Hi, I am trying to create binary mask across Z timepoints. I googled and read that it can be doned using Image -> Adjust -> Threshold and Process -> Binary -> Convert to mask. However, this are not returning the right mask. After adjusting my threshold i get this.
Hi and welcome to the forum,
the first image is already the binary mask.
A binary mask is simply an 8-bit image where there are just 0 and 255 values with the 255 grey value being the 1 thus the foreground or objects of interest.
I would suggest also to use a filter before you do the thresholding, depending on the application either a Gaussian Blur or a Median Filter (https://imagej.nih.gov/ij/docs/menus/process.html#filters). It avoids these fuzzy segmentations that you have there especially at the edges of your objects.
For using thresholding and binary options properly, make sure you have the settings under control that influence the outcome:
Edit > Options > Colors…
Set forground to white and background to black
Process > Binary > Options
Tick the box Black background.
When you perform
Wich options did you ticked ?