0 particles found when running easymode pick

[andreanans]

Hi,

We have used easymode to segment some ribosomes in a tomogram and it worked fairly well. However, easymode pick also finds 0 particles, regardless of input parameters. We've played around with size and threshold, but so far nothing has worked. Do you have any suggestions for this case?

EDIT: turns out the threshold needs to be decreased significantly (to 0.2). Min density 0, mean is 0.005, max is 88. Any idea why this happened?

EDIT2: The command only works if we run it via ais. The equivalent command run in easymode already locates 0 particles.

Thanks
Andrea

[mgflast]

Hi Andrea,

I think this is a mismatch between Ais and easymode versions - easymode outputs uint8 by default, but old Ais versions expect int16.

I'll upload the latest version of both to PyPi tomorrow and think that should fix it.

Would you mind sharing the command and resulting output?

Thanks for reporting the issue! Best,
Mart

[mgflast]

Allright if you install the latest version of Ais:

pip install Ais-cryoET==1.0.47

And of easymode (I didn't upload a new version to pypi yet):

pip install git+https://github.com/mgflast/easymode.git

Then I think the easymode pick ... should work. If not I'd need to have a look at the commands you tried

[andreanans]

Thanks for the fast response. The picking is now working in easymode and ais. However, Easymode is still writing out the segmentation files with very low mean densities, like 0.6.

[mgflast]

A low mean might make sense if there simply aren't a lot of ribosomes in the tomograms. But the max of 88 is a bit odd, I would expect it to be 127 (with --format int8).

What is the pixel size of your tomograms?

[andreanans]

We have tried 10A and 12A tomograms. They have ribosomes and appear to be segmented well.

[mgflast]

I've just made the first version of the documentation available and it includes a ribosome tutorial - maybe this helps?

https://mgflast.github.io/easymode/user_guide/examples/ribosome/

One thing that might be going wrong: are you pointing easymode pick at the segmentation directory, or the tomogram directory? After running:

easymode segment ribosome --data tomograms/ --output segmented/

You would then run:

easymode pick ribosome --data segmented/

If the tutorial doesn't hlep solve the problem, could you share the commands you are running and the output it gives? Then I should be able to figure out what's going wrong.

[andreanans]

We're pointing to the segmentation directory. I'll have a look at the tutorial and see if I'm doing anything wrong. Otherwise maybe I can send you one of our tomograms. Thanks!

[mgflast]

Sure, if you send me a tomogram and/or a __ribosome volume I’ll see whether it works for me. Alternatively the command you used and the resulting output would be helpful.

…

On Fri, 14 Nov 2025 at 15:53, andreanans ***@***.***> wrote: *andreanans* left a comment (mgflast/easymode#2) <#2 (comment)> We're pointing to the segmentation directory. I'll have a look at the tutorial and see if I'm doing anything wrong. Otherwise maybe I can send you one of our tomograms. Thanks! — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BSQIFOEIGKGGYKBVCMQ5JEL34XUGLAVCNFSM6AAAAACMAWU33KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKMZTGE2DSOBWHA> . You are receiving this because you commented.Message ID: ***@***.***>

[andreanans]

Just letting you know I sent a message to your gmail with links to a tomogram and the segmented output. Cheers.