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juglab / cryoCARE_T2T

Singularity image for cryo-CARE
BSD 2-Clause "Simplified" License
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IMOD version #3

Open sbliven opened 5 years ago

sbliven commented 5 years ago

I noticed that the singularity container uses IMOD 4.10.16. This is an older beta release (latest stable: 4.9.12, beta: 4.10.32). I was wondering if there were specific features of IMOD 4.10 that are especially important for cryoCARE, or if it would also work with the 4.9 series.

I did come across one difference already (the new -dfixed parameter of mtffilter)

tibuch commented 5 years ago

Hello @sbliven

I only use IMOD 4.10.x because of the new mtffilter command. Essentially you can use the IMOD version which you use for tomogram reconstruction. This would also mean that you have to adapt the reconstruction jupyter notebook. But from experience this has to be done anyway. Or at least it has to be verified that the reconstructions are still looking as expected. Every user/group/lab seems to have a slightly different reconstruction protocol. It is only important that the two tomograms, which get reconstructed, are identical up to noise.

sbliven commented 5 years ago

I don't have experience with the mtffilter changes. Is the dose weighting essential?

I experimented in my imod_4_9 fork with allowing None for the dfix and ini parameters; in this case they are not passed through so it works with 4.9. Would this be useful to include upstream? If so I can make a PR (but depends on #4 currently).