Change in measurements after Fiji update

I did some fluorescence analysis on FIJI a few weeks ago and went back to it today, after updating FIJI, and the measurements are coming out differently. They aren’t just different hugely different numbers (8.5 v 92.2), but the intensity ratios between two comparable images isn’t the same either?

I’ve kept the threshold the same before I have created the selection, so that shouldn’t be the issue.

Example 2

It seems you are not replicating the exact same measurement, given that e.g. the measured area (IntDen divided by Mean) is very different between the two results tables. In general, you can use Plugins > Macros > Record... to record which ImageJ/FIJI-commands were used to obtain a certain measurement result and with this reproduce measurements later more easily.


To me it looks like as if in your image you actually selected the background instead of the foreground (you see this because of the yellow line around the outer border of the image). This can happen if you determined the selection via a binary image or a thresholding and your background settings are different (►Process ►Binary ►Options…, here the black background option decides which part of the image will be thresholded as foreground and background when creating binary images). Another potential mistake could be that you (de)select dark background when performing a manual thresholding from which you deduce your selection.

Since one of your two separate measurements does not show the selection area it is not possible to determine if your selection is exactly of the same size. Potentially you can always switch on all measurements (►Analyze ►Set Measurements…) to get a consistent output table to check this.


I feel like such an idiot, thank you so much!