Inspect Picks "Done Picking! Extract Particles" is not working

Particle Picking
1

Hi
I am trying to pick particles through template picking and extraction.
All of sudden, “Done Picking! Extract Particles” in the Inspect Particle Pick job is not responsive.
Since it was working for the Manual Picker job, I went back there and tried again with other test data set.
Then this one also did not work.

I have updated the Version 2.3.2, which did not fix the problem.
Should I reinstall the whole package again?

Thanks

Joseph

2

Hey @Joseph,

We haven’t encountered this issue before. Can you try restarting cryoSPARC again, then restart your browser and check again?

cryosparcm restart

3

Hi Stephan,
I have tried but it is still not working.
So far, other jobs are functional, though.

Do you have any idea?

Joseph

4

Hi @Joseph,

Did you try clearing the job or creating a new one? Please note this will remove your manual particle picking progress.

5

Hi Stephan,

I have tried with a new project using a small data set.
It was successful for “import movies”, “motion correction” and “ctf estimation”
However, it failed again in Manual picker job.

Am I doing something wrong?

I only applied the ctf estimated output to the manual picker, leaving “particles” section blank.
I followed the T20S tutorial.

Thanks

Joseph

6

Hi Stephan,

I have just found how to fix the issue.
I was using an odd number for box size, but when I changed it to an even number, it worked.
The difference was quite clear.
I think you may want to add this information somewhere in the protocol.

Thanks

Joseph

7

Hi @Joseph,

The T20s tutorial states the box size should be double the diameter:

Screen Shot 2018-10-17 at 11.24.04 AM.png2414×170 32 KB

Thank you for following up!

8

Check again:
"* Adjust the box size to make it easier to see the location of picks. Often a very small box size (32) can be helpful. The box size is not used in the outputs of this job, as this job only outputs particle locations. "

If you don’t follow the tutorial to the letter, it won’t work. You have a 50/50 chance of picking and odd number.

9

Hey @satyshur,

After reading this post I went back to the initial problem and realized what the issue was. The box size you select to paint the particles in the Inspect Picks job should not matter when extracting the locations. Sorry for the inconvenience. I’ve fixed this bug, and it has now been released in the latest version of cryoSPARC (v2.15.0).

Also, in order to find the actual traceback, I used cryosparcm joblog Px Jx, which returns the log file for the job process.