http://imagej.273.s1.nabble.com/Plugin-macro-to-calculate-cell-area-perimeter-circularity-automatically-tp3696263p3696265.html
Thanks for your mail. I tried the following
open image, find edges(process-find edges) adjust threshold (image-adjust -threshold) and then choosing analyze particles (analyze-analyze particles) this seems to work , but ofcourse my images are not high quality , so with better images it might work better. But even with higher qualty images there may be uneven illumination so uneven background , so how should I adjust the threshold locally ( if that is what you mean). What would be the best magnification for taking a overview of many cells at time 10X or 20X. The images that I uploaded are taken with 4X and a low reslotion camera attached to the mini microscope in cell lab. Now i will try with standerd microscope.
> From: Frederick Ross <
[hidden email]>
> Subject: Re: Plugin/ macro to calculate cell area,perimeter circularity automatically
> To:
[hidden email]
> Date: Monday, May 12, 2008, 11:13 AM
> 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
____________________________________________________________________________________
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