m[38;5;12m [39m[38;5;12mbiology)[39m[38;5;12m [39m[38;5;12mis[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mmachine[39m[38;5;12m [39m[38;5;12mlearning[39m[38;5;12m [39m[38;5;12mapproach[39m[38;5;12m [39m[38;5;12mfacilitating[39m[38;5;12m [39m[38;5;12mrapid[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mprecise[39m[38;5;12m [39m[38;5;12mcell[39m[38;5;12m [39m[38;5;12mtype[39m[38;5;12m [39m[38;5;12midentification[39m[38;5;12m [39m[38;5;12mwith[39m[38;5;12m [39m[38;5;12mhuman-level[39m[38;5;12m [39m[38;5;12maccuracy[39m[38;5;12m [39m[38;5;12mfrom[39m[38;5;12m [39m
[38;5;12mspatial[39m[38;5;12m [39m[38;5;12mproteomics[39m[38;5;12m [39m[38;5;12mdata.[39m
[38;5;12m- [39m[38;5;14m[1mMicroSAM[0m[38;5;12m (https://github.com/computational-cell-analytics/micro-sam) - Tools for segmentation and tracking in microscopy build on top of SegmentAnything. Segment and track objects in microscopy images interactively.[39m
[38;5;12m- [39m[38;5;14m[1mMorpholibJ[0m[38;5;12m (https://github.com/ijpb/MorphoLibJ) - Collection of mathematical morphology methods and plugins for ImageJ.[39m
[38;5;12m- [39m[38;5;14m[1mPartSeg[0m[38;5;12m (https://github.com/4DNucleome/PartSeg) - A GUI and a library for segmentation algorithms.[39m
[38;5;12m- [39m[38;5;14m[1mPyImSegm[0m[38;5;12m (https://github.com/Borda/pyImSegm) - Image segmentation - general superpixel segmentation and center detection and region growing.[39m
[38;5;12m- [39m[38;5;14m[1mSquidpy[0m[38;5;12m (https://github.com/scverse/squidpy) - 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.[39m
[38;5;12m- [39m[38;5;14m[1mStarDist[0m[38;5;12m (https://github.com/stardist/stardist) - Object detection with Star-convex shapes.[39m
[38;5;12m- [39m[38;5;14m[1mSuite2p[0m[38;5;12m (https://github.com/MouseLand/suite2p) - Pipeline for processing two-photon calcium imaging data.[39m
[38;5;12m- [39m[38;5;14m[1mSyMBac[0m[38;5;12m (https://github.com/georgeoshardo/SyMBac) - Accurate segmentation of bacterial microscope images using synthetically generated image data.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mTrainable[0m[38;5;14m[1m [0m[38;5;14m[1mWeka[0m[38;5;14m[1m [0m[38;5;14m[1mSegmentation[0m[38;5;12m [39m[38;5;12m(https://github.com/fiji/Trainable_Segmentation)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mFiji[39m[38;5;12m [39m[38;5;12mplugin[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mlibrary[39m[38;5;12m [39m[38;5;12mthat[39m[38;5;12m [39m[38;5;12mcombines[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mcollection[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mmachine[39m[38;5;12m [39m[38;5;12mlearning[39m[38;5;12m [39m[38;5;12malgorithms[39m[38;5;12m [39m[38;5;12mwith[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mset[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mselected[39m[38;5;12m [39m[38;5;12mimage[39m[38;5;12m [39m[38;5;12mfeatures[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12mproduce[39m[38;5;12m [39m[38;5;12mpixel-based[39m[38;5;12m [39m
[38;5;12msegmentations.[39m

[38;2;255;187;0m[4mEcology[0m
[38;5;12m- [39m[38;5;14m[1mPAT-GEOM[0m[38;5;12m (http://ianzwchan.com/my-research/pat-geom/) - A software package for the analysis of animal colour pattern.[39m
[38;5;12m- [39m[38;5;14m[1mThermImageJ[0m[38;5;12m (https://github.com/gtatters/ThermImageJ) - ImageJ functions and macros for working with thermal image files.[39m


