Kaziaa / awesome-biological-image-analysis

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

Awesome Biological Image Analysis

List of software, tools, pipelines, plugins etc. for image analysis related to biological questions. Contributions are welcome.

Contents

• General image analysis software
• Image processing and segmentation
• Ecology
• Neuroscience
• Plant science
• Fluoresence in situ hybridization
• Electron and super resolution microscopy
• Image restoration and quality assessment
• Cell migration and particle tracking
• Pathology
• Mycology
• Microbiology
• Yeast imaging
• Other
• Publications
• Similar lists and repositories

General image analysis software

• 3D Slicer - 3D Slicer is a free, open source and multi-platform software package widely used for medical, biomedical, and related imaging research.
• Bioimagetools - Bioimagetools is an R package for working with images in 3D and 4D, mostly for biology/microscopy.
• BioImageXD - BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images.
• BioProfiling.jl - A flexible Julia toolkit for high-dimensional cellular profiles.
• Cell-ACDC - A GUI-based Python framework for segmentation, tracking, cell cycle annotations and quantification of microscopy data.
• CellProfiler - CellProfiler is open-source software helping biologists turn images into cell measurements.
• CellProfiler Analyst - Open-source software for exploring and analyzing large, high-dimensional image-derived data.
• Fiji - Fiji is a "batteries-included" distribution of ImageJ—a popular, free scientific image processing application.
• Flika - An interactive image processing program for biologists written in Python.
• Icy - Icy is an open community platform for bioimage informatics, providing software resources to visualize, annotate and quantify bioimaging data.
• Ilastik - Ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.
• ImageJ - ImageJ is public domain software for processing and analyzing scientific images.
• ImageJ2 - ImageJ2 is a rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging.
• ImageJ.JS - Image analysis in the browser with ImageJ.
• ImagePy - ImagePy is an open source image processing framework written in Python.
• MIPLIB - A Python software library with a variety of functions for (optical) microscopy image restoration, reconstruction and analysis.
• Napari - Napari is a fast, interactive, multi-dimensional image viewer for Python.
• Napari-J - A plugin to exchange data with FIJI and to use FIJI image analysis from napari.
• OpenCV - OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.
• PYME - An open-source application suite for light microscopy acquisition, data storage, visualization, and analysis.
• Scikit-image - Scikit-image is a collection of algorithms for image processing.

Image processing and segmentation

• Ark-Analysis - A pipeline toolbox for analyzing multiplexed imaging data.
• AtomAI - AtomAI is a Pytorch-based package for deep/machine learning analysis of microscopy data.
• CakeCell - Segmenting cells (and other objects!) in microscopy images via neural networks.
• Cellpose - A generalist algorithm for cell and nucleus segmentation.
• Cellshape - 3D single-cell shape analysis of cancer cells using geometric deep learning.
• CellSighter - CellSighter is an ensemble of convolutional neural networks to perform supervised cell classification in multiplexed images.
• CLIJ2 - CLIJ2 is a GPU-accelerated image processing library for ImageJ/Fiji, Icy, Matlab and Java.
• Deep Lipid - Machine learning for semantic segmentation of lipid droplets within quantitative phase images (QPI) of yeast cells.
• DeepCell - Deep Learning Library for Single Cell Analysis.
• DeepSlide - A Sliding Window Framework for Classification of High Resolution Microscopy Images.
• EBImage - Image processing toolbox for R.
• ERNet - ERNet: Segmentation of Endoplasmic Reticulum microscopy images using modified CNN-based image restoration models.
• GPim - Gaussian processes and Bayesian optimization for images and hyperspectral data.
• Ijp-DeBayer2SX - Bayer-pattern image to color image converters.
• MitoSegNet - Easy-to-use Deep Learning Segmentation for Analyzing Mitochondrial Morphology.
• MorpholibJ - MorpholibJ Collection of mathematical morphology methods and plugins for ImageJ.
• PartSeg - PartSeg is a GUI and a library for segmentation algorithms.
• PyImSegm - Image segmentation - general superpixel segmentation & center detection & region growing.
• Sequitr - Microscopy image processing with TensorFlow.
• Squidpy - Squidpy, a 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 - Object Detection with Star-convex Shapes.
• Suite2p - Pipeline for processing two-photon calcium imaging data.
• SyMBac - Accurate segmentation of bacterial microscope images using synthetically generated image data.
• TensorFlow-MIL - TF Implementation of Multiple Instance Learning FCN.
• Trainable Weka Segmentation - The Trainable Weka Segmentation is a Fiji plugin and library that combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations.
• U-shape3D - Designed to detect morphological motifs, such as blebs, filopodia, and lamellipodia, from 3D images of surfaces, particularly images of cell surfaces.
• VAMPIRE - VAMPIRE (Visually Aided Morpho-Phenotyping Image Recognition) analysis quantifies and visualizes heterogeneity of cell and nucleus morphology.

