Published in Nature Methods
Microscopy analysis, reimagined for the cloud
Why NimbusImage
A modern platform designed around how scientists actually work with microscopy data today.
Runs entirely in your browser. No downloads, no dependency nightmares, no out-of-memory crashes. Process images that would never fit in local RAM.
See what algorithms are doing and correct them in real time. Adjust segmentation boundaries, add missed cells, remove false positives — all visually.
Apache 2.0 licensed. Inspect every line, self-host on your own infrastructure, and extend it to fit your exact research needs.
Capabilities
State-of-the-art algorithms, accessible through an interface designed for biologists.
Cellpose, Piscis, and SAM built in. Detect cells, nuclei, and organelles with a single click — then refine the results interactively.
Quantify RNA FISH spots, protein aggregates, and other punctate signals with sub-pixel precision across entire tissue sections.
Follow cells through time-lapse sequences, build lineage trees, and measure dynamics across division events.
Extract morphology, intensity statistics, spatial relationships, and hundreds of features per object automatically.
Full support for volumetric data and multi-channel colocalization. Navigate Z-stacks and overlay channels seamlessly.
Apply workflows to hundreds of images at once. Automated pipelines keep your analysis consistent and reproducible.
Publication
NimbusImage was developed at the Raj Lab at the University of Pennsylvania, in collaboration with Kitware. It grew from years of experience building tools for quantitative imaging in biology — and the frustration of watching students struggle with installation and memory limits.
Read the Nature Methods paperPlans
Start free with our hosted platform. Scale when you need to.
Individual
Free to start
For individual researchers exploring NimbusImage.
Small Group
Free to start
For labs and small teams collaborating on projects.
Institutional
Custom
For core facilities and departments with specific needs.
Desktop App
The same cloud-powered platform, wrapped in a native app for a dedicated experience.
A native window with its own process — no browser tab competition for memory or CPU.
Available for Windows, macOS (Apple Silicon), and Linux. Same experience everywhere.
Your projects, data, and settings stay in the cloud. Switch between desktop and browser seamlessly.
Open Source
NimbusImage is Apache 2.0 licensed because we believe scientific tools should be inspectable, reproducible, and free from vendor lock-in. Every algorithm, every pipeline, every line of code is available for you to audit, modify, and extend.
Self-host on your own infrastructure for complete data sovereignty, or use our managed cloud platform and focus on your research.
View on GitHubStart analyzing microscopy images in your browser today. No credit card, no installation, no commitment.
