Login  Register

Plugin/ macro to calculate cell area,perimeter circularity automatically

Posted by venukesireddy on May 10, 2008; 12:27pm
URL: http://imagej.273.s1.nabble.com/Plugin-macro-to-calculate-cell-area-perimeter-circularity-automatically-tp3696263.html

Dear experienced list memebrs ,

I am looking for a plugin /macro which can automatically identify cells in a phase contrast image ( often the quality of the image is not good, uneven illumination etc)  calculate cell area shape and perimeter,circularity for each and every cell in the image, and also give a statistical distribution of cells parameters say x% of cells have this characteristic and y % cells have another characteristic and so on..


I am a newbi to Image J and i have no programming experience so I would be very glad if you can provide a step by step protocol of how to to use such a plugin and macro.

From the littile things i have tried I can find the edges of the cells  (ImageJ-process-find edges) but do not know how to proceed furthur, I can draw Region of Interset ( ROI) with free hand selection tool then I can calculate area, perimeter ,circularity etc but in this case I have to manually draw the ROI around each cell (very laborious work). So if I can do everything automatically it would be of great help.
  Alternatively I have come across another program called " cell profiler" but this program is bit complicated for me to learn. As I do not know exactly which modules to apply it is giving error messages and I have no experience with it. Any suggestions on how to use this are also highly appreciated.

Here I am giving links to some example images taken at low magnification and low resloution camera.

Download-Link #1: http://rapidshare.com/files/113891406/0____Control_cells.avi.html

Download-Link #4: http://rapidshare.com/files/113891409/1___control_cells.tif.html

Download-Link #5: http://rapidshare.com/files/113891410/2___mir_3.tif.html

Download-Link #2: http://rapidshare.com/files/113891407/2____mir2.avi.html

the avi files contain single images ( i can open them with AVI reader plugin)


sincerely
venu