Ecology

• PAT-GEOM - PAT-GEOM: a software package for the analysis of animal colour pattern.
• ThermImageJ - ImageJ functions and macros for working with thermal image files.

Neuroscience

• Automated Neuronal Differentiation Analyzer - Automated Neuronal Differentiation Analyzer: An open-source tool for high-throughput image analysis of neuronal differentiation.
• AxonDeepSeg - Segment axon and myelin from microscopy data using deep learning.
• BG-atlasAPI - A lightweight python module to interact with atlases for systems neuroscience.
• Brainreg - Automated 3D brain registration with support for multiple species and atlases.
• Brainreg-napari - Automated 3D brain registration in napari with support for multiple species and atlases.
• Brainrender - brainrender is a python package for the visualization of three dimensional neuro-anatomical data.
• Cellfinder - Automated 3D cell detection and registration of whole-brain images.
• Cellfinder-napari - Efficient cell detection in large images using cellfinder in napari.
• CloudVolume - Read and write Neuroglancer datasets programmatically.
• ExplantAnalyzer - ExplantAnalyzer: An advanced automated neurite outgrowth analysis evaluated by means of organotypic auditory neuron explant cultures.
• L-Measure - a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies.
• NeuroAnatomy Toolbox - NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
• Neuroglancer - Neuroglancer is a WebGL-based viewer for volumetric data.
• NeuronJ - NeuronJ: An ImageJ Plugin for Neurite Tracing and Analysis.
• Panda - PANDA (Pipeline for Analyzing braiN Diffusion imAges) is a matlab toolbox for pipeline processing of diffusion MRI images.
• PyTorch Connectomics - PyTorch Connectomics is a deep learning framework for automatic and semi-automatic annotation of connectomics datasets, powered by PyTorch.
• RivuletPy - Robust 3D Neuron Tracing / General 3D tree structure extraction in Python for 3D images powered by the Rivulet2 algorithm.
• SliceMap - SliceMap: An Algorithm for Automated Brain Region Annotation, implemented as FIJI(ImageJ) plugin.
• SNT - The ImageJ framework for semi-automated tracing and analysis of neurons.
• TrailMap - TRAILMAP is a software package to extract axonal data from cleared brains.
• Wholebrain - Automated cell detection and registration of whole-brain images with plot of cell counts per region and Hemishpere.
• ZVQ - Zebrafish Vascular Quantification - Image analysis pipeline to perform 3D quantification of the total or regional zebrafish brain vasculature using the image analysis software Fiji.

