As described in #16 and #19, the settings displayed for the user to adjust should be improved in two ways:
The Small Objects Threshold has a non-linear effect and is therefore hard to tune. Its name is also ambiguous.
The name of the Fiber Threshold and Nuclei Threshold settings are ambiguous, and equivalent settings adjusting the maximum intensity for fibers or nuclei to be detected could be a simple yet nice improvement.
This PR addresses these two problems:
The Small Objects Threshold was renamed to Minimum nucleus diameter (px).
It now drives the minimum equivalent diameter a nucleus must have to be detected. Previously, it was directly driving the minimum area of detected nuclei.
The Fiber Threshold and Nuclei Threshold settings were renamed to Minimum fiber intensity and Minimum nucleus intensity, for more clarity.
Two new Maximum fiber intensity and Maximum nucleus intensity settings were added, symmetrical to the Minimum fiber intensity and Minimum nucleus intensity ones but for maximum intensities.
A check was added when loading the settings.pickle file, so that unrecognized settings are ignored instead of raising an exception.
With this PR, the settings.pickle file now becomes forward- and backward-compatible for versions greater than 1.0.6. Unrecognized settings are ignored, and unprovided one are set to default.
As described in #16 and #19, the settings displayed for the user to adjust should be improved in two ways:
Small Objects Thresholdhas a non-linear effect and is therefore hard to tune. Its name is also ambiguous.Fiber ThresholdandNuclei Thresholdsettings are ambiguous, and equivalent settings adjusting the maximum intensity for fibers or nuclei to be detected could be a simple yet nice improvement.This PR addresses these two problems:
Small Objects Thresholdwas renamed toMinimum nucleus diameter (px).Fiber ThresholdandNuclei Thresholdsettings were renamed toMinimum fiber intensityandMinimum nucleus intensity, for more clarity.Maximum fiber intensityandMaximum nucleus intensitysettings were added, symmetrical to theMinimum fiber intensityandMinimum nucleus intensityones but for maximum intensities.settings.picklefile, so that unrecognized settings are ignored instead of raising an exception.With this PR, the
settings.picklefile now becomes forward- and backward-compatible for versions greater than 1.0.6. Unrecognized settings are ignored, and unprovided one are set to default.Closes #16 Closes #19