Hi Ricardo, I’m glad to hear that someone out there is getting use out of these tools, and thank you for your enthusiasm and suggestions. They are definitely on our roadmap; users have been requesting them. I'm currently focused on improvements to our lighting model for volumes, but may revisit these additional segmentation techniques in a couple of weeks. If you want to hack on them yourself, all code relevant to segmentations is contained within the segmentation bundle. You would need to define additional segmentation mouse modes that would be activated by buttons you click on the segmentation tool, and then different segmentation algorithms that those mouse modes would call. I would prefer if you made pull requests to the ChimeraX repo to implement these, but I’m not sure what our policy on accepting external code is. I’ve CCed Scooter Morris, the RBVI’s main administrator/project manager, in case he has any knowledge that could help us. — Zach

On 21 Jun 2024, at 08:36, Ricardo Righetto via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

Thanks a lot for adding the Segmentations mode in v1.8, this is very much welcomed for cryo-ET data!

Are there any plans for expanding the capabilities of this tool? If possible, I would like to suggest some features for manual segmentation:

* Segment contiguous density in 3D by clicking on it (akin to the blob selector in the "Right Mouse" options, which operates on surfaces) * Related: threshold-based segmentation i.e. segment in 3D all contiguous density between selected minimum and maximum density thresholds * 2D/3D Lasso-based segmentation * Dilation, erosion and smoothening of segmentations

Some of these things are already possible by combining volume and surface operations or with external tools, but it would be very nice to have everything streamlined in one click (or a few) through the GUI.

Alternatively, I would appreciate pointers on how to implement these features as a ChimeraX plugin. Happy to discuss more.

Thank you and have a nice weekend!

-- Ricardo Diogo Righetto _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Hi Ricardo,

On 27 Jun 2024, at 02:46, Ricardo Righetto <ricardorighetto@gmail.com> wrote:

Dear Zach,

Thank you so much for your answer, it's great to know that the segmentation bundle is under active development.

I'll see what I can come up with myself from my list of feature requests, and will likely contact you for advice in the process. Also happy to test any new developments of this bundle. Let's stay in touch!

Please do, I’m always around to answer questions and looking forward to working with you. The circular cursor that already exists is hard coded into the 2D slice viewers in segmentations/src/ui/orthoplanes.py so abstracting that so it can be swapped out for another algorithm would be a good place to start. If you’ve never built ChimeraX before, the programming manual has what you need to start. If you notice deficiencies in it, take note of your workarounds and we can use them to improve the documentation.

About contributing code directly to ChimeraX or via an external bundle, it might be a bit early, but it's good to know what the preferred course of action would be.

Best wishes,

-- Ricardo Diogo Righetto

Em ter., 25 de jun. de 2024 às 20:46, Zach Pearson <zjp@cgl.ucsf.edu> escreveu: Hi Ricardo,

I’m glad to hear that someone out there is getting use out of these tools, and thank you for your enthusiasm and suggestions. They are definitely on our roadmap; users have been requesting them. I'm currently focused on improvements to our lighting model for volumes, but may revisit these additional segmentation techniques in a couple of weeks.

If you want to hack on them yourself, all code relevant to segmentations is contained within the segmentation bundle. You would need to define additional segmentation mouse modes that would be activated by buttons you click on the segmentation tool, and then different segmentation algorithms that those mouse modes would call.

I would prefer if you made pull requests to the ChimeraX repo to implement these, but I’m not sure what our policy on accepting external code is. I’ve CCed Scooter Morris, the RBVI’s main administrator/project manager, in case he has any knowledge that could help us.

— Zach

...

On 21 Jun 2024, at 08:36, Ricardo Righetto via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

Thanks a lot for adding the Segmentations mode in v1.8, this is very much welcomed for cryo-ET data!

Are there any plans for expanding the capabilities of this tool? If possible, I would like to suggest some features for manual segmentation:

* Segment contiguous density in 3D by clicking on it (akin to the blob selector in the "Right Mouse" options, which operates on surfaces) * Related: threshold-based segmentation i.e. segment in 3D all contiguous density between selected minimum and maximum density thresholds * 2D/3D Lasso-based segmentation * Dilation, erosion and smoothening of segmentations

Some of these things are already possible by combining volume and surface operations or with external tools, but it would be very nice to have everything streamlined in one click (or a few) through the GUI.

Alternatively, I would appreciate pointers on how to implement these features as a ChimeraX plugin. Happy to discuss more.

Thank you and have a nice weekend!

-- Ricardo Diogo Righetto _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

— Zach