Plant science

• Aradeepopsis - A versatile, fully open-source pipeline to extract phenotypic measurements from plant images.
• ArchiDART - ArchiDART is an R package that was developed for the automated analysis of plant root system architectures using Data Analysis of Root Tracings (DART) and Root System Markup Language (RSML) files.
• Black Spot - Black Spot is a free stand alone software and method to estimate leaf area from images of leaves captured using any standard flatbed scanner.
• DIRT - Digital Imaging of Root Traits: Extract trait measurements from images of monocot and dicot roots.
• EasyPCC_V2 - Easy Plant Phenotyping Tool for both indoor and outdoor use.
• GLO-Roots - GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems.
• KymoRod - Graphical User Interface for studying the growth of plant hypocotyl and root.
• LeafByte - LeafByte is a free and open source mobile app for measuring herbivory quickly and accurately.
• LeafGP - Leaf-GP, is a comprehensive software application for analysing large growth image series.
• LeafJ - LeafJ is a plugin for ImageJ that aids in the measurement of plant leafs.
• PaCeQuant - PaCeQuant, an ImageJ-based tool, which provides a fully automatic image analysis workflow for PC shape quantification.
• PhenotyperCV - Header-only C++11 library using OpenCV for high-throughput image-based plant phenotyping.
• PlantCV - PlantCV is an open-source image analysis software package targeted for plant phenotyping.
• PlantSeg - PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images.
• RhizoTrak - An open source tool for flexible and efficient manual annotation of complex time-series minirhizotron images.
• Rhizovision Explorer - RhizoVision Explorer is free and open-source software developed for estimating root traits from images acquired from a flatbed scanner or camera.
• RootPainter - RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation.
• Sato-folium - Image Recognition of Plant Leaves for Species Identification.
• TRiP - Tracking Rhythms in Plants: A motion detection algorithm for estimating circadian period from leaf movement data.

Fluoresence in situ hybridization

• Big-fish - Big-FISH is a python package for the analysis of smFISH images.
• ChromaWizard - A tool for creating karyotypes of M-FISH images.
• FISHcount - Software for counting single RNA molecules using analysis of FISH data.
• RS-FISH - RS-FISH is a Fiji plugin to detect FISH spots in 2D/3D images which scales to very large images.
• ThunderFish - ThunderFISH is a pre-processing tool that extracts 2D single-cell RNA-FISH images from your 3D microscopy images of large field of view.
• TissUUmaps - Visualizer of NGS data, plot millions of points and interact, gate, export. ISS rounds and base visualization.

Electron and super resolution microscopy

• ASI_MTF - Imagej macro to calculate the modulation transfer function (MTF) based on a knife edge (or slanted edge) measurement.
• DECODE - DECODE is a Python and Pytorch based deep learning tool for single molecule localization microscopy.
• Empanada - Panoptic segmentation algorithms for 2D and 3D electron microscopy images.
• Em-scalebartools - Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image.
• MSSR - MSSR for single image super-resolution.
• Picasso - A collection of tools for painting super-resolution images.
• SASS - Toolkit for simulating real-time control systems for super-resolution microscopy.
• SMAP - A modular super-resolution microscopy analysis platform for SMLM data.
• ThunderSTORM - A comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging.

Image restoration and quality assessment

• CSBDeep - A deep learning toolbox for microscopy image restoration and analysis.
• Ijp-color - Plugins for ImageJ - color space conversions and color calibration.
• Image Quality - Image quality is an open source software library for Image Quality Assessment (IQA).
• LLSpy - LLSpy is a python library to facilitate lattice light sheet data processing.
• NanoJ-SQUIRREL - An ImageJ-based analytical approach that provides quantitative assessment of super-resolution image quality.
• NCS - NCS is a Noise Correction Algorithm for sCMOS cameras.
• Noise2Void - Learning Denoising from Single Noisy Images.

Cell migration and particle tracking

• CellMigration - Analysis of 2D cell migration in Igor.
• TrackMate - TrackMate has a user-friendly interface that allows for performing tracking, data visualization, editing results and track analysis in a convenient way.
• TrackMateR - An R package to analyze cell migration and particle tracking experiments using outputs from TrackMate.
• TracX - TracX is a 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 - This Fiji plugin loads trajectories from TrackMate, characterize them using TraJ and classifiy them into normal diffusion, subdiffusion, confined diffusion and directed/active motion by a random forest approach (through Renjin).
• QuimP - QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.
• Usiigaci - Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning.

Pathology

• FastPathology - Open-source software for deep learning-based digital pathology.
• HistoClean - HistoClean is a tool for the preprocessing and augmentation of images used in deep learning models.
• Minerva - Minerva Story is an image viewer that is 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 - An open-source toolkit for computational pathology and machine learning.
• PAQUO - A library for interacting with QuPath from Python.
• QuPath - Open source software for digital pathology image analysis.

