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Hi!
I'm converting the ZCDL4M 3D U-Net notebook with the bioimageio.core code and I see that 3D images are not properly stored. This also happened to StarDist as far as I remember when the images we…
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Hi Maria,
I have been trying to set up pycurv to analyze some mitochondria which have complex cristae morphology, which makes compartment segmentation difficult to borderline impossible, so I am us…
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I have 512x512 greyscale images I want to annotate using brush masks by humans and automatically segment later on using a UNet ML backend.
Versions:
label-studio: 1.4
label-studio-sdk: 0.0.4
lab…
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**incomplete read extraction within a genomic range**
*(Error with `pyega3 fetch`)*
**Description of the bug**
Tried to extract reads mapped to mitochondria genome using command below:
$ pyeg…
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Is it possible to segment bodies within a cell? My data is a set of TEM images. I am looking to segment autophagic bodies inside the vacuole of the cell. When I tried it on my images, it highlighted t…
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On the earlier version of Mobie one could change the opacity of a segmentation in Settings -> brightness & color
in Mobie 2.0.0 the segmentations do not appear here anymore.
I would be very useful…
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Hi,
Julian @jhennies has the segmentations almost ready.
What would be the workflow to add those? I saw that it is basically additional datasets (xml). But how does MoBIE know that it is a segmen…
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Hi,
I am rendering organelle meshes along with the segmentation data, skeletons, and object meshes. The latter three are wrapped in a `LocalVolume` source inside a `SegmentationLayer`. Everything w…
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I am interested to use the ISTN to try aligning brain scans, leveraging the location of mitochondria as landmarks. However I have run into issues in the code. In my understanding from the ISTN paper t…
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I run your code MitoEM-R-A.yaml in the MitoEM challenge, but many H5 files appear in the inference time . How can I merge them? The H5 file list is as follow:
![image](https://user-images.githubuserc…