How to count particle in a stack under different background brightness for beginner

Hello guys, I am a beginner and I am counting particle and their position in a stack, but now the problem is that the background brightness is different in each slice that I can not set a suitable threshold for whole stack. Do You know how to solve this or how to choose a suitable threshold for each slice automatically?
Thanks a lotpic001.tif (2.2 MB) pic002.tif (2.2 MB)
Here is the sample of different slices, Thanks!

This plugin homogenizes the brightness of a stack, aligning distribution functions of image pairs:

https://imagej.nih.gov/ij/plugins/stack-contrast/index.htm

It is designed for images captured by a confocal laser scanning microscope but I think it can also work on your images as appear a sequence of a flow and image pairs are similar locally.

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Cool BORJA,
Thanks for the heads up.
Bob

Hello! I’m also working with stacks and I need to quantify the signal at a particular position and make the calibration bar to show how often/how many slices a signal can be found in a particular position. Would you mind sharing how you take note the position of the signal?

Thanks BORJA, that’s quite useful!

Hello, ojacopiado. For take the position, you should Analyze-set measurement, and then choose centroid, which can give you the position of particle