algorithms for detecting fluorescently labeled nuclei in microscope images
operator supports different detection modes based on binary morphology
output data are masks of detected nuclei and statistical measures
Input image
the single-channel image to be analyzed
if the image contains multiple channels, only the first one is processed
Operator mode
mode to use for detection, each mode subsumes a specific list of thresholding and morphological operations
the default mode OTSU OPENCLOSE has proven most reliable, but the results are highly data specific - probably some tests with different settings are necessary to achieve satisfactory results on your data
available modes:
OTSU OPENCLOSE: combines Otsu thresholding with opening and closing operations
OTSU ERODEDILATE: combines Otsu thresholding with erosion and dilation operations
NIBLACK: applies Niblack thresholding and morphological post-processing
Min. nuclei size
minimum size of nuclei regions in pixel, smaller regions are removed
Apply morpholigical operations
disables/enables morphological post-processing
if disabled nuclei images are only thresholded, small regions are removed and holes are filled
Masksize
mask size of squared structuring element for morphological operations
Fill holes
enables/disables hole filling in nuclei regions after thresholding
Niblack operator
thresholding operator to be used in mode NIBLACK, see Niblack Thresholding for details
Units
currently not used
Verbose
disables/enables output of additional messages on console