[38;2;255;187;0m[4mNeuroscience[0m
[38;5;12m- [39m[38;5;14m[1mAxonDeepSeg[0m[38;5;12m (https://github.com/axondeepseg/axondeepseg) - Segment axon and myelin from microscopy data using deep learning.[39m
[38;5;12m- [39m[38;5;14m[1mBG-atlasAPI[0m[38;5;12m (https://github.com/brainglobe/bg-atlasapi) - A lightweight Python module to interact with atlases for systems neuroscience.[39m
[38;5;12m- [39m[38;5;14m[1mBrainreg[0m[38;5;12m (https://github.com/brainglobe/brainreg) - Automated 3D brain registration with support for multiple species and atlases.[39m
[38;5;12m- [39m[38;5;14m[1mBrainreg-napari[0m[38;5;12m (https://github.com/brainglobe/brainreg-napari) - Automated 3D brain registration in napari with support for multiple species and atlases.[39m
[38;5;12m- [39m[38;5;14m[1mBrainrender[0m[38;5;12m (https://github.com/brainglobe/brainrender) - Python package for the visualization of three dimensional neuro-anatomical data.[39m
[38;5;12m- [39m[38;5;14m[1mCaImAn[0m[38;5;12m (https://github.com/flatironinstitute/CaImAn) - Computational toolbox for large scale Calcium Imaging Analysis.[39m
[38;5;12m- [39m[38;5;14m[1mCellfinder[0m[38;5;12m (https://github.com/brainglobe/cellfinder) - Automated 3D cell detection and registration of whole-brain images.[39m
[38;5;12m- [39m[38;5;14m[1mCellfinder-napari[0m[38;5;12m (https://github.com/brainglobe/cellfinder-napari) - Efficient cell detection in large images using [39m[38;5;14m[1mcellfinder[0m[38;5;12m (https://brainglobe.info/cellfinder) in napari.[39m
[38;5;12m- [39m[38;5;14m[1mCloudVolume[0m[38;5;12m (https://github.com/seung-lab/cloud-volume) - Read and write Neuroglancer datasets programmatically.[39m
[38;5;12m- [39m[38;5;14m[1mNeuroAnatomy Toolbox[0m[38;5;12m (https://github.com/natverse/nat) - R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.[39m
[38;5;12m- [39m[38;5;14m[1mNeuroglancer[0m[38;5;12m (https://github.com/google/neuroglancer/) - WebGL-based viewer for volumetric data.[39m
[38;5;12m- [39m[38;5;14m[1mNeuronJ[0m[38;5;12m (https://imagescience.org/meijering/software/neuronj/) - An ImageJ plugin for neurite tracing and analysis.[39m
[38;5;12m- [39m[38;5;14m[1mPanda[0m[38;5;12m (https://www.nitrc.org/projects/panda/) - Pipeline for Analyzing braiN Diffusion imAges: A MATLAB toolbox for pipeline processing of diffusion MRI images.[39m
[38;5;12m- [39m[38;5;14m[1mPyTorch Connectomics[0m[38;5;12m (https://github.com/zudi-lin/pytorch_connectomics) - Deep learning framework for automatic and semi-automatic annotation of connectomics datasets, powered by PyTorch.[39m
[38;5;12m- [39m[38;5;14m[1mRivuletPy[0m[38;5;12m (https://github.com/RivuletStudio/rivuletpy) - Robust 3D Neuron Tracing / General 3D tree structure extraction in Python for 3D images powered by the Rivulet2 algorithm.[39m
[38;5;12m- [39m[38;5;14m[1mSNT[0m[38;5;12m (https://github.com/morphonets/SNT/) - ImageJ framework for semi-automated tracing and analysis of neurons.[39m
[38;5;12m- [39m[38;5;14m[1mTrailMap[0m[38;5;12m (https://github.com/AlbertPun/TRAILMAP/) - Software package to extract axonal data from cleared brains.[39m
[38;5;12m- [39m[38;5;14m[1mWholebrain[0m[38;5;12m (https://github.com/tractatus/wholebrain) - Automated cell detection and registration of whole-brain images with plot of cell counts per region and Hemishpere.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mZVQ[0m[38;5;14m[1m [0m[38;5;14m[1m-[0m[38;5;14m[1m [0m[38;5;14m[1mZebrafish[0m[38;5;14m[1m [0m[38;5;14m[1mVascular[0m[38;5;14m[1m [0m[38;5;14m[1mQuantification[0m[38;5;12m [39m[38;5;12m(https://github.com/ElisabethKugler/ZFVascularQuantification)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mImage[39m[38;5;12m [39m[38;5;12manalysis[39m[38;5;12m [39m[38;5;12mpipeline[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12mperform[39m[38;5;12m [39m[38;5;12m3D[39m[38;5;12m [39m[38;5;12mquantification[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12mtotal[39m[38;5;12m [39m[38;5;12mor[39m[38;5;12m [39m[38;5;12mregional[39m[38;5;12m [39m[38;5;12mzebrafish[39m[38;5;12m [39m[38;5;12mbrain[39m[38;5;12m [39m[38;5;12mvasculature[39m[38;5;12m [39m[38;5;12musing[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12mimage[39m[38;5;12m [39m[38;5;12manalysis[39m
[38;5;12msoftware[39m[38;5;12m [39m[38;5;12mFiji.[39m



