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E.g. After GASP, the "Run Segmentation Fix from Nuclei" widget doesn't find the immediate GASP output in the drop down list. But if I GASP again, the previous renamed GASP output shows up.
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Hi,
I specified `segmented_custom` in the following code
```
sq.im.segment(img=img2, layer="image_smooth", channel=None, method=cellpose_he, channel_cellpose=0, flow_threshold=1)
…
WT215 updated
2 months ago
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To get the correct segmentation it's important that the objects on the new image are approximately the same size as in the training data. This doesn't necessarily mean that the voxel size should be th…
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Hi,
I am using Mesmer to segment cell nuclei of multiplexed immunofluorescence images.
To check if the segmentation works well, is it possible to obtain the segmentation outlines overlaid on the c…
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Hi there,
I've been using the plugging previously with no problem. Things has been fine until recently I run into a problem of Part 2 . The interface keep showing up an error of "macro error no summ…
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When executing the python code:
`model = fast.DataHub().download('nuclei-segmentation-model')`
I get the error:
`Traceback (most recent call last):
File "C:\Users\etiennp\PycharmProjects\RACE\…
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Hi
That's a great method! I'm wondering if, without the reference data and positive/negative markers (I only have the DAPI image and transcripts.csv), this method is still viable for cell segmentati…
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Aim is to use SpatialData is the data storage backend underlying the SPARCS workflow. This allows us to interface with many existing software solutions and build up on the existing software frameworks…
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if not manually set, the default color for segmentation is green. (so far so good)
1) if I click on export or upload the geojson, it does not contain the color if all the same nuclei have the same …
tdefa updated
3 years ago
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A couple of cool examples of napari, which is brilliant to display labels and annotate images.
https://napari.org/tutorials/applications/annotate_segmentation
https://napari.org/tutorials/gallery#…