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I see, it looks like your results are pretty good.

Regarding your comment about training the classifier, I agree that you probably need more training material. 1500 annotations per class isn't bad to start with, but 6 images for training are too few. I imagine that if those 1500 annotations/class were spread among more images (keeping the training volume the same while...


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import qupath.ext.stardist.StarDist2D // Specify the model file (you will need to change this!) def pathModel = '/Users//alvinair//Documents//HbH//dsb2018_heavy_augment.pb' // <- change the model to the HE trained model, and then remove the channel option in the builder like below. The HE model works on RGB images, like your data. The dsb2018 model works with fluorescence im...

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Hi!

I’m applying a Cell Painting approach to preview what (unknown) biological side-reactions may occur over time when I over-express fluorescent proteins of interest in mammalian cells. As a result, I’m using a mix of ‘canonical’ Cell Painting dyes alongside probes that are unique to my experimental setup. Right now I have adapted a JUMP morphological profiling pipeli...


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Hi @Rdornier - The failure to access ROIs feels like a permissions issue of some sort - although it's strange that it works with Shapes.

I wonder if the difference on your production server is that you have different users/groups, whereas test server is just you? Is the ROI in y...


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Brian Northan:

So I am still trying to figure out why these changes make big differences for me, but don't change the results for the study Authors.

@haesleinhuepf suggested Dunning Kruger for the earlier expertise-confidence relationship, but perhaps Dunning Kruger ...


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