[38;2;255;187;0m[4mPlant science[0m

[38;5;12m- [39m[38;5;14m[1mAradeepopsis[0m[38;5;12m (https://github.com/Gregor-Mendel-Institute/aradeepopsis) - A versatile, fully open-source pipeline to extract phenotypic measurements from plant images.[39m
[38;5;12m- [39m[38;5;14m[1mDIRT[0m[38;5;12m (https://github.com/Computational-Plant-Science/DIRT) - Digital Imaging of Root Traits: Extract trait measurements from images of monocot and dicot roots.[39m
[38;5;12m- [39m[38;5;14m[1mLeafByte[0m[38;5;12m (https://zoegp.science/leafbyte) - Free and open source mobile app for measuring herbivory quickly and accurately.[39m
[38;5;12m- [39m[38;5;14m[1mPaCeQuant[0m[38;5;12m (https://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant) - An ImageJ-based tool which provides a fully automatic image analysis workflow for PC shape quantification.[39m
[38;5;12m- [39m[38;5;14m[1mPhenotyperCV[0m[38;5;12m (https://github.com/jberry47/ddpsc_phenotypercv) - Header-only C++11 library using OpenCV for high-throughput image-based plant phenotyping.[39m
[38;5;12m- [39m[38;5;14m[1mPlantCV[0m[38;5;12m (https://github.com/danforthcenter/plantcv) - Open-source image analysis software package targeted for plant phenotyping.[39m
[38;5;12m- [39m[38;5;14m[1mPlantSeg[0m[38;5;12m (https://github.com/hci-unihd/plant-seg) - Tool for cell instance aware segmentation in densely packed 3D volumetric images.[39m
[38;5;12m- [39m[38;5;14m[1mRhizoTrak[0m[38;5;12m (https://prbio-hub.github.io/rhizoTrak/) - Open source tool for flexible and efficient manual annotation of complex time-series minirhizotron images.[39m
[38;5;12m- [39m[38;5;14m[1mRhizovision Explorer[0m[38;5;12m (https://github.com/rootphenomicslab/RhizoVisionExplorer) - Free and open-source software developed for estimating root traits from images acquired from a flatbed scanner or camera.[39m
[38;5;12m- [39m[38;5;14m[1mRootPainter[0m[38;5;12m (https://github.com/Abe404/root_painter) - Deep learning segmentation of biological images with corrective annotation.[39m


