2D classification counts all particles as duplicates after reextraction and deletion of original extraction

Particle Picking
1

Hi there!

I have a project where I extracted tons of particles in the first round (ca. 10 million) and heavily down selected afterwards with 2D and 3D classification. I then reextracted the particles. To save space, I cleared the original extraction job. Now, when I do either remove duplicates or 2D classification, almost all my particles I have are removed (I get exactly 1 per micrograph). If I add micrograph pixel size to remove duplicates, it works as it does normally and I keep most of my particles. However, my department runs cryosparc 4.4.1, so that is not an option for 2D classification jobs (I believe it’s implemented in 4.5+).

I’ve tried “Reassign particles”, but to no avail. Any idea what to do from here?

2

Hi there @kbjoernsson,

Thanks for the post. The suggested procedure for handling this issue, for CryoSPARC v4.4.1, has been described here. In short: Remove duplicate particles can be done via the standalone job with a specified micrograph pixel size, and the remove duplicates parameter in the 2D classification job can be disabled.

The reason for this was due to a bug that existed for particle datasets picked before version v4.4.1, in which not all metadata including the micrograph pixel size was tracked.

Let me know if this answers your question
Michael

1 Like
3

Hi Michael,

That fixed the issue - thanks!

Best
Kasper