Smart Markers for Watershed-Based
Cell Segmentation
Can Fahrettin Koyuncu1, Salim Arslan1, Irem Durmaz2, Rengul Cetin-Atalay2,
Cigdem Gunduz-Demir1*
Present by: Xinyu Chang
Email:xchang@kent.edu
Marker-Controlled Watershed Segmentation
The watershed transform is often applied to separating
touching objects in an image problem.
The watershed transform finds "catchment basins" and
"watershed ridge lines" in an image by treating it as a
surface where light pixels are high and dark pixels are low.
The watershed transform works better if you can identify,
or "mark," foreground objects and background locations
3 types of pixels
(1) Bright pixels, pixels region with high intensity.
(2) Dark-center pixels, pixels with low intensity
fully surrounded by bright pixels
(3) Dark pixels, , pixels with low intensity partially
surrounded by bright pixels
4 types of cell
(1) Bright pixels represent type I cells and boundary.
(2) Dark-center pixels for type II cells
(3) Dark pixels for both type III (darker none circular
cell )and type IV (apoptosis)
Process chart
Otsu thresholding with Sobel operator
In order to apply a Otsu
thresholding to obtain
all the foreground, yet
the dark pixels would
not get lost. With a
Sobel operator The
gradient has been take
into consideration.
Dark pixels regions is defined as intensity smaller than
the Threshold of Otsu and larger than k・tsobel
Noise and artifacts elimination
1. Eliminate narrow
dark pixel regions
around the boundary.
2. Majority filter
3. Fill holes under
certain area
4. Erase dark pixel
region without any
bright pixel
Majority filter
The Majority Filter tool has two criteria to satisfy before a replacement
can occur: the number of neighboring cells of a similar value must be
large enough (Majority or Half), and those cells must be contiguous
about the center of the filter kernel. The second criteria concerning
the spatial connectivity of the cells minimizes the corruption of cellular
spatial patterns.
Smart marker extraction
For dark pixels and dark-center pixels
Smart marker extraction
For Bright pixels
1. Dilate to get rid of the boundary
2. A bright pixel cell has a circle area beyond a
threshold
Result and comparison
Thank you