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juglab / cryoCARE_pip

PIP package of cryoCARE
BSD 3-Clause "New" or "Revised" License
25 stars 14 forks source link

mrc data mode? #31

Closed Dan-Zed closed 1 year ago

Dan-Zed commented 1 year ago

Can cryoCARE use tomograms in byte i.e. mode 0 format? This apparently works for a colleague but not for me. When I try mode 0 or 1 it fails during the training step.
More importantly, does it matter what the pixel size is? I was told <10 A pix size is ideal, which I can only achieve with bin2 but a smaller file size. My bin4 tomograms are 1024x1440x400, pixel size 13.34, and about 2.3GB in mode 2. Bin2 is about 18GB in mode 2.

While I'm here: I'd love to know if there are any parameters that should be adjusted for tomograms of the nucleus, a rather busy place.

rdrighetto commented 1 year ago

Hi @Dan-Zed

Training with odd/even tomograms both in MODE 0 (byte) and in MODE 1 (int16) works fine here using cryo-CARE v0.2.1. Perhaps your environment has an older version of mrcfile?

Regarding the pixel size, never heard of such a constraint, we typically use cryo-CARE on bin4 tomograms at a pixel size of 14.08 Å and it works great.

thorstenwagner commented 1 year ago

No reaction since a while. I gonna close it.