COLLECTION 03 / Measure what you see

Bioimage Analysis.

Choose software for interactive microscopy, digital pathology, and repeatable image quantification.

Where to start

Check your image format, dimensionality, and desired output first. Try a small representative image and inspect masks or measurements before running an entire batch.

Tools in this collection

41 EDITORIAL LISTINGS

Open source

Fiji

Open, inspect, and measure microscopy images in an ImageJ distribution that bundles common plugins.

Bioimage AnalysisDesktop app

Open source

QuPath

Annotate whole-slide images, measure objects, and export measurements from tissue image projects.

Bioimage AnalysisDesktop app

Open source

CellProfiler

Build reusable image-processing pipelines and export object measurements from batches of microscopy images.

Bioimage AnalysisDesktop app

Open source

napari

Explore multidimensional images, overlay segmentation masks, and edit annotations in interactive layers.

Bioimage AnalysisDesktop app / Python package

Open source

ilastik

Train image classifiers interactively by marking examples in a desktop interface, then export predictions for review.

Bioimage AnalysisDesktop app

Open source

OMERO

Store microscopy images and metadata in a central repository for viewing, organization, and controlled sharing.

Bioimage AnalysisServer / web app

Open source

Bio-Formats

Read image pixels and acquisition metadata from many microscope formats and export to formats such as OME-TIFF.

Bioimage AnalysisLibrary / plugin

Open source

TrackMate

Link detected objects across time-lapse frames and inspect or export the resulting trajectories.

Bioimage AnalysisFiji plugin

Open source

Cellpose

Generate instance masks for cells or nuclei in microscopy images and inspect them in a graphical interface.

Bioimage AnalysisDesktop app / Python package

Open source

StarDist

Detect and segment individual nuclei and other compact objects using learned star-convex shapes.

Bioimage AnalysisPython package

Open source

InstanSeg

Run pretrained instance segmentation models on fluorescence or brightfield microscopy images to delineate cells and nuclei.

Bioimage AnalysisPython package / QuPath extension

Open source

μSAM

Prompt a microscopy segmentation model with points or boxes to outline objects and refine them interactively.

Bioimage Analysisnapari plugin / Python package

Open source

DeepImageJ

Run compatible pretrained models inside ImageJ for tasks such as microscopy segmentation or image restoration.

Bioimage AnalysisImageJ plugin

Open source

BigStitcher

Bioimage AnalysisFiji plugin

Open source

BigDataViewer

Navigate large multiview volumes at several resolutions without loading the entire image into memory.

Bioimage AnalysisFiji plugin / Java library

Open source

MorphoLibJ

Apply mathematical morphology to clean masks, separate touching objects, and measure labeled structures in 2D or 3D.

Bioimage AnalysisImageJ plugin

Open source

CLIJ2

Run filtering, labeling, and measurement operations on an OpenCL-compatible GPU from Fiji workflows.

Bioimage AnalysisFiji plugin

Open source

BaSiCPy

Estimate and correct uneven illumination and background variation across microscopy images.

Bioimage AnalysisPython package

Open source

ModularImageAnalysis (MIA)

Assemble reusable image and object analysis workflows from modules for loading, segmentation, measurement, and output.

Bioimage AnalysisFiji plugin

Open source

OpenSlide

Read regions of multiresolution whole-slide images without loading the full slide.

Bioimage AnalysisLibrary / Python bindings

Open source

Slideflow

Extract tiles from whole-slide images and organize research workflows for model training and evaluation.

Bioimage AnalysisPython package

Open source

HistomicsTK

Process histology images with tools for stain handling, nuclei analysis, and feature extraction.

Bioimage AnalysisPython package

Open source

3D Slicer

Visualize, segment, and register volumetric images in an interactive research application.

Bioimage AnalysisDesktop app

Open source

ITK-SNAP

Inspect 3D image stacks and create segmentation masks using manual editing or semi-automatic tools.

Bioimage AnalysisDesktop app

Open source

Neuroglancer

Explore very large volumes, label layers, and meshes in a browser using multiresolution data sources.

Bioimage AnalysisBrowser viewer

Open source

CVAT Community Edition

Create and review image or video labels in a browser and export them for model development.

Bioimage AnalysisSelf-hosted web app

Open source

OME-Zarr Python

Read, write, and inspect OME-Zarr image pyramids and labels from a Python workflow.

Bioimage AnalysisPython package / CLI

Open source

BioIO

Load multidimensional microscopy images through format-specific readers and access their dimensions and metadata in Python.

Bioimage AnalysisPython package

Open source

scikit-image

Combine filtering, segmentation, morphology, and region measurement in array-based image analysis scripts.

Bioimage AnalysisPython package

Open source

SimpleITK

Apply image filtering and registration while retaining physical image geometry in scripted workflows.

Bioimage AnalysisPython / multi-language library

Free

BioImage Archive

Search and download published biological imaging datasets with study metadata.

Bioimage AnalysisPublic data repository

Free

Image Data Resource (IDR)

Browse curated imaging studies and their metadata in a public OMERO-based resource.

Bioimage AnalysisPublic image repository

Open source

Cytomine Community

Browse large biomedical images and collaborate on regions and annotations in browser-based projects.

Bioimage AnalysisSelf-hosted web app

Commercial

Huygens

Restore microscopy images using deconvolution and inspect the results in a scientific imaging suite.