hi, I have used FV3000(Olympus) to scan the mouse brain slices and I am trying to find the best step size of Z section to get a good quality of image as well as save time. I tried to used the step size of 1.8, 1.5, 1, 0.8, 0.5 for the same region (Midbrain, i used tyrosine hydrolase to stain dopamine neurons), and they have different slices due to different step size. (step size 1.8 has 25 slcies, 1.5 has 31, 1 has 46, 0.8 has 58, 0.5 has 93). But when i open them in Fiji ImageJ, they all have 25 slices and the quality of the images look similar. I don't know what happen. Can anyone help me with this problem? Thanks.
I suggest you follow this thread https://www.researchgate.net/post/How_to_Confocal_image_analysis_on_FIJI_ImageJ
See also https://confocal.uconn.edu/wp-content/uploads/sites/1081/2016/02/2014-05_Analyzing_fluorescence_microscopy_images.pdf
Ummmm...it's very unusual that this is happening. Usually reading z-stacks in image J is very straight forward. May be update your Image J version or re-check if the saved files have not be overwritten by the 1.8 stepwise stack.
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