Add possibility to delete 3D labels which have only few layers

[dfgdgdfgd]

Description:

Hi Francesco, i noticed that when segmenting 3D data with Cellpose, it is often the case that labels end after only 1-3 layers and the rest of the nuclei are assigned to a new label. Do you think there might be a possibility to implement a function to delete 3D labels with only a few layers?

Thanks and best regards Mario

[ElpadoCan]

Hi Mario, by "a few layers" do you mean a few z-slices? If yes, then surely we can implement that function.

Do you think it should also have a minimum area threshold? I was thinking that some objects made of three z-slices might be legit if they are big enough, right?

Did you try filtering by minimum size? You can test this in the GUI from the menu in the top menu bar Segment --> Segmentation post-processing... and then you play with the sliders and numeric controls.

Anyway, we can add a "minimum number of z-slices" numeric control in that window, what do you think?

Cheers, Francesco

[dfgdgdfgd]

Hi Francesco,

yes, i meant a few z-slices. And yes, indeed, you´re right, a minimum area would certainly make sense, since the thickness of the z-slices is variable.

Filtering by minimum size is a really useful option, but sometimes wrong segmented structures exceed the adjusted minimum size, but they have only a fraction of the volume of a whole nucleus. A slider for "minimum number of z-slices" would be great, since that would give the user more flexibility to delete over-segmented nuclei.

Thanks and best regards, Mario

[ElpadoCan]

Hi Mario,

I just release v1.2.4rc56 with the feature that we discussed.

There is now a new slider in the post-processing parameters to set the minimum number of z-slices per object. This can also be set when you segment multiple positions at once with the segmentation module.

To update, activate the acdc environment and then run the command pip install --upgrade cellacdc.

Let me know if it works, thanks!

Have a good Christmas break and a happy new year!

Cheers, Francesco

[dfgdgdfgd]

Salve Francesco,

great, mille grazie, provo domani.

Buon natale anche a te é un buon anno nuovo!!

Saluti Mario

Am Tue, 20 Dec 2022 11:20:07 -0800 schrieb Francesco Padovani :

Hi Mario,

I just release v1.2.4rc56 with the feature that we discussed.

There is now a new slider in the post-processing parameters to set the minimum number of z-slices per object. This can also be set when you segment multiple positions at once with the segmentation module.

To update, activate the acdc environment and then run the command pip install --upgrade cellacdc.

Let me know if it works, thanks!

Have a good Christmas break and a happy new year!

Cheers,Francesco

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