Hi, I have been trying to analyze an image for positive cell detection in the new version of Qupath but it is unable to do so. However when I tried to use an older version-0.1.2, it worked. I am interested in using the new version for all my analysis, how do I do it?
I think more information will be needed here.
You haven’t given any information about what the project is, whether you converted the project from a 0.1.2 project to a 0.2.0 (File menu), if you started a completely new project with the same images… or much else, like what error messages you are getting. Please provide more info
The project is to detect positive and negative cell detection-CD8 and CD20 for B cells and T-cells. I am new to Qupath and started working on the version 0.2.0 .
The process followed was simple-open the image, set the stain and analyze for positive cell detection. So, when I opened it on this version, it could analyze the slide i.e., the positive and negative cells were not highlighted(purple and pink stain). I then downloaded the version 0.1.2 the sample analysis with detection worked. However, I want to use the latest software but as mentioned it is not working.
Hope this information helps or else will be willing to provide any other information you need.
Sorry, this is a bit confusing and you still have provided no screenshots or images (as mentioned by the forum when you create a post for the first time). Can you show that you were using the same settings in both versions, and that the image data was being read in the same way (Image tab)? Is the Image Type the same in both cases?
If you are using an image type that can be opened by both BioFormats and Openslide, which server is being used for 0.2.0 where things don’t work?
Also, you still have not said exactly what wasn’t working. Highlighting you can turn on and off yourself. Were the cells generated? Are they classified? Were you using the same threshold for classification?
The first screen shot is on version 0.1.2 where it was able to positive detect the sample, the same image on version 0.2.0 could not.
The work flow is File—Open—The image opens in the software—Select Analyze----select positive cell detection—Run
Not sure if it is just me, but I do not see any images hosted.
From the specific steps you listed, you would not expect to get any cells. You need an annotation object to find cells within. This has not changed between 0.1.2 and 0.2.0, though.
Generally speaking, I recommend doing all analysis within a project, unless you are just testing something and intend not to save any results.