(no subject)

[mohamed kenawy]

Hello all,
I am new with ImageJ. Can someone help me how can I count the number and sizes of the air bubbles in this slide ?
Is there a way to extrapolate the results on an Excel sheet ?
Regards,
Kenawy.

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[nhotaling]

Hello Mohamed,

I'd suggest looking into image segmentation techniques that are used in
ImageJ.  A couple great links are http://fiji.sc/Segmentation and
http://ij-plugins.sourceforge.net/plugins/segmentation/ .  Because you have
uneven back lighting I'd probably go for "local" thresholding/segmentation
techniques.  Your general procedure would look something like, convert your
image into an 8 bit (grayscale) tif file. Select your region of interest.
Segment using a variety of algorithms (whatever works best).  Remove noise,
and errant bubbles from image.  and then. depending on how you segment, the
air bubbles will come out as white or black.  If they are black, then
great, use the analyze particle function in ImageJ and you'll get all the
information you need about them.  If they are white, select your area of
interest and invert the image.  Then use the analyze particle command.

Its going to be a lot more work than it sounds to do that.  But try
Googling/searching the forum for segmentation and/or thresholding, ROI
(regions of interest), analyze particle, and noise removal.  If you have to
do this on many images also google macro creation in ImageJ and batch
processing in imagej.

Good luck!

Nathan

On Fri, Mar 27, 