I have posted this also on GitHub (#2035 on GitHub), but when I didn’t get any response there I also try to post it here.
I have tried to do a new pull request but it seemed like I didn’t have permission send it. How is the procedure for pull requests?
This one is about an Object Feature based Gray-level Threshold using optimized global precision. It computes the threshold level that optimized the global precision with regards to a given expected object size range.
Implemented from Ranefall P and Wählby C, “Global Gray-level Thresholding Based on Object Size”, Cytometry Part A, 89:4, 2016, pp. 385-390. In this paper we show that the method performs better that all global threshold methods in CellProfiler and ImageJ, given that you can input a range of expected object sizes.
In my pull request I have incorporated it into ApplyThreshold, IdentifyPrimaryObjects, and IdentifySecondaryObjects.
The following files are modified: applythreshold.py, identify.py, threshold.py, test_threshold.py
New files: sizeintervalprecision.py, _sizeIntervalPrecision.c
Earlier I have been in contact with Lee regarding a plugin based on this, but it would be nice to have it integrated into the IdentifyPrimaryObjects and ApplyThreshold modules.