Thumbnails in CPA don't reflect the analysed data

cellprofiler-analyst
#1

Hello everyone!

I’m a new user of CP. I have problems with using classifier module in CPA and I even have no idea what I am doing wrong. It seems that I miss something obvious…

I have some ND2 images and each contains about 20 slices Z-stack in 2 separate channels (DAPI and 488). What I want is to make CP analyse only the middle of the cell which is 10th slice (in both channels). I use metadata module to extract data only about the 10th slice. It seems that CP really analyses and writes to SQLite database only the 10th slice.

Then I want to use training module in Classifier in CPA and I need to see only the 10th as I primarily classify cells by my eyes.

BUT when I open this database in CPA it shows me thumbnails of the 1st slice when I try to use classifier. Is there any way to make CPA show me only the 10th slice?

What I tried (but it also didn’t work properly): I supposed that the thumbnails from CPA may not reflect the database information. In ExportToDatabase module there is “select the images for which you want to save thumbnails” and there are options “DAPI” and “488” (my 2 channels). I tried to add module “Convert objects to image” which makes a picture “example” of the 10th slice. And then I selected this “example” as a thumbnail instead of DAPI and 488. BUT classifier still showed the 1st slice…

I use CellProfiler 3.1.5 and CP Analyst 2.2.1.

Any help is appreciated.

Thank you in advance.

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#2

Hi, welcome!
I’m not an expert on this, but I can at least say that the thumbnail options in the ExportToDatabase module are irrelevant to what you see within CPA’s Classifier. Those are thumbnails of the ENTIRE image and are only used, to my knowledge, in the PlateViewer tool.

It’s possible that there is a clever way to do what you want but I’m not sure (it’s possible the fancy metadata technique you are using just isn’t replicated in CPA, only in CP). I would suggest checking the CPA properties file because that is where you choose which images to view in CPA’s Classifier.

A potential workaround: in CP, can you use SaveImages to save just the 10th slice (the one of interest) as a separate file? Then you could tell CPA to load that image file in Classifier instead of the original Z-stacks.

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