Only partial conversion of membrane segments to meshes

[JuhaHuiskonen]

Hi,

I have complete membrane segentations of my tomograms.

I am now trying to convert the segments to meshes with the command "membrain_pick convert_file". When I open the OBJ file in Napari, I see that some segments, but not all, have been converted to a triangulated surface.

Any idea why the conversion is only partial?

Cheers,
Juha

[LorenzLamm]

Hi Juha,

Thanks for raising this issue.
Hm, I'm not sure what could be the issue for you. One possible reason I can see is that you have multiple connected components in your segmentation. The membrain_pick convert_file functionality will only process the largest connected component of the segmentation it can find. So the ideal format of your input would be one .mrc segmentation file per connected component.
Could this be the reason that some segments are not properly converted for you?

Best,
Lorenz

[JuhaHuiskonen]

Hi Lorenz,

That explains it. My tomograms include multiple membrane viruses, resulting in as many membranes that are not connected. Would it be possible to return all components with a size larger than a user-given value?

Best wishes,
Juha

[LorenzLamm]

Hi Juha,

You could use the lasso-3d Napari plugin. Here, you can load your segmentation, crop out areas of interest (optional), and do the connected component computation you mentioned, i.e. also with filtering out small components. Afterwards, you can save out the resulting components (or choose a subset to save).

Downside of this is that you need to open the segmentations in Napari, which makes it difficult to process large batchs of tomograms.

We do have a connected components functionality in MemBrain-seg, you can find more info here. However, this functionality will only store one .mrc file with all different components assigned to a different integer value.

So I realize maybe it makes sense to also have this functionality available to store out each connected component as a separate file. Or better: Make membrain-pick also usable with the multi-integer output of the MemBrain-seg connected components functionality.

Please let me know if this helps :)

Best,
Lorenz

[JuhaHuiskonen]

Hi Lorenz,

As my dataset includes nearly 500 tomograms, I am looking for an automated solution. I have around 10 disconnected, spherical membrane components in each tomogram. So ideally, there would be a way to return a mesh for each of these, in a single OBJ or H5 file per tomogram, so that I can proceed picking particles on all of these meshes using surforama.

Best wishes,
Juha