Hi @Dmitry,
Thanks for the information. We’ve been noticing some issues with negative stained data during particle picking, and one symptom of this is that picking tends to pick in the spaces between actual particles/filaments. There was a recent thread discussing some workarounds with negative stain picking: Blob picker missing highest contrast particles (negative stain) – I believe the main suggestion here was ensuring the micrographs are imported with “negative stain” activated. If that still doesn’t work, it seemed like some users had success with pre-multiplying the micrographs by -1 when importing, and then processing as normal (i.e. with negative stain off).
Please let me know if either of these options helps improve the particle picker!
EDIT: I stand corrected, please see Oli’s suggestion below. We’re planning to re-visit our negative stain workflow to iron out the bugs here.
Best,
Michael