QuPath misses cells in cropped image that were detected in full image


I’m running cell detection in QuPath and I see differences when I run it on a full image vs. a cropped region:

It detects additonal cells in the full image, even though the same local information is present in the cropped image; they’re both 8-bit and I did not re-scale intensity or anything like that.

Cell detection settings:
requested pixel size: 0
background: 8
median filter: 0
sigma: 1.5
min. area: 10
max. area: 75
threshold: 1
split: yes
expansion: 0
include nucleus: yes
smooth: yes
measure: yes

Any ideas why this occurs and how I can ensure consistent results? Thanks!


It is most likely the variation in the tiling.

There are a few more posts like this but I failed to quickly dig them up. If you change the image, you change the tiling, and may not get the same results, at least as far as I understand it.