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

8 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