Negative stain reconstruction

request_recorded

#1

Is there a way to tell a cryosparc project at the beginning or at steps like ctf and blob picking etc that it’s already inverted data?


#2

You can set the data sign to +1 or set “negative stain” in some job types.

These options are not consistent, however, and I recommend you manually invert your micrographs before import.

parallel -j 8 e2proc2d.py --mult=-1 {.} {}_inv.mrc ::: *.mrc

You can search for my post with my negative stain approach in cryoSPARC, it seems to work well for most data. I usually collect ~10 images on a T12 and have 2D classes and a 3D reconstruction within 30 - 45 minutes.


#3

Hi @hansenbry, @DanielAsarnow

Thanks for reporting - indeed the options needed for dealing with NS data are present but not consistent or obvious… we will improve this so that NS data can be specified at import time and then everything should just work.