Actin segmentation

[delnianzri]

Hi Mart,

I am currently using EasyMode for actin segmentation in my mammalian cell tomograms. EasyMode has a lot of background after segmentation, and it also misclassifies microtubules and some membranes as actin. How can I optimize it?
It actually works perfectly for microtubules and intermediate filaments.

Thank you in advance.

Best,
Delnia

[mgflast]

Hey Delnia! I'm currently working out some issues with the actin model, but it'll be a while before that is online. Meanwhile, you can try the alternative 2d model: easymode segment actin --data <> --2d; I'm guessing you're running segmentation on your IsoNet2-denoised tomos? I originally didn't include any missing-wedge-inpainted tomogram style in the training, so sometimes the networks struggle with those. I've since generated two pretrained wedge correctors (IsoNet2 style and DeepDeWedge style) which I will using during training to augment the input subtomograms; meaning the networks should be more robust to different tomogram styles. With that and some other edits the actin network should get much better - in a week or two. Op do 9 jul 2026 om 08:28 schreef Delnia Nazari ***@***.***>:

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*delnianzri* created an issue (mgflast/easymode#24) <#24> Hi Mart, I am currently using EasyMode for actin segmentation in my mammalian cell tomograms. EasyMode has a lot of background after segmentation, and it also misclassifies microtubules and some membranes as actin. How can I optimize it? It actually works perfectly for microtubules and intermediate filaments. Thank you in advance. Best, Delnia — Reply to this email directly, view it on GitHub <#24?email_source=notifications&email_token=BSQIFOCTXNAUENCWOKO45QD5D5CSZA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBYGQ2DCNZXGM2DDJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BSQIFOEASIWFPVSA5PY7Y3T5D5CSZAVCNFSNUABGKJSXA33TNF2G64TZHMYTANJUGI2TGOJYGY5US43TOVSTWNBYGQ2DCNZXGM2DDILWAI> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/BSQIFOGRV2H64MOVBEVUZIL5D5CSZA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBYGQ2DCNZXGM2DDJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/BSQIFOFDUSEDPWQL22MKKXL5D5CSZA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBYGQ2DCNZXGM2DDJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[delnianzri]

Thanks. I will try the 2D then; I only checked the 3D and the Isonet2 denoised version tbh. Looking forward to the new model:)