I’m quite new to this community so forgive any incompleteness or naiveness of the questions
I have a set of 150 slide scan images acquired using Zeiss Axio Scan. I would like to do some faily basic quantification with basic thresholding and Analyze particles.
The problem I run into is that the size of the .tiff files created by ZEN software’s export function exceeds the dimension limitations of ImageJ (Fiji in my case) that are (as I found on one of the forum posts here) imposed by Java. I have tried various combinations of BioFormats and BigData viewer to no avail.
I tried to circumvent this using QuPath, but if I want to do any sort of ImageJ mediated approach from within the QuPath, I have to downsample by a factor larger than 4 which renders the final file unusable for my application. The only solution that I can think of now is to go and manually chop all the scans into 4 pieces in ZEN Blue, and analyze them separately. This would not in itself be a problem if I didn’t have to do it 150 times over and be extremely careful that I don’t have an overlap between the segments because it will introduce errors into my measurements.
Does any of your brilliant brains have a better idea on how I can solve this problem and not spend weeks in front of a monitor doing a job of a well trained monkey?