Mycology

• DeepMushroom - DeepMushroom Image classification of Fungus using ResNet.
• Fungal Feature Tracker (FFT) - Fungal Feature Tracker (FFT): A tool to quantitatively characterize morphology and growth of filamentous fungi.

Microbiology

• 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.
• BacStalk - BacStalk is an interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial species.
• BiofilmQ - BiofilmQ is an advanced biofilm analysis tool for quantifying the properties of cells inside large 3-dimensional biofilm communities in space and time.

Yeast imaging

• BABY - An image processing pipeline for accurate single-cell growth estimation of budding cells from bright-field stacks.
• YeastMate - Neural network-assisted segmentation of mating and budding events in S. cerevisiae.
• YeaZ - An interactive tool for segmenting yeast cells using deep learning.

Other

• AICSImageIO - Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python.
• Biobeam - Biobeam is an 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 - BoneJ is a collection of Fiji/ImageJ plug-ins for skeletal biology.
• B-Store - Lightweight data management and analysis tools for single-molecule microscopy.
• Calipy - Real-time, interactive exploration of 3D image stacks.
• CaPTk - Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks.
• ColiCoords - ColiCoords is a python project for analysis of fluorescence microscopy data from rodlike cells.
• CompactionAnalyzer - 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.
• Correlescence - This is open-source ImageJ plugin for different spatial/temporal correlation analysis of images (stacks and hyperstacks).
• Cytominer-database - Cytominer-database provides command-line tools for organizing measurements extracted from images.
• DetecDiv - DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods.
• MIA - MIA is a Fiji plugin which provides a modular framework for assembling image and object analysis workflows.
• MicroscPSF-Py - Fast and Accurate 3D PSF Computation for Fluorescence Microscopy.
• MorphoGraphX - MorphoGraphX is an open source application for the visualization and analysis of 4D biological datasets.
• Napari-aicsimageio - Multiple file format reading directly into napari using pure Python.
• NEFI2 - NEFI2 is a Python tool created to extract networks from images.
• Neurite - Neural networks toolbox focused on medical image analysis.
• Nd2reader - nd2reader is a pure-Python package that reads images produced by NIS Elements 4.0+.
• NUKE-BREAK - Automated detection of nuclei and DNA damage in Caenorhabditis elegans germline.
• OAD - Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools.
• PAM - PAM is a software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with a focus on experiments using pulsed interleaved excitation.
• Pycytominer - Data processing functions for profiling perturbations.
• Pyotf - A simulation software package for modelling optical transfer functions (OTF)/point spread functions (PSF) of optical microscopes written in python.
• PyScratch - PyScratch is an open source tool that autonomously performs quantitative analysis of in vitro scratch assays.
• Quanfima - Quanfima (quantitative analysis of fibrous materials) is a collection of useful functions for morphological analysis and visualization of 2D/3D data from various areas of material science.
• Sbt-imagej - Sbt-imagej is an SBT (Simple Build Tool) plugin that helps with development of ImageJ plugins.
• SimpleElastix - Multi-lingual medical image registration library.
• Vaa3D - Vaa3D is open-source software for 3D/4D/5D image visualization and analysis.
• XitoSBML - XitoSBML is an ImageJ plugin which creates a Spatial SBML model from segmented images.
• Z-stack Depth Color Code - ImageJ/FIJI plugin to colorcode Z-stacks/hyperstacks.
• ZeroCostDL4Mic - Exploiting Google Colab to develop a free and open-source toolbox for Deep-Learning in microscopy.
• ZetaStitcher - ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

Publications

• A Hitchhiker's guide through the bio-image analysis software universe.
• Biological imaging software tools.
• Data-analysis strategies for image-based cell profiling.
• Large-scale image-based screening and profiling of cellular phenotypes.
• Workflow and metrics for image quality control in large-scale high-content screens.

Similar lists and repositories

• BIII - Repository of bioimage analysis tools.
• Napari hub - Collection of napari plugins.
• OpenMicroscopy - Non-comprehensive list of projects and resources related to open microscopy.