algorithms for detecting fluorescently labeled nuclei in microscope images
operator supports different detection modes combining binary morphology, local contrast enhancement and active contours
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
CONTRAST ANALYSIS: applies a local contrast-enhancement to the image and then does an Otsu thresholding followed by some post-processing;
for details on the contrast enhancement see section Locally Adaptive Contrast Enhancement for details
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
not used in CONTRAST ANALYSIS mode
Masksize
mask size of squared structuring element for morphological operations
not used in CONTRAST ANALYSIS mode
Fill holes
enables/disables hole filling in nuclei regions after thresholding
not used in CONTRAST ANALYSIS mode
Niblack operator
thresholding operator to be used in mode NIBLACK, see Niblack Thresholding for details
Operator for local contrast improvement
operator for locally adaptive contrast enhancement, refer to section Locally Adaptive Contrast Enhancement for details on the operator
Note: if the operator is not applied in component-wise mode (which is the default), processing an image may take up to a few minutes...
Try Nuclei Separation
applies one of the operators for nucleus region separation to the binary nuclei mask to re-split nuclei regions which might have been merged during prior detection steps
Nucleus Separator
the operator for separation to be applied;
for details, refer to section Nucleus Region Separation
Units
currently not used
Verbose
disables/enables output of additional messages on console