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Showing posts from April, 2014

Basic cell counting and segmentation in Matlab

Counting cells manually is a tedious error prone process for humans. Given a large data set of microscopy images this task can be achieved much faster by means of basic computer vision techniques. In this tutorial we will segment cells from an image following a method similar to the one presented by Yongming Chen in 1999. The method uses basic morphological operations and the watershed algorithm to segment the cells. Nowadays better methods for cell segmentation exist. This method was chosen for its simplicity and ease of implementation.

We start with an image of cell-like structures by Anna-Katerina Hadjantonakis and Virginia E Papaioannou.

A = imread('cells.jpg');
We convert the image to grayscale:
I = rgb2gray(A);

To be able to extract the dimmer cells, it is necessary to perform some local contrast adjustments
I = adapthisteq(I);


Objects on the borders can be caused by noise and other artifacts. We can eliminate objects on the borders of the image like this:
I = imclearborder(…