Black Micrograph Preview

CryoSPARC Live
1

Hi All,

Ive got an issue where all (or sometimes a few) micrographs show up as black in cryoSPARC live. The micrographs seem OK in all other ways. Live picks particles, and the small preview image at the top show up fine. But the main image is black. If I do pre-processing offline, all seems normal.

Falcon 3 linear mode, Arctica. I did a new gain of the F3 to ensure that wasn’t the issue.

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2

@simonbrown Please can you collect browser diagnostics while you are observing this issue and email the compressed HAR file for the debugging of potential network issues.

3

Hi,

Sorry for the slow reply. I have collected these diagnostics, where can I email them to?

Thanks!

4

Thanks for collecting the diagnostics. I sent you a direct message regarding the email address.

5

@simonbrown Thanks for sending us the browser debugging information. Please can you also email a compressed copy of the file

/path/to/cryosparc_master/run/command_vis.log

to the same address. Please check the first timestamp inside that file that the file includes the time frame during which you observed the black preview(s). If necessary, please instead send us the compressed copy of the relevant older version (command_vis.log.1, command_vis.log.2, etc.) and include in your email

  1. The relevant project and Live session IDs.
  2. A link to this forum topic.
6

Hi,

Following up on the above. I figured out that this was only an issue with Falcon 3 movies in linear mode, specifically at higher dose rates. I changed our collection parameters to lower dose rates and now all the movies show up as expected. Our guess is that pixels may have been saturated and were compromising some sort of normalisation in the micrograph image in cryoSPARC.

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