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## Use Case
Requested by Jessica and Graham!
They described an issue where, when doing a max-projection through a volume, cell nuclei (or cells) may be overlapping in the projection. Currently, th…
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@Mava04 did @k-dominik get back to you about the feasibility of segmenting the nuclei with ilastik?
I think other options could be [CellPose](http://www.cellpose.org/static/docs/index.html) or [St…
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Hi! Thanks for designing this great tool. I've been using it quite a bit on Visium slides and it seems to have worked really well in the past. Currently I'm trying to use this on tissue slides that ha…
ssobt updated
7 months ago
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Dear Kwok,
After running SEPIA for the participants, now I want to corregister the subject Chimap to AHEAD template. So, I used the SEPIA GUI for this but the problem is, it is very slow. I have used…
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Hi, I had some questions about the cluster annotation after cell segmentation
I tried to map the single-cell data to Visium and got the probability of the spatial location of cell group ExcNeurons3…
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As far as I can tell, most of the outputs are per-observation files/information (like expression per nuclei, boundary, membrane etc. per cell) which fits well into the AnnData model i.e each `obs` var…
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I tried CZI from our confocal with z-stack and I got this error:
Performing segmentation on file 1 of 2
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UnboundLocal…
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Nice work!
The listed experiments shown the U-shape Swin Transformer could capture global and local information. However, its ability to capture small target information has not yet been shown, i.e…
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**Is your feature request related to a problem? Please describe.**
create_test_image_2d is great, but at the moment, you can get the class ID, but not the object instance ID. This means that two over…
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If the user calculates Max Intensity Projection on every channel for every FOV, along with maybe some segmentation results, what would be the best way to store them in the new version of zarr store?
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