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Surforama

Surforama is a napari plugin for interactively exploring volumetric data by leveraging 3D surfaces. Given a membrane surface mesh, it projects the local tomogram density onto the surface so you can see what's sitting on (or in) the membrane, annotate and pick particles directly on the surface, and export oriented particles as RELION-formatted STAR files for subtomogram averaging.

It pairs naturally with the surfaces we build in Surface Morphometrics: once you have a clean membrane mesh, Surforama turns it into a tool for finding and orienting membrane-associated proteins. Developed by Kevin Yamauchi, Kyle Harrington, and collaborators (teamtomo / cellcanvas).

When to use it

  • You have a membrane surface mesh and want to see densities on it in context.
  • You want to pick particles on a membrane surface with sensible orientations (normal to the membrane).
  • You want oriented particles exported to RELION STAR files to feed subtomogram averaging.

Setup

Unfortunately, I introduced a scaling bug in my code this week, so you won't be able to make an obj scaled correctly for Surforama. Whoops! Instead, go ahead and grab surforama.obj

For surforama, its also helpful to have some deconvolution (or denoising!) done on your data. Since we have imod handy and its fast, we'll just do deconvolution quickly: 

module load imod
mtffilter tomograms/YTC041_1_lam4_2_ts_002.mrc -dec 0.5 -def 5 YTC041_1_lam4_2_ts_002_dec.mrc


conda activate surforama    
surforama --image-path YTC041_1_lam4_2_ts_002_dec.mrc --mesh-path surforama.obj

Try changing the parameters of the offset and the thickness to project - you should be able to find some dark spots at an offset around 5-8 that correspond to membrane-associated ribosomes!

If you want, you can try setting up a star file and picking those particles - these get their initial orientations directly from the surface normals, so you get a lot of the geometric advantages Mart and Will talked about for contextual particle picking.

  1. Click "Enable" under pick on surface
  2. Click points on the surface where you see ribosomes
  3. Click "Select File" next to file path and choose a star file name.
  4. Click "Save" to save the picked particles.
  5. Examine your particle picks - they should have phi and psi but rot should be 180/-180 for all!

Outputs

  • Surface-projected views of the tomogram density for inspection/figures.
  • Picked particles with positions and orientations on the membrane.
  • RELION-formatted STAR files ready for subtomogram averaging.

Tips

  • Surface normals give you orientation priors "for free," which is a big head start for averaging membrane proteins.
  • You can also generate isosurfaces for this in membrain - it doesnt have to be fancy morphometrics surfaces. With that said, we love our fancy surfaces!