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?
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.
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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.
@apunjani is there any new information on this? We have several projects that we would like to use cryoSPARC for that are “simple” negative stain reconstructions that we keep needing to take to other programs.
@hansenbry It only takes a few seconds to invert the micrographs before importing in cryoSPARC. Well worth it considering the time saving in using cryoSPARC for picking, 2D classification and 3D reconstruction…
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Hey @hansenbry,
With the latest release of cryoSPARC (v2.13.0, January 28, 2020), we added full support for negative stain data. Just flip the toggle in the Import Movies/Import Micrographs job. We’re open to any suggestions so please let us know! For more information, please see the tutorial here:
For more information on whats new in cryoSPARC v2.13.0, see here:
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