[38;2;255;187;0m[4mFluoresence in situ hybridization[0m
[38;5;12m- [39m[38;5;14m[1mBig-fish[0m[38;5;12m (https://github.com/fish-quant/big-fish) - Python package for the analysis of smFISH images.[39m
[38;5;12m- [39m[38;5;14m[1mDypFISH[0m[38;5;12m (https://github.com/cbib/dypfish) - Python library for spatial analysis of smFISH images.[39m
[38;5;12m- [39m[38;5;14m[1mRS-FISH[0m[38;5;12m (https://github.com/PreibischLab/RS-FISH) - Fiji plugin to detect FISH spots in 2D/3D images which scales to very large images.[39m
[38;5;12m- [39m[38;5;14m[1mSpotiflow[0m[38;5;12m (https://github.com/weigertlab/spotiflow) -  A deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method developed for spatial transcriptomics workflows.[39m
[38;5;12m- [39m[38;5;14m[1mTissUUmaps[0m[38;5;12m (https://tissuumaps.github.io/) - Visualizer of NGS data, plot millions of points and interact, gate, export. ISS rounds and base visualization.[39m



[38;2;255;187;0m[4mElectron and super resolution microscopy[0m
[38;5;12m- [39m[38;5;14m[1mASI_MTF[0m[38;5;12m (https://github.com/emx77/ASI_MTF) - ImageJ macro to calculate the modulation transfer function (MTF) based on a knife edge (or slanted edge) measurement.[39m
[38;5;12m- [39m[38;5;14m[1mDECODE[0m[38;5;12m (https://github.com/TuragaLab/DECODE) - Python and PyTorch based deep learning tool for single molecule localization microscopy.[39m
[38;5;12m- [39m[38;5;14m[1mEmpanada[0m[38;5;12m (https://github.com/volume-em/empanada) - Panoptic segmentation algorithms for 2D and 3D electron microscopy images.[39m
[38;5;12m- [39m[38;5;14m[1mEm-scalebartools[0m[38;5;12m (https://github.com/lukmuk/em-scalebartools) - Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image.[39m
[38;5;12m- [39m[38;5;14m[1mPicasso[0m[38;5;12m (https://github.com/jungmannlab/picasso) - A collection of tools for painting super-resolution images.[39m
[38;5;12m- [39m[38;5;14m[1mSMAP[0m[38;5;12m (https://github.com/jries/SMAP) - A modular super-resolution microscopy analysis platform for SMLM data.[39m
[38;5;12m- [39m[38;5;14m[1mThunderSTORM[0m[38;5;12m (https://github.com/zitmen/thunderstorm) - A comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging.[39m


[38;2;255;187;0m[4mImage restoration and quality assessment[0m
[38;5;12m- [39m[38;5;14m[1mCSBDeep[0m[38;5;12m (https://github.com/CSBDeep/CSBDeep) - A deep learning toolbox for microscopy image restoration and analysis.[39m
[38;5;12m- [39m[38;5;14m[1mIjp-color[0m[38;5;12m (https://github.com/ij-plugins/ijp-color) - Plugins for ImageJ - color space conversions and color calibration.[39m
[38;5;12m- [39m[38;5;14m[1mImage Quality[0m[38;5;12m (https://github.com/ocampor/image-quality) - Open source software library for Image Quality Assessment (IQA).[39m
[38;5;12m- [39m[38;5;14m[1mLLSpy[0m[38;5;12m (https://github.com/tlambert03/LLSpy) - Python library to facilitate lattice light sheet data processing.[39m
[38;5;12m- [39m[38;5;14m[1mNCS[0m[38;5;12m (https://github.com/HuanglabPurdue/NCS) - Noise correction algorithm for sCMOS cameras.[39m
[38;5;12m- [39m[38;5;14m[1mNoise2Void[0m[38;5;12m (https://github.com/juglab/n2v) - Learning denoising from single noisy images.[39m


