Present by: Xinyu Chang Email:xchang@kent

Smart Markers for Watershed-Based Cell Segmentation

Can Fahrettin Koyuncu1, Salim Arslan1, Irem Durmaz2, Rengul Cetin-Atalay2, Cigdem Gunduz-Demir1*

Present by: Xinyu ChangEmail:[email protected]

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

(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

3 types of 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 elimination1. Eliminate narrow dark

pixel regions around the boundary.

2. Majority filter3. Fill holes under

certain area4. 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 extractionFor dark pixels and dark-center pixels

Smart marker extractionFor Bright pixels

1. Dilate to get rid of the boundary2. A bright pixel cell has a circle area beyond a

threshold

Result and comparison

Thank you