How to remove some bad quality images

I have 4000 frames now, but some have very thick ice and huge cracks, so I want to go through each frame one by one in cryosparc and make a selection. How can I achieve this functionality? In relion I usually do it in the manual picker program.

For micrographs, the equivalent would probably be the Manually Curate Exposures jobtype.

@zhe, to chime in, you can definitely use Manually Curate Exposures as suggested by @leetleyang, and you could also load your dataset into cryoSPARC Live and use the Overview Tab to view individual exposures and reject them manually and/or using threshold criteria:
(Scroll to 4. Exclude Poor Quality Exposures from Downstream Processing)

Once satisfied with your selection, you can Export Exposures ( and this will make the accepted and rejected exposure outputs available in the corresponding Project in your regular cryoSPARC interface for use in downstream processing.


The problem I’ve had with looking through a large number of micrograph in CryoSparc is that it may take >1 s for it to load a specific micrograph, which is much longer than you need to look at the image to assess quality. Thus, my solution, albeit much less elegant, has been to do a Generate Thumbnails job to a low resolution (let’s say @1 of 170) and then open the output folder, delete all the @1 thumbs and load the resulting @2 thumbs in an image viewer in batches of 50. In this way, for me at least, this means I can get through them a lot faster by just closing the viewer windows while scanning over the images briefly and saving the bad ones in a subfolder. Then, as Manually Curate Exposures can sort the micrographs alphabetically, it’s just a matter of finding the names in the subfolder and rejecting them.

How do you generate the thumbnails from mrc files? What I did is converge the mrc image to jpg with low resolution. Do you have any convenient ways?
Thank you so much.

thank you verymuch!!!!!I have made it

Thank you very much, very good solution! I spent over 10 hours yesterday looking at my pictures and it was really eye consuming. But how exactly does your solution work? Use that program? I’m just starting to learn cryosparc, so there are many, many things I don’t understand, thank you very much for your help

CryoSparc has a job under “Utilities” that is called “Generate Micrograph Thumbnails”, which only parameter is the requested resolution. The thumbnails are then output in a subfolder of the job folder as .png’s. For actually viewing the images, I work on a Windows PC connected by FTP to our CryoSparc server from which I used to download small batches into a cache of the FTP program and open them directly in individual viewer windows. A better solution, however, is probably to download all the .png’s and open the first one with the default Windows image viewer because that let’s you scroll through the folder with just the arrow keys.

Good to know. Thank you.