[38;2;255;187;0m[4mCell migration and particle tracking[0m
[38;5;12m- [39m[38;5;14m[1mCellMigration[0m[38;5;12m (https://github.com/quantixed/CellMigration) - Analysis of 2D cell migration in Igor.[39m
[38;5;12m- [39m[38;5;14m[1mTrackMate[0m[38;5;12m (https://github.com/fiji/TrackMate) - User-friendly interface that allows for performing tracking, data visualization, editing results and track analysis in a convenient way.[39m
[38;5;12m- [39m[38;5;14m[1mTrackMateR[0m[38;5;12m (https://github.com/quantixed/TrackMateR) - R package to analyze cell migration and particle tracking experiments using outputs from TrackMate.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mTracX[0m[38;5;12m [39m[38;5;12m(https://gitlab.com/csb.ethz/tracx)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mMATLAB[39m[38;5;12m [39m[38;5;12mgeneric[39m[38;5;12m [39m[38;5;12mtoolbox[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mcell[39m[38;5;12m [39m[38;5;12mtracking[39m[38;5;12m [39m[38;5;12mfrom[39m[38;5;12m [39m[38;5;12mvarious[39m[38;5;12m [39m[38;5;12mmicroscopy[39m[38;5;12m [39m[38;5;12mimage[39m[38;5;12m [39m[38;5;12mmodalities[39m[38;5;12m [39m[38;5;12msuch[39m[38;5;12m [39m[38;5;12mas[39m[38;5;12m [39m[38;5;12mBright-field[39m[38;5;12m [39m[38;5;12m(BF),[39m[38;5;12m [39m[38;5;12mphase[39m[38;5;12m [39m[38;5;12mcontrast[39m[38;5;12m [39m[38;5;12m(PhC)[39m[38;5;12m [39m[38;5;12mor[39m[38;5;12m [39m[38;5;12mfluorescence[39m[38;5;12m [39m[38;5;12m(FL)[39m[38;5;12m [39m[38;5;12mwith[39m[38;5;12m [39m[38;5;12man[39m[38;5;12m [39m[38;5;12mautomated[39m[38;5;12m [39m[38;5;12mtrack[39m[38;5;12m [39m[38;5;12mquality[39m[38;5;12m [39m
[38;5;12massessment[39m[38;5;12m [39m[38;5;12min[39m
[38;5;12mabsence of a ground truth.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mTraJClassifier[0m[38;5;12m [39m[38;5;12m(https://imagej.net/plugins/trajclassifier)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mFiji[39m[38;5;12m [39m[38;5;12mplugin[39m[38;5;12m [39m[38;5;12mthat[39m[38;5;12m [39m[38;5;12mloads[39m[38;5;12m [39m[38;5;12mtrajectories[39m[38;5;12m [39m[38;5;12mfrom[39m[38;5;12m [39m[38;5;12mTrackMate,[39m[38;5;12m [39m[38;5;12mcharacterizes[39m[38;5;12m [39m[38;5;12mthem[39m[38;5;12m [39m[38;5;12musing[39m[38;5;12m [39m[38;5;12mTraJ[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mclassifiies[39m[38;5;12m [39m[38;5;12mthem[39m[38;5;12m [39m[38;5;12minto[39m[38;5;12m [39m[38;5;12mnormal[39m[38;5;12m [39m[38;5;12mdiffusion,[39m[38;5;12m [39m[38;5;12msubdiffusion,[39m[38;5;12m [39m[38;5;12mconfined[39m[38;5;12m [39m[38;5;12mdiffusion[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m
[38;5;12mdirected/active[39m[38;5;12m [39m[38;5;12mmotion[39m[38;5;12m [39m[38;5;12mby[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mrandom[39m[38;5;12m [39m[38;5;12mforest[39m[38;5;12m [39m[38;5;12mapproach[39m[38;5;12m [39m[38;5;12m(through[39m[38;5;12m [39m[38;5;12mRenjin).[39m
[38;5;12m- [39m[38;5;14m[1mQuimP[0m[38;5;12m (https://github.com/CellDynamics/QuimP) - Software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.[39m
[38;5;12m- [39m[38;5;14m[1mUsiigaci[0m[38;5;12m (https://github.com/oist/usiigaci) - Stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning.[39m

