Request: Manual Picker jobs shouldn't take so much disk space

Particle Picking
1

Hello,

I’ve noticed while cleaning up several projects that Manual Picker jobs use an excessive amount of disk space. For example, I have a project with 2800 micrographs and 600000 particle picks and for some reason it takes up 300GB of disk space. The particle blob/location .cs file containing coordinates takes up 230MB. Can this job-type be cleaned up so that it doesn’t use so much space?

Thank you,
-Alex

2 Likes
2

I’ve also noticed this. Seems that the new manual picker in v4 extracts particles based on the box size specified in the interactive interface. Whenever I just want the particle coordinates (e.g. for Topaz training), I just set the box size to 4 to minimize the disk space taken.

Best,
Kookjoo

3 Likes
3

Hi Kookjoo,

That’s a good idea. Do you set the box size to 4 just re-extracting with box size 4 or is there a better way?

Best,
-Alex

4

Hi Alex,

Yes, that’s what I did when I wanted to combine the good set of particles with some manually picked ones for Topaz training purposes. I set the box size to 4 in the interactive interface of manual picker. I knew I wouldn’t need the extracted particle stack except for the particle locations.

There isn’t a way to bypass extraction when you click the “Done Picking” button. It would be great to have the option to turn off extraction. At least in my mind, this is similar to what one would expect from particle pickers - get the coordinates then extract particles with Fourier crop / flip micrographs / etc in a downstream extraction job.

Best,
Kookjoo

2 Likes
5

Oh! I thought the box size option at the top of a running manual picker job was just for visualization. I learned something new=)

1 Like
6

It was a random discovery that turned out to be useful in my case :innocent:

7

Hi all,

Thanks for the suggestion! We’ll work on making extraction an optional step in the manual picker so you can just output particle locations instead.

- Suhail

2 Likes