awesome-biological-image-analysis

3D Slicer

Free, open source and multi-platform software package widely used for medical, biomedical, and related imaging research

Open source ready-to-use all-in-one library that provides deep-learning workflows for a large variety of bioimage analysis tasks

Free, open source software package for analyzing, processing and visualizing multi-dimensional microscopy images

Cell-ACDC

A GUI-based Python framework for segmentation, tracking, cell cycle annotations and quantification of microscopy data

CellProfiler

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

A "batteries-included" distribution of ImageJ — a popular, free scientific image processing application

Flika

An interactive image processing program for biologists written in Python

Open community platform for bioimage informatics, providing software resources to visualize, annotate and quantify bioimaging data

Ilastik

Simple, user-friendly tool for interactive image classification, segmentation and analysis

ImageJ

Public domain software for processing and analyzing scientific images

ImageJ2

A Rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging

ImagePy

Open source image processing framework written in Python

Napari

Fast, interactive, multi-dimensional image viewer for Python

OpenCV

Open source computer vision and machine learning software library

PYME

Open-source application suite for light microscopy acquisition, data storage, visualization, and analysis

Scikit-image

Collection of algorithms for image processing

Ark-Analysis

A pipeline toolbox for analyzing multiplexed imaging data

AtomAI

PyTorch-based package for deep/machine learning analysis of microscopy data

Cellpose

A generalist algorithm for cell and nucleus segmentation

CellSAM

A foundation model for cell segmentation trained on a diverse range of cells and data types

Cellshape

3D single-cell shape analysis of cancer cells using geometric deep learning

GPU-accelerated image processing library for ImageJ/Fiji, Icy, MATLAB and Java

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

GPim

Gaussian processes and Bayesian optimization for images and hyperspectral data

MAPS

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

Tools for segmentation and tracking in microscopy build on top of SegmentAnything. Segment and track objects in microscopy images interactively

MorpholibJ

Collection of mathematical morphology methods and plugins for ImageJ

PartSeg

A GUI and a library for segmentation algorithms

Proseg

: A cell segmentation method for in situ spatial transcriptomics

PyImSegm

Image segmentation - general superpixel segmentation and center detection and region growing

Salem²

Segment Anything in Light and Electron Microscopy via Membrane Guidance

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

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

Trainable Weka Segmentation

Fiji plugin and library that combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations

A software package for the analysis of animal colour pattern

ThermImageJ

ImageJ functions and macros for working with thermal image files

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

Python package for the visualization of three dimensional neuro-anatomical data

CaImAn

Computational toolbox for large scale Calcium Imaging Analysis

Cellfinder

Automated 3D cell detection and registration of whole-brain images

Cellfinder-napari

Efficient cell detection in large images using in napari

CloudVolume

Read and write Neuroglancer datasets programmatically

NeuroAnatomy Toolbox

R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons

Neuroglancer

WebGL-based viewer for volumetric data

An ImageJ plugin for neurite tracing and analysis

Pipeline for Analyzing braiN Diffusion imAges: A MATLAB toolbox for pipeline processing of diffusion MRI images

PyTorch Connectomics

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

SNT

ImageJ framework for semi-automated tracing and analysis of neurons

TrailMap

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

Aradeepopsis

A versatile, fully open-source pipeline to extract phenotypic measurements from plant images

DIRT

Digital Imaging of Root Traits: Extract trait measurements from images of monocot and dicot roots

Free and open source mobile app for measuring herbivory quickly and accurately

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

Open-source image analysis software package targeted for plant phenotyping

PlantSeg

Tool for cell instance aware segmentation in densely packed 3D volumetric images

Open source tool for flexible and efficient manual annotation of complex time-series minirhizotron images

Rhizovision Explorer

Free and open-source software developed for estimating root traits from images acquired from a flatbed scanner or camera

RootPainter

Deep learning segmentation of biological images with corrective annotation

Big-fish

Python package for the analysis of smFISH images

DypFISH

Python library for spatial analysis of smFISH images

RS-FISH

Fiji plugin to detect FISH spots in 2D/3D images which scales to very large images

