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Hi, I am curious about the AJI calculation of prediction images and the ground truth.
From the code, looks like you are using binary predictions with binary masks to calculate the AJI.
Would this …
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old workflows that were added before the “workflow type” field was added for each workflow step (before March 2019) need to be curated to update the workflow type. e.g. all the workflow steps in http…
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Hi,
Is there a way to put stardist in a macro to apply the segmentation for each slice and recombine them to reconstruct 3D nuclei ?
It would be great, I try but don't find the command to skip the i…
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I am working on cell counting model and using DSA+Histomics for it, Can i also include a text number in the middle of the region of interest for which the nuclei segmentation boundaries are generated?…
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Is it possible to do segmentation on syllable level? thanks in advance.
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Reported by Raffa: after re-running a (modified) pipeline, the metadata download apparently succeeds but the CSV file is empty (consists of just the header). In the server logs we could find::
```…
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@ArneDefauw I have a weird bug where `allocate_intensity` is very slow. When looking at the Dask dashboard, it seems to not use the segmentation_mask already in the SpatialData object from the `segmen…
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Hi, I tried using the original Cellpose for 3D stack tif segmentation. The majority of the DAPI nuclei could not be identified in the first try. However, after adjusting the stitch_threshold from 0 to…
rmd13 updated
5 months ago
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I noticed that IdentifySecondaryObjects should support volumes was marked as done. I am getting the following error message when I try to use the IdentifySecondaryObjects module which is downstream f…
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Hello,
I am trying to import a multiframe tiff file in ilastik.
You only choose a single file. If your stack is contained in a single file (e.g. a multi-page tiff) please use the "Add File" butt…