Posted by
Frederick Ross on
May 12, 2008; 8:13am
URL: http://imagej.273.s1.nabble.com/Plugin-macro-to-calculate-cell-area-perimeter-circularity-automatically-tp3696263p3696264.html
Looking at these images, you are probably going to do at least a lot
of correction by hand, and if you have no programming experience,
you're going to do the outlining by hand. I recommend you get a Wacom
tablet, as it makes it about 25% faster and a lot less fatiguing.
The cells are darker, so a local threshold would be the easiest way to
go about this. I don't know if there is an existing plugin for this,
but there probably is. That might give you seeds for a watershed,
which you can combine with a background cut with a general threshold
(once you flat-field the image).
Automatic segmentation requires very high image quality and an
algorithm specialized to your particular purpose.
On Sat, May 10, 2008 at 2:27 PM, venukesireddy <
[hidden email]> wrote:
> 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
>
> --
> View this message in context:
http://www.nabble.com/Plugin--macro-to-calculate-cell-area%2Cperimeter-circularity-automatically-tp17162804p17162804.html> Sent from the ImageJ mailing list archive at Nabble.com.
>
--
Frederick Ross
Doctorant, SV/GHI/UPKIN, EPFL
Graduate Fellow, The Rockefeller University