Hi all, Wondering if there’s a way to get the new open source segment anything model that meta ai released recently integrated into the AIAA server? The model seems incredibly powerful and integration with Slicer seems like it would be a godsend to those of us in the natural history space utilizin…

It should be pretty easy to integrate, but does anyone know if it would work well on 3D data? I’d be afraid that each slice would segment differently and you’d end up with jagged segmentations in 3D.

Maybe? My thought was that I could pretty easily import an image of a single slice into the model and using the segment from prompt functionality was able to mask out the outline of entire organs trivially. Youre right that as currently implemented the automatic mask generator in SAM doesnt really…

The prompt for a segmentation can be a mask. For 3D images it would be reasonable to have the user segment one slice, then use that slice’s segmentation as a prompt to segment adjacent slices, and so on recursively. Some special logic would be needed to handle multiple user-segmented slices, which w…

At the minimum it would be a great seeding tool for fill between the slices.

I can only use it via a screen capture module snapshots, and while playing with window/level settings, it seems to capture different features. These are all same slice. I couldn’t figure out how to do multiple masks manually. All from automatic parsing of the images. [image] [image] [image]

That’s about where I am with it running it through google colab and just seeing how the model behaves with cephalopod contrast enhanced CT images. Unfortunately I’m not in the position to host my own server for implementing the backend of the AIAA and rather than developing an extension around the …

“Segment anything” works considerably better than “Remove background” function in PowePoint and it is nice that it is made easily accessible in a web application and that the training data is published as well. But I don’t really get the excitement about using it for medical images. To me it its pe…

Perhaps im misguided in thinking that models trained on human and mouse data are not gonna work well for segmenting unconventional organisms. I work on cephalopods and other mollusks (ex vivo CEμCT) and have found flood filling and grow from seeds to be inconsistent/needing a lot of correction but …

Integration of “Segment Anything Model”?

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Dominick_Dickerson (Dominick Dickerson) April 7, 2023, 10:41pm 5

Could it use a similar logic to what is used during the “fill between slices” tool to handle multiple slices?

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Integration of “Segment Anything Model”?

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