Open access to annotated cryoET tomograms







or explore via API

Welcome to the CryoET Data Portal, a project built by the Chan Zuckerberg Imaging Institute and the Chan Zuckerberg Initiative.

Currently, annotating tomograms from cryo-electron tomography (cryoET) experiments is a tedious, time-consuming, and often manual process. Our goal is to accelerate this process by catalyzing the development of sophisticated machine-learning methods for automatic annotation, helping researchers find scientific insights faster.

The portal provides biologists and developers open access to high-quality, standardized, annotated data they can readily use to retrain or develop new annotation models and algorithms. Currently, the portal contains 15,218 tomograms from 300 datasets contributed by the groups of Julia Mahamid, Jürgen Plitzko, David Agard, John Briggs, Abhay Kotecha, Ben Engel, Danielle Grotjahn, and Grant Jensen.

All tomograms include rich standardized metadata such as data tree structure and naming conventions. Most groups have already provided annotations for their data, and there is a structure to add new annotations to existing tomograms.

We are actively growing the number of annotated datasets on the portal and encourage researchers to share their data. We are working with EMPIAR to host the data and support annotation.

Ultimately, our vision is to contribute to developing a large, open-access database of annotated and validated 3D structural information for cells that researchers can use to gain new insights into cellular and structural biology.

Help us achieve this vision

View and Download Datasets

Find and visualize cryoET datasets in the portal and download to use for your work.

Contribute your Data

We encourage you to share datasets and/or annotations to existing data. Click below to fill out the inquiry form.

Participate in our ML competition

Develop a ML model for annotating subcellular structures and proteins in CryoET data.

Thank You to our Data Contributors…

  • David Agard
  • Ben Barad
  • Florian Bec
  • John Briggs
  • Zhen Chen
  • Jane Ding
  • Ben Engel
  • Ryan Feathers
  • Sara Goetz
  • Danielle Grotjahn
  • Gus Hart
  • Grant Jensen
  • Mohammed Kaplan
  • Zunlong Ke
  • Sagar Khavnekar
  • Abhay Kotecha
  • Jun Liu
  • Julia Mahamid
  • Michaela Medina
  • Jürgen Plitzko
  • Ricardo Righetto
  • Kem Sochacki
  • Matt Swulius
  • Liang Xue
  • Huaxin Yu
  • Ellen Zhong

Top Image: The inner workings of an algal cell as depicted with cryo-electron tomography, which aggregates multiple snapshots of a single piece of material. Visible are the Golgi apparatus (green and magenta), and vesicles (multi-colored circles). | Photo credit: Y. S. Bykkov et al./eLIFE (CC BY 4.0)