Image segmentation based on finding the maximum mean intensity path

The program finds the membrane in a fluorescence image using a modified Dijkstra algorithm.

The program can be used for detecting the cell membrane in microscopic images in which the cell membrane is stained. The user must provide the coordinates of a couple of seeds placed on the membrane. The program finds the maximum mean intensity path between the seeds using a modified version of Dijkstra's algorithm (https://en.wikipedia.org/wiki/Dijkstra%27s_algorithm).
The package contains four files:
1. allBorders=determineAllBoundaries(imagedata,vertices)
Determines the cell membrane in cells in an image.
imagedata - a 2D array of pixel intensities
vertices - a cell array in which each cell contains the coordinates of seeds placed on the membrane of a cell
allBorders - a cell array in which each cell contains the coordinates of membrane pixels of a cell
2. bestPathXY=calculateOneMembrane(imageData,allPointsXYForOneCell)
Determines the cell membrane of a single cell.
imageData- a 2D array of pixel intensities
allPointsXYForOneCell - a 2-column matrix with every row corresponding to the coordinates of a seed
bestPathXY - the XY coordinates of membrane pixels of a single cell

3. bestPathXY=findMaxMeanPath_DijkstraNagy(imageData,startXYorig,endXYorig)
Determines the maximum mean intensity path between two points in an image.
imageData - a 2D array of pixel intensities
startXYorig , endXYorig - the X-Y coordinates of the two points between which the maximum mean intensity path is to be determined
bestPathXY - the XY coordinates of the maximum mean intensity path.

4. testdata.mat - containing an image and another file defining the seeds for two cells in the image.
The program can be tested with the following command using the data in testdata.mat:
allBorders=determineAllBoundaries(imagedata,vertices);

A GUI-controlled version of the application is available at
http://peternagy.webs.com/image-analysis-with-matlab
http://peternagy.webs.com/Matlab/DijkstraNagy/DijkstraNagy.p