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Hi,
Thanks for this super helpful tool, but I have some problems running deepcell mesmer, it would be great if you can help me.
1. When I run the following code to identify cytoplasm, I find that …
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Issue was raised on imagesc thread https://forum.image.sc/t/qupath-not-opening-bif-z-stacks/50674
A sample file along with a related `tifp` file have been provided which reproduce the issue (tested w…
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https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/model_spec_latest.md
Beware that this might not include microns resolution yet.
what we should probably do is be able to convert our…
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Hello,
I wanted to convert an MRXS file which has 4 channels and is fluorescent to OME.TIFF, I first went through Bioformats2raw to get a ZARR file which seems to have gone well. Then I wanted to c…
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This issue was first raised on image.sc thread: https://forum.image.sc/t/axioscan-7-fluorescent-channels-not-displaying-in-qupath/94615/15
A sample files showing the issue is available on Zenodo: h…
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## Bug report
**Describe the bug**
See https://forum.image.sc/t/qupath-negative-array-size-exception-during-fast-cell-counts/36332
**To Reproduce**
Try Fast Cell Counts with a low Gaussian sig…
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- if you specify downsample on init then the coords of all geometries are transformed, which makes the whole affair very confusing, since now the server coordinates don't correspond to anything in the…
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This issue was raised on forum thread https://forum.image.sc/t/qupath-cant-open-svs-images-from-aperio-versa-slide-scanner/93502/8 and appears to be very similar to issues seen with other formats such…
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Thank you for making a very interesting tool.
I've been working through the tutorial and noticed that the datasets already include segmentation masks. Can you provide advice on how to create masks …
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Thank you again for the hard work on this.
There is a discrepancy between the colors of the images extracted and the optimal colors such as the one seen in Leica Imagescope. Are you able to incorpora…