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.htmlDownload-Link #4:
http://rapidshare.com/files/113891409/1___control_cells.tif.htmlDownload-Link #5:
http://rapidshare.com/files/113891410/2___mir_3.tif.htmlDownload-Link #2:
http://rapidshare.com/files/113891407/2____mir2.avi.htmlthe avi files contain single images ( i can open them with AVI reader plugin)
sincerely
venu