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tischi / fiji-plugin-morphometry

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Microglia: Working with 3d images #80

Open m-albert opened 5 years ago

m-albert commented 5 years ago

Hi Tischi, nice plugin!

Does the plugin work with 3d(+t) images? If not do you plan to extend it to 3d?

Cheers!

tischi commented 5 years ago

Hi Marvin,

Which part of the repo do you mean? There are currently several plugins hosted:

https://github.com/tischi/fiji-plugin-morphometry/tree/master/src/main/java/de/embl/cba/morphometry/commands

m-albert commented 5 years ago

Which part of the repo do you mean?

Oh, I wasn't aware there are several plugins. I'm referring to the Microglia Morphometry part.

tischi commented 5 years ago

Ok! The code base of the tracking and feature measurements is, I hope, written in a way that it should be easily usable in 3D as well; at least that was my plan from the beginning :-) The code for the interactive segmentation could also work in 3D, however the part of manually correcting boundaries of wrong segmentations is of course more hassle in 3D. Do you know of a project where people you would need it?

m-albert commented 5 years ago

Ok! The code base of the tracking and feature measurements is, I hope, written in a way that it should be easily usable in 3D as well; at least that was my plan from the beginning :-)

Nice! But I guess it's not readily usable in 3d yet? Because I just tried with a 3d image and it threw an error saying that only 2d is supported.

The code for the interactive segmentation could also work in 3D, however the part of manually correcting boundaries of wrong segmentations is of course more hassle in 3D.

Yeah in 3d these things become difficult. But maybe in Fiji there'd some other plugin which could take care of that?

Do you know of a project where people you would need it?

For now I'm just playing around and seeing what other approaches there are for measuring things on microglia :)

tischi commented 5 years ago

OK! I don't have time right now to add anything for 3-D unless it is kind of high priority... Let me know if you "really need it" :-)