The ImageJ user guide states:
"[Find Maxima] Determines the local maxima in an image and creates a binary (mask-like) image of the same size with the maxima, or one segmented particle per maximum, marked . Analysis is performed on the existing rectangular selection or on the entire image if no selection is present. […]
Noise Tolerance: Maxima are ignored if they do not stand out from the surroundings by more than this value (calibrated units for calibrated images). In other words, a threshold is set at the maximum value minus noise tolerance and the contiguous area around the maximum above the threshold is analyzed. For accepting a maximum, this area must not contain any point with a value higher than the maximum. Only one maximum within this area is accepted."
I’m interested in the output “Maxima within Tolerance”, which is: “All points within the Noise Tolerance for each maximum.”
Can anyone help me understand how this is different from binarizing a photo using the Threshold function?
In the end I will use the Analyze Particles function to count the number of cells in a photograph. It seems like Find Maxima and Adjust/Threshold are two paths to the same place.
When would I use one, and when the other? I’m having trouble understanding which is best for me and it isn’t yet clear in experimenting what provides better results.
(Threshold: “Use this tool to automatically or interactively set lower and upper threshold values, segmenting grayscale images into features of interest and background.”)
Thanks in advance for all your help!