I have been having this issue for a while, and I could not find previous reports of it.
Since the “Report Bug…” feature in FIJI is not working, I can’t provide full details of my install here. Working in Windows 8.1. I tested it with a freshly downloaded 64-bit Windows FIJI, ImageJ 1.52c and got the same result:
To reproduce bug:
Open the sample image M51 Galaxy (16-bit)
Draw a rectangular selection around a visible feature. The selection should not start in the top left corner.
Crop the image using either Ctrl+Shift+X or using the menu
FIJI crops the image to the size of my selection, but shifts the cropped region to the top left corner. As a result, the selected feature is not in the cropped image. In the galaxy sample file, I end up with a black crop.
This happens with every 16-bit grayscale TIFF image, and has been happening in the current and previous version (1.52b and 1.52c). I am not sure when exactly the bug appeared.
Please let me know if important information is missing, or if I missed a previous report of this issue.