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GrotjahnLab / surface_morphometrics

Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging.
GNU General Public License v3.0
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Tutorial Design #4

Closed bbarad closed 2 years ago

bbarad commented 2 years ago

I want to write a tutorial jupyter notebook. This will be timed well with uploading preliminary tomos, labels, and surfaces to Zenodo.

  1. Download a single label file
  2. Generate surfaces from the label file
  3. Run pycurv and surface_to_surface.py
  4. Generate a few nice plots.

This will be very dependent on:

  1. Getting quick generation of a functional environment for pycurv
  2. Figuring out how to make pycurv run FAST - maybe reduced number of triangles? 150,000 runs in 4 hours on a cluster w/ 128GB ram but 50,000 would be considerably faster and could probably run on a 32GB RAM machine... find an example where 50,000 gives a real robust result - probably not too wild in terms of cristae!
  3. generalizing plotting code to be easier to import - right now its a bit of a hairball.
bbarad commented 2 years ago

Because segmentations compress impressively well (thanks, LZW), I am just uploading a tarball with a couple of them to the github. The generalize branch is where I am working on tutorial development, as well as some other updates.

bbarad commented 2 years ago

Tutorial (in the form of example data and an example config file) is included in Version 0.2 release onwards!