[38;2;255;187;0m[4mPathology[0m
[38;5;12m- [39m[38;5;14m[1mFastPathology[0m[38;5;12m (https://github.com/AICAN-Research/FAST-Pathology) - Open-source software for deep learning-based digital pathology.[39m
[38;5;12m- [39m[38;5;14m[1mHistoClean[0m[38;5;12m (https://github.com/HistoCleanQUB/HistoClean) - Tool for the preprocessing and augmentation of images used in deep learning models.[39m
[38;5;12m- [39m[38;5;14m[1mMinerva[0m[38;5;12m (https://github.com/labsyspharm/minerva-story) - Image viewer designed specifically to make it easy for non-expert users to interact with complex tissue images.[39m
[38;5;12m- [39m[38;5;14m[1mOrbit[0m[38;5;12m (http://www.orbit.bio) - A versatile image analysis software for biological image-based quantification using machine learning, especially for whole slide imaging.[39m
[38;5;12m- [39m[38;5;14m[1mPathML[0m[38;5;12m (https://github.com/Dana-Farber-AIOS/pathml) - An open-source toolkit for computational pathology and machine learning.[39m
[38;5;12m- [39m[38;5;14m[1mPAQUO[0m[38;5;12m (https://github.com/bayer-science-for-a-better-life/paquo) - A library for interacting with QuPath from Python.[39m
[38;5;12m- [39m[38;5;14m[1mQuPath[0m[38;5;12m (https://qupath.github.io/) - Open source software for digital pathology image analysis.[39m

[38;2;255;187;0m[4mMycology[0m
[38;5;12m- [39m[38;5;14m[1mDeepMushroom[0m[38;5;12m (https://github.com/Olament/DeepMushroom) - Image classification of fungus using ResNet.[39m
[38;5;12m- [39m[38;5;14m[1mFungal Feature Tracker (FFT)[0m[38;5;12m (https://github.com/hsueh-lab/FFT) - Tool to quantitatively characterize morphology and growth of filamentous fungi.[39m

[38;2;255;187;0m[4mMicrobiology[0m
[38;5;12m- [39m[38;5;14m[1mBactMap[0m[38;5;12m (https://github.com/vrrenske/BactMAP) - A command-line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs into various plots.[39m
[38;5;12m- [39m[38;5;14m[1mBacStalk[0m[38;5;12m (https://drescherlab.org/data/bacstalk/docs/index.html) - Interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial species.[39m
[38;5;12m- [39m[38;5;14m[1mBiofilmQ[0m[38;5;12m (https://drescherlab.org/data/biofilmQ/docs/) - Advanced biofilm analysis tool for quantifying the properties of cells inside large 3-dimensional biofilm communities in space and time.[39m

[38;2;255;187;0m[4mYeast imaging[0m
[38;5;12m- [39m[38;5;14m[1mBABY[0m[38;5;12m (https://git.ecdf.ed.ac.uk/swain-lab/baby/) - An image processing pipeline for accurate single-cell growth estimation of[39m
[38;5;12mbudding cells from bright-field stacks.[39m
[38;5;12m- [39m[38;5;14m[1mYeastMate[0m[38;5;12m (https://yeastmate.readthedocs.io/en/latest/) - Neural network-assisted segmentation of mating and budding events in S. cerevisiae.[39m
[38;5;12m- [39m[38;5;14m[1mYeaZ[0m[38;5;12m (https://github.com/lpbsscientist/YeaZ-GUI) - An interactive tool for segmenting yeast cells using deep learning.[39m



