Tomogram reconstruction

Although the core of easymode is really just about feature detection, we've included a couple of tools to facilitate cryoET data preprocessing. These are built on Warp and AreTomo3.

Fully automated tomogram reconstruction

Use easymode reconstruct to convert input frames and mdoc files into tomograms fully automatically. This command simply wraps around Warp and AreTomo3, so all credit goes to those authors! Requires setting up Warp and AreTomo3 as described on the installation page.

easymode reconstruct --frames frames/ --mdocs mdocs/ --apix 1.56 --dose 3.20

Optional arguments:

--thickness <int>         Thickness of the tomogram in Å (default: 3000)
--extension <str>         File extension of the input frames (default: auto-detected)
--tomo_apix <float>       Output pixel size in Å (default is 10 Å/px).
--shape <int>x<int>       Size (in pixels) of the tilt images (default: auto-detected)
--no_halfmaps             Include this flag in order NOT to generate even/odd frame and volume splits

Tip: skip the halfmaps

If you plan to use one the easymode general pretrained denoisers, you can save a lot of time and memory by skipping the generation of the halfmaps with --no_halfmaps. See the general denoisers page for details.