CIF Tutorials | QuPath : Counting and classifying cells in multiple brain regions

[@danidaje]

Thanks for the great and valuable tutorial! Really appreciate it!

[@jesuchristopherjoseph3884]

Very useful tutorial.

[@sanfire00]

very nice, thank you!

[@Svipuls]

Thank you for this super useful tutorial!

[@ilajoshi1384]

Hi Thank you so much for such an amazing video. I am trying to use this video for my cells analaysis. However I am not able to run classifier to detect particular channel. Could you please tell me what should I do

[@UniversalBuilder]

I assume you are trying to use StarDist? If yes look at the code part halfway through this video (e.g at 21:30). At some point you have to specify on which channel you want to work with. In this example it's 'DAPI'. It may be different for you, you can look for the channel names in the Brightness/Contrast tool (the half black circle in the toolbar next to the drawing tools). If you are asking about running a classifier you have trained, make sure you apply it on objects detected in the same way as the objects used for the training. For instance the StarDist script doesn't always include the "measureIntensity()" command, meaning a classifier trained on detections which have an Intensity feature will not work on detections that have not this feature. One common issue is that the Analyze>Cell detection command adds the intensity features by default, but not the StarDist code snippet. Another common mistake is trying to apply a classifier trained on images with certain channel names on images which have other channel names (for instance, DAPI became Alexa405nm or something similar). There are many potential issues like that, the key being to try your best to stay consistent.

[@ilajoshi1384]

@@UniversalBuilder Hi, Thank you for your reply. I am having problems training classifiers for different channels. I do not understand why despite making it to annotate cells to identify classifer, command live update is not working for me

[@tamarsegal3985]

Thanks! very useful! There is an option to change the radius of the detecting cells with Stardist?

[@UniversalBuilder]

All the available parameters are listed here: qupath.readthedocs.io/en/stable/docs/deep/stardist.html You can change the cell expansion radius, but not the nuclei. I suppose you could filter out later nuclei out of your target range. Something like that: forum.image.sc/t/select-delete-objects-that-are-above-a-specific-area/38229