[38;2;255;187;0m[4mOther[0m
[38;5;12m- [39m[38;5;14m[1mAICSImageIO[0m[38;5;12m (https://github.com/AllenCellModeling/aicsimageio) - Image reading, metadata conversion, and image writing for nicroscopy images in Python.[39m
[38;5;12m- [39m[38;5;14m[1mBiobeam[0m[38;5;12m (https://maweigert.github.io/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.[39m
[38;5;12m- [39m[38;5;14m[1mBoneJ[0m[38;5;12m (https://github.com/bonej-org/BoneJ2) - Collection of Fiji/ImageJ plug-ins for skeletal biology.[39m
[38;5;12m- [39m[38;5;14m[1mCaPTk[0m[38;5;12m (https://github.com/CBICA/CaPTk) - Cancer Imaging Phenomics Toolkit: A software platform to perform image analysis and predictive modeling tasks.[39m
[38;5;12m- [39m[38;5;14m[1mColiCoords[0m[38;5;12m (https://github.com/Jhsmit/ColiCoords) - Python project for analysis of fluorescence microscopy data from rodlike cells.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mCompactionAnalyzer[0m[38;5;12m [39m[38;5;12m(https://github.com/davidbhr/CompactionAnalyzer)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mPython[39m[38;5;12m [39m[38;5;12mpackage[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12mquantify[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12mtissue[39m[38;5;12m [39m[38;5;12mcompaction[39m[38;5;12m [39m[38;5;12m(as[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mmeasure[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12mcontractile[39m[38;5;12m [39m[38;5;12mstrength)[39m[38;5;12m [39m[38;5;12mgenerated[39m[38;5;12m [39m[38;5;12mby[39m[38;5;12m [39m[38;5;12mcells[39m[38;5;12m [39m[38;5;12mor[39m[38;5;12m [39m[38;5;12mmulticellular[39m[38;5;12m [39m[38;5;12mspheroids[39m[38;5;12m [39m[38;5;12mthat[39m[38;5;12m [39m[38;5;12mare[39m[38;5;12m [39m[38;5;12membedded[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mfiber[39m
[38;5;12mmaterials.[39m
[38;5;12m- [39m[38;5;14m[1mCytominer-database[0m[38;5;12m (https://github.com/cytomining/cytominer-database) - Command-line tools for organizing measurements extracted from images.[39m
[38;5;12m- [39m[38;5;14m[1mDetecDiv[0m[38;5;12m (https://github.com/gcharvin/DetecDiv) - Comprehensive set of tools to analyze time microscopy images using deep learning methods.[39m
[38;5;12m- [39m[38;5;14m[1mMIA[0m[38;5;12m (https://github.com/mianalysis/mia) - Fiji plugin which provides a modular framework for assembling image and object analysis workflows.[39m
[38;5;12m- [39m[38;5;14m[1mMorphoGraphX[0m[38;5;12m (https://morphographx.org) - Open source application for the visualization and analysis of 4D biological datasets.[39m
[38;5;12m- [39m[38;5;14m[1mNapari-aicsimageio[0m[38;5;12m (https://github.com/AllenCellModeling/napari-aicsimageio) - Multiple file format reading directly into napari using pure Python.[39m
[38;5;12m- [39m[38;5;14m[1mNEFI2[0m[38;5;12m (https://github.com/05dirnbe/nefi) - Python tool created to extract networks from images.[39m
[38;5;12m- [39m[38;5;14m[1mNeurite[0m[38;5;12m (https://github.com/adalca/neurite) - Neural networks toolbox focused on medical image analysis.[39m
[38;5;12m- [39m[38;5;14m[1mNd2reader[0m[38;5;12m (https://github.com/Open-Science-Tools/nd2reader) - A pure-Python package that reads images produced by NIS Elements 4.0+.[39m
[38;5;12m- [39m[38;5;14m[1mOAD[0m[38;5;12m (https://github.com/zeiss-microscopy/OAD) - Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools.[39m
[38;5;12m- [39m[38;5;14m[1mPycytominer[0m[38;5;12m (https://github.com/cytomining/pycytominer) - Data processing functions for profiling perturbations.[39m
[38;5;12m- [39m[38;5;14m[1mPyotf[0m[38;5;12m (https://github.com/david-hoffman/pyotf) - A simulation software package for modelling optical transfer functions (OTF)/point spread functions (PSF) of optical microscopes written in Python.[39m
[38;5;12m- [39m[38;5;14m[1mPyScratch[0m[38;5;12m (https://bitbucket.org/vladgaal/pyscratch_public.git/src) - Open source tool that autonomously performs quantitative analysis of in vitro scratch assays.[39m
[38;5;12m- [39m[38;5;14m[1mQuanfima[0m[38;5;12m (https://github.com/rshkarin/quanfima) - 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.[39m
[38;5;12m- [39m[38;5;14m[1mSimpleElastix[0m[38;5;12m (https://github.com/SuperElastix/SimpleElastix) - Multi-lingual medical image registration library.[39m
[38;5;12m- [39m[38;5;14m[1mVaa3D[0m[38;5;12m (https://alleninstitute.org/what-we-do/brain-science/research/products-tools/vaa3d/) - Open-source software for 3D/4D/5D image visualization and analysis.[39m
[38;5;12m- [39m[38;5;14m[1mXitoSBML[0m[38;5;12m (https://github.com/spatialsimulator/XitoSBML) - ImageJ plugin which creates a Spatial SBML model from segmented images.[39m
[38;5;12m- [39m[38;5;14m[1mZ-stack Depth Color Code[0m[38;5;12m (https://github.com/ekatrukha/ZstackDepthColorCode) - ImageJ/Fiji plugin to colorcode Z-stacks/hyperstacks.[39m
[38;5;12m- [39m[38;5;14m[1mZeroCostDL4Mic[0m[38;5;12m (https://github.com/HenriquesLab/ZeroCostDL4Mic) - Google Colab to develop a free and open-source toolbox for deep-Learning in microscopy.[39m
[38;5;12m- [39m[38;5;14m[1mZetaStitcher[0m[38;5;12m (https://github.com/lens-biophotonics/ZetaStitcher) - Tool designed to stitch large volumetric images such as those produced by light-sheet fluorescence microscopes.[39m



