I am very new to image analysis using Fiji and would appreciate your help a lot.
I have over 30 images of embryonic mouse tails and I need to count macrophages on each z-stack. Each image have 24 z-stacks and 2 channels. I have a set workflow where I arrange threshold, brightness and colour etc. To avoid bias, for each image and for each z-stack I am using the same B&C and same auto-threshold (Intermodes). However it is very time consuming to go over each z-stack of each image and currently is taking me a day per image but I need to do all my data analysis in a very short time period.
How can I automatically do this type of counting per each z-stack using the same settings?
My analysis goals is to count macrophages on each z-stack for each image using the same threshold/B&C/etc.
Thank you for the help!