Plugin/ macro to calculate cell area,perimeter circularity automatically

[venukesireddy]

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

[Frederick Ross]

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

[venukesireddy]

Hi Frederick Ross,

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.

Do you have any comments and suggestions on this.

sincerely
venu

--- On Mon, 5/12/08, Frederick Ross <[hidden email]> wrote:

> 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

      ____________________________________________________________________________________
Be a better friend, newshound, and
know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