I’m currently working with czi files on the 0.1.2 version of qupath. This is the first time this issue has occurred. TMA dearrayer can’t detect cores, it only leaves one circle in the middle of the screen.
I was wondering if there is any way of fixing this? If not, would you be so kind to send me script to perform the dearrayer manually?
Please include the QuPath tag in posts so that they can be found more easily. I only saw this one when I woke up and checked all new posts! I added the tag for now.
I recommend creating a fixed sized TMA, which you can see here.
Your whole slide scanner looks like ours before we cleaned, white balanced and maybe replaced the bulb. IE, the background is too dark.
The other possibility is that the size is very sensitive, and even 0.1mm can make a big difference in the detection. Though, I suspect it is the background.
Also check the image type under the ‘Image’ tab. If it doesn’t say brightfield, double-click to change that.
Thank you, I sent the slides for re scanning to get the background lines out of the image. I completely forgot to check the image type so I suspect that could be why dearraying didn’t work. Thank you.