Blob Picker picking around particles in v2.13.2

hansenbry · February 14, 2020, 5:44pm

I’m trying to do a negative stain reconstruction, with v2.13.2 but I’m having an odd issue where the blob picker and even the template picker seem to be picking around my white particles in the image. Is there a secondary setting or something other than selecting negative stain at input that I should be doing?

sdawood · February 14, 2020, 6:46pm

Hi @hansenbry,

Can you make sure you create a new blob picker or template picker job instead of cloning an existing job? Also, please attach a screenshot if possible.

Regards,
Suhail

hansenbry · February 14, 2020, 6:57pm

Hi Yes I created a new job and didn’t clone a job.

Here is a screen shot of one of the outputs

Feng10 · February 17, 2020, 1:56am

Hi @hansenbry,

I think CryoSPARC only finds dark particles, rather than white particles.

One solution is to invert the contrast of your images, so your particles will be black, and cryosparc can find them. For example, use e2proc2d:

e2proc2d.py raw_image.tif inverted_image.tif --mult -1

https://blake.bcm.edu/emanwiki/EMAN2/Programs/e2proc2d