open source · cloud native · apache 2.0
Sharper structures. Faster pipelines.
CryoApex is production-ready software for cryo-EM data processing. Plugin-driven, cloud-native, and built to scale from a single workstation to a global compute cluster. More information can be found in the documentation.
$ git clone https://github.com/cryoapex/CryoApex
$ cd CryoApex && bash start.shFig. 01 Backdrop — micrograph from the bundled demo session.
First impression
The CryoApex workspace.
Open a session and CryoApex shows you everything in one place — the active micrograph, the navigator, the plugin tabs for your workflow, and result thumbnails as they come in.
What it does
A platform shaped like the cryo-EM workflow.
Drop in algorithms, configure them through generated forms, submit jobs at session scale, and inspect results in views designed for the result. The pieces fit because they share a model.
Plugin platform
Drop a Python plugin with Pydantic schemas; the UI renders forms automatically. CTF estimation, motion correction, particle picking — all under one roof, with a consistent submission and result UX.
Read moreBatch processing
Submit work on a single image or an entire session. Progress streams live over Socket.IO, and every result is persisted to the database — so you can come back later and find exactly what ran.
Read morePer-plugin result views
Tailored visualizations, not raw JSON. Thon-ring sketches for CTF fits, drift trajectories for motion correction, particle overlays for pickers — every plugin gets a view designed for its result.
Read moreCloud native
Containerized end-to-end. Run the same images on your workstation, an HPC cluster, or in the cloud — reproducible from one environment to the next. One command brings the full stack up.
Read moreAt a glance
Built in the open. Engineered for cryo-EM.
- Open source
- Apache 2.0 on GitHub
- Cloud native
- Workstation, cluster, or cloud
- Plugin SDK
- Python + Pydantic schemas
- Cryo-EM focused
- CTF · motion · picking
Start here
Pick the path that fits.
Try the bundled demo first if you want to see CryoApex end-to-end. Then point it at your own session when you're ready.
Get started
Ready to run CryoApex on your data?
Spin it up locally, on your cluster, or in the cloud — the same containers run everywhere.