Spotiflow

A deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method developed for spatial transcriptomics workflows

Visualizer of NGS data, plot millions of points and interact, gate, export. ISS rounds and base visualization

ASI_MTF

ImageJ macro to calculate the modulation transfer function (MTF) based on a knife edge (or slanted edge) measurement

DECODE

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

Picasso

A collection of tools for painting super-resolution images

SMAP

A modular super-resolution microscopy analysis platform for SMLM data

ThunderSTORM

A comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging

CSBDeep

A deep learning toolbox for microscopy image restoration and analysis

Ijp-color

Plugins for ImageJ - color space conversions and color calibration

Image Quality

Open source software library for Image Quality Assessment (IQA)

LLSpy

Python library to facilitate lattice light sheet data processing

NCS

Noise correction algorithm for sCMOS cameras

Noise2Void

Learning denoising from single noisy images

CellMigration

Analysis of 2D cell migration in Igor

TrackMate

User-friendly interface that allows for performing tracking, data visualization, editing results and track analysis in a convenient way

TrackMateR

R package to analyze cell migration and particle tracking experiments using outputs from TrackMate

Fast and Flexible Particle-Tracking Toolkit

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

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

Software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane

Ultrack

Versatile cell tracking method for 2D, 3D, and multichannel timelapses, overcoming segmentation challenges in complex tissues

Usiigaci

Stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

FastPathology

Open-source software for deep learning-based digital pathology

HistoClean

Tool for the preprocessing and augmentation of images used in deep learning models

Minerva

Image viewer designed specifically to make it easy for non-expert users to interact with complex tissue images

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

Open source software for digital pathology image analysis

DeepMushroom

Image classification of fungus using ResNet

Fungal Feature Tracker (FFT)

Tool to quantitatively characterize morphology and growth of filamentous fungi

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

Interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial species

Advanced biofilm analysis tool for quantifying the properties of cells inside large 3-dimensional biofilm communities in space and time

An image processing pipeline for accurate single-cell growth estimation of budding cells from bright-field stacks

htsimaging

Python package for high-throughput single-cell imaging analysis

Neural network-assisted segmentation of mating and budding events in S. cerevisiae

YeaZ

An interactive tool for segmenting yeast cells using deep learning

AICSImageIO

Image reading, metadata conversion, and image writing for nicroscopy images in Python

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

Collection of Fiji/ImageJ plug-ins for skeletal biology

CaPTk

Cancer Imaging Phenomics Toolkit: A software platform to perform image analysis and predictive modeling tasks

ColiCoords

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

Cytominer-database

Command-line tools for organizing measurements extracted from images

DetecDiv

Comprehensive set of tools to analyze time microscopy images using deep learning methods

MIA

Fiji plugin which provides a modular framework for assembling image and object analysis workflows

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

Python tool created to extract networks from images

Neurite

Neural networks toolbox focused on medical image analysis

Nd2reader

A pure-Python package that reads images produced by NIS Elements 4.0+

OAD

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools

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

Open source tool that autonomously performs quantitative analysis of in vitro scratch assays

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

SimpleElastix

Multi-lingual medical image registration library

Open-source software for 3D/4D/5D image visualization and analysis

XitoSBML

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

Google Colab to develop a free and open-source toolbox for deep-Learning in microscopy

ZetaStitcher

Tool designed to stitch large volumetric images such as those produced by light-sheet fluorescence microscopes

An article presenting a curated guide and glossary of bio-image analysis terms and tools

The steps of biological image analysis and the appropriate tools for each step

In-detail explanations of image analysis pipelines

A workflow for phenotype extraction from high throughput imaging experiments

Approaches for quality control in high-content imaging screens

Repository of bioimage analysis tools

Notebooks for bioimage analysis in Python

Microscopy for beginners reference guide

Cytodata

A curated list of awesome cytodata resources

Collection of napari plugins

OpenMicroscopy

Non-comprehensive list of projects and resources related to open microscopy