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easymode + Warp/RELION/M

easymode was designed within the Warp/RELION/M workflow. All training data was processed using WarpTools and AreTomo3, and for validation via subtomogram averaging we used RELION5 and M.

Where easymode fits in

After generating tomograms with Warp, you can begin using easymode to denoise and/or segment your data (and tilt selection, if desired). easymode IO is straightforward: tomogram .mrc file in, segmentation .mrc volume out. After running segmentation for your features of interest, you will have your original tomograms in their original directory and segmentation volumes elsewhere (e.g. segmented/).

What to do with segmentations

You can use the resulting segmentation volumes in several ways:

  • Visualization and data exploration — use segmentations with Pom for tomogram composition analysis, dataset browsing, and data curation.
  • Particle picking — use easymode pick to automatically generate STAR files from segmented volumes, using either globular picking or filament tracing.

Particle picking and subtomogram averaging

The STAR files generated by easymode pick are directly compatible with WarpTools' ts_export_particles function. This means you can go from segmentation to particle export in just two steps:

  1. Run easymode pick on your segmentation volumes to generate particle STAR files.
  2. Use ts_export_particles to create the particle data and STAR file required for RELION jobs such as Refine3D, Class3D, and InitialModel.

After subtomogram averaging, the final STAR files can also be used with easymode + Pom to take measurements of the biological content of tomograms at or around your particle coordinates.