Hello, I am somewhat new to using imageJ for scientific analysis. I am quantifying images taken of tissue IF stains on a confocal microscope. I quantifying dapi on 10x images so I created a square selection that I have saved and have been applying to each image to assure the hpf I quantify is the same in each image. However, I am encountering an issue. It seems within my set of images some are opening up at a 75% zoom while others are opening up at a 33% zoom. I took all images at 10x and am confused at why this is occurring. The selection was created on the 33% images, and when i apply to the 75% images it looks larger. Is it okay to quantify 75% images with this selection? Is there a way to make them all open up on the same zoom percentage? I tried setting the 75% images to 33% and they get really small. Thanks in advance!
If the image has more pixels than your monitor, Fiji will decrease the zoom level by default so that you can see the entire image. (Note, the optical or digital zoom settings you used on the microscope are irrelevant… it only matters how many pixels are in the image).
Zoom in ImageJ doesn’t affect the underlying data in any way and will not affect your analysis… it’s just how the image looks on the monitor.
The only thing that might be relevant here is to make sure that you are aware of the absolute area in your sample represented by a given region in the image (by taking not of the pixel size calibrations, etc…).