Global Scale Automatically Resetting Itself


I am having trouble with Fiji on Windows 7. I have been setting the scale to 10 pixels per 4 micrometers (2.5 pixels/micrometer) and checking the box that says “Global”. If I close the image and use DiameterJ to segment it, the scale is reset to the default (96 pixels/inch). If I reopen the image, I get a message that says “The calibration of this image conflicts with the current global calibration.” I have searched online, and cannot seem to find any troubleshooting tips for this issue. Has anyone else experienced anything similar to this?


Adilm (?),
I’m not a user of DiameterJ, but I don’t think that’s a bug. Rather, it’s a consequence of how DiameterJ is designed. If you look at the documentation, All measures given by DiameterJ are in pixels by default.

Several places in the macro code, it indeed sets a global scale to pixels (i.e., 1 pixel = 1 pixel), so the scale you set and saved with the image (assuming it’s saved in a format that stores the scale!) does conflict with the new global calibration set afterwards by DiameterJ. I believe you can check Disable Global Calibration and ImageJ will keep the calibration saved with the image. See here for one previous discussion.