Cryo-ET

Cryogenic electron tomography (cryo-ET) sits between single particle cryo-EM and volume EM. Cryo-ET involves the collection of tilt series of images from vitrified samples, which are then computationally reconstructed into 3D volumes.

Here are some resources in the intersection of cryo-ET and OME-Zarr.

Tools

• ChimeraX OME-Zarr - A plugin for ChimeraX to read and visualize OME-Zarr datasets designed for cryo-ET data.

• copick - CryoET annotation framework built upon OME-Zarr data. [paper]

• zarr-particle-tools - CryoET data analysis package (subtomogram averaging) based on OME-Zarr

Data

• Cryo-ET Data Portal - Cryo-ET data portal, with datasets shared as OME-Zarr (arguably EM and volumetric, but usually not considered ‘volume EM’ in the sense of serial sectioning or block-face imaging). [paper]

Other

• Cryo-ET Object Identification Kaggle Challenge - Kaggle competition for cryo-ET object identification, with OME-Zarr datasets.