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BIOP / qupath-extension-cellpose

an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.
Apache License 2.0
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Specify intensity measurements in CellposeBuilder #49

Closed RouvenHoefflin closed 2 months ago

RouvenHoefflin commented 3 months ago

Hi,

Thanks a lot for that amazing plugin! I’m using the cellpose extension (v0.9) in QuPath (v0.5.1) to run nucelar segmentation on very large super high-plex immunofluorescence images (>70plex). To reduce the number of measurments, I want to specify the intensity measurments for the segmented cell compartments using the cellpose builder as described here (and not measure everything using the default code: “measureIntensity()”:

biop.github.io CellposeBuilder (qupath-extension-cellpose 0.9.3 API) declaration: package: qupath.ext.biop.cellpose, class: CellposeBuilder

However, I don’t fully understand the syntax and couldn’t find examples online. Could you provide a line of code as example, in which the specified following intensity features get measured:

Compartments: Nucleus, Cytoplasm (exclude e.g. Membrane, Cell etc.) Markers/channels: DAPI, CD45 (exclude all others) Stats: Mean, Median, Max (exclude e.g. Min, STDV etc.) This will help to reduce the data burden by a lot, which is importent for downstream analysis.

Thanks a lot for your help.

Rouven

lacan commented 2 months ago

Hi, We've discussed the issue in the forum here https://forum.image.sc/t/specify-intensity-measurements-for-cellpose-extension-in-qupath/99814/2?u=oburri So I am closing this ticket :)