[38;2;255;187;0m[4mPublications[0m

[38;5;12m- [39m[38;5;14m[1mA Hitchhiker's guide through the bio-image analysis software universe[0m[38;5;12m (https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14451) - An article presenting a curated guide and glossary of bio-image analysis terms and tools.[39m
[38;5;12m- [39m[38;5;14m[1mBiological imaging software tools[0m[38;5;12m (https://dx.doi.org/10.1038%2Fnmeth.2084) - The steps of biological image analysis and the appropriate tools for each step.[39m
[38;5;12m- [39m[38;5;14m[1mData-analysis strategies for image-based cell profiling[0m[38;5;12m (https://doi.org/10.1038/nmeth.4397) - In-detail explanations of image analysis pipelines.[39m
[38;5;12m- [39m[38;5;14m[1mLarge-scale image-based screening and profiling of cellular phenotypes[0m[38;5;12m (https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22909) - A workflow for phenotype extraction from high throughput imaging experiments.[39m
[38;5;12m- [39m[38;5;14m[1mWorkflow and metrics for image quality control in large-scale high-content screens[0m[38;5;12m (https://linkinghub.elsevier.com/retrieve/pii/S2472555222075943) - Approaches for quality control in high-content imaging screens.[39m

[38;2;255;187;0m[4mFootnotes[0m
[38;2;255;187;0m[4mSimilar lists and repositories[0m

[38;5;12m- [39m[38;5;14m[1mBIII[0m[38;5;12m (https://biii.eu) - Repository of bioimage analysis tools.[39m
[38;5;12m- [39m[38;5;14m[1mBio-image Analysis Notebooks[0m[38;5;12m (https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/intro.html) - Notebooks for bioimage analysis in Python.[39m
[38;5;12m- [39m[38;5;14m[1mBioimaging Guide[0m[38;5;12m (https://www.bioimagingguide.org) - Microscopy for beginners reference guide.[39m
[38;5;12m- [39m[38;5;14m[1mCytodata[0m[38;5;12m (https://github.com/cytodata/awesome-cytodata) - A curated list of awesome cytodata resources.[39m
[38;5;12m- [39m[38;5;14m[1mNapari hub[0m[38;5;12m (https://www.napari-hub.org) - Collection of napari plugins.[39m
[38;5;12m- [39m[38;5;14m[1mOpenMicroscopy[0m[38;5;12m (https://github.com/HohlbeinLab/OpenMicroscopy) - Non-comprehensive list of projects and resources related to open microscopy.[39m
