Measurement map shows different outputs between slides of same project

Hello! I’ve been running projects containing ~13 slides for different stains for a few months. Recently, I ran into a problem where the output for positive pixel count that I expected changed between slides. For example: instead of receiving Stained area, I received stained pixels. All of the headers changed and I’m unsure as to how to get similar outputs. I tried to check the measurement manager to see if I could change something, but did not have any options there. When I get a final file, I end up with a lot of NAs in columns where there should be data.

How would I be able to change the output to be the same?

Thank you!

It sounds like perhaps one image is missing the pixel size information in microns.

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Oh, okay. I attached a picture of what output I’m getting if that helps. Would you know how I would be able to overcome this and get the same output for all of the slides in my project. It isn’t just one slide, but rather 7 or 8 out of 13.

Thank you so much! image

As Pete said, if you don’t have the same data input, you won’t get the same data output. Without QuPath being given any information on how large each pixel is, it will not be able to output the areas in square microns. If you know the pixel areas but aren’t able to create the images in the same way, you might want to create two different projects and then create an additional spreadsheet column with a conversion to or from pixels so that all of your data is the same type.

Or basically, if you want the columns to all be the same, the images also need to all have metadata, or all have no metadata. There are several other posts on metadata around the forums.

If you think you are adding the same types of images into the project, then something is likely going wrong on the image creation end.