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.
Tilt selection
Use easymode select_tilts to automatically identify bad tilt images and exclude them from tomogram reconstruction. To avoid repeating tomogram reconstruction, you could run the above easymode reconstruct with argument --steps 11100000 first, then run tilt selection, and then reconstruct with --steps 00011111. Or just reconstruct and think about tilt selection later.
easymode select_tilts --tomostar tomostar/ --output tomostar/selected_tilts/
Optional arguments:
--tiltstack <string> Path to a single tilt stack file OR glob pattern for multiple tilt stacks (*.st) OR directory containing tilt stacks (default: warp_tiltseries/tiltstacks/).
--tomostar <string> Directory containing Warp-style tomogram star files.
--xml <string> Path to a directory containing Warp-style tilt series .xml files. The 'UseTilt' parameter in these files will be updated based on the tilt selection (default: warp_tiltseries/xml/).
--tta <int> Test-time augmentation factor (default: 1, max 8). The model will predict multiple augmented versions of each tilt image and average the results.
--gpu <int> GPU id(s) to use for inference.
--extension <str> Extension of the tomogram star files in --tomostar. Default is '*.tomostar'.
--threshold <float> Threshold for tilt exclusion (default: 0.5). Tilt images with a predicted quality score below this value will be excluded. Score range is 1.0 to 0.0, with 1.0 being good.
--overwrite If used, if output star files already exist in --output, they will be overwritten.