trouble with NPC segmentation

[redsoul233]

Hi there! I'm using NPC segmentation on my 3D SMLM data. However, no matter which SMAP version I use ( source code or compiled), it will have bugs.
I follow the "SMAP_Manual_NPC.pdf" step 3.

When I clicked redraw, the software did nothing, and I saw this information:

What should I do? Is the data I use wrong?

By the way, the npc image is shown below:

Thanks a lot!

[Rieslab]

Hi Lucas, Can you try the develop branch of the MATLAB version of SMAP?

On 14.01.2026, at 15:40, hex ***@***.***> wrote: redsoul233 created an issue (jries/SMAP#31) <#31> Hi there! I'm using NPC segmentation on my 3D SMLM data. However, no matter which SMAP version I use ( source code or compiled), it will have bugs. I follow the "SMAP_Manual_NPC.pdf" step 3. image.png (view on web) <https://github.com/user-attachments/assets/f0554389-50fb-4172-9c67-877d8646a1ec> When I clicked redraw, the software did nothing, and I saw this information:

Can you check if in the Cell list the cells appear (on the right side)? Can you press the upd button and see if then you see the cells? If you do a File redraw, you should see the boxes with the cells (the grid). 

image.png (view on web) <https://github.com/user-attachments/assets/f286583f-3593-4635-86de-379f886c1962>Do the Chinese words indicate what error this is? Or are they meaningless?

Best, Jonas

What should I do? Is the data I use wrong? By the way, the npc image is shown below: image.png (view on web) <https://github.com/user-attachments/assets/3f06f72b-ee73-4197-be7c-0850b696f4fa> Thanks a lot! — Reply to this email directly, view it on GitHub <#31>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZ52BTSAGMM2SA7RCADYST4GZIPJAVCNFSM6AAAAACRVVZXAOVHI2DSMVQWIX3LMV43ASLTON2WKOZTHAYTGNJQGE3TGNY>. You are receiving this because you are subscribed to this thread.

— Prof. Dr. Jonas Ries Professor for Advanced Microscopy and Cellular Dynamics Max Perutz Labs University of Vienna Vienna-Biocenter-Campus 5, 1030 Vienna, Austria Phone: +43 1 4277 74380 Mobile: +43 660 896 0663 Email: ***@***.*** https://www.maxperutzlabs.ac.at/research/research-groups/ries

[redsoul233]

Hi! Thanks for your reply. Fortunately, after I used the develop branch and conducted continuous trials, I finally segmented my NPC.
If you don't mind, I have another question: how to use particle averaging in your paper "Maximum-likelihood model fitting for quantitative analysis of SMLM data", Fig. 5, and Extended Fig. 10. The result is amazing, but I didn't find the tutorial and entrance.
I appreciate any reply. Thanks you.

[Rieslab]

Hi, can I refer you to the first author of that paper, Yu-Le Wu? Best, Jonas

…

On 21.01.2026, at 14:17, hex ***@***.***> wrote: redsoul233 left a comment (jries/SMAP#31) <#31 (comment)> Hi! Thanks for your reply. Fortunately, after I used the develop branch and conducted continuous trials, I finally segmented my NPC. If you don't mind, I have another question: how to use particle averaging in your paper "Maximum-likelihood model fitting for quantitative analysis of SMLM data", Fig. 5, and Extended Fig. 10. The result is amazing, but I didn't find the tutorial and entrance. I appreciate any reply. Thanks you. — Reply to this email directly, view it on GitHub <#31 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZ52BXMUV4YTWOAHEMD65T4H54ALAVCNFSM6AAAAACRVVZXAOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTONZYGA4TKMRQHE>. You are receiving this because you commented.

[redsoul233]

Great! I will contact the author for further help. Thanks for your help. My email is zjuenxinghe@gmail.com, and you can tell me the author's email or copy him on the email, because I can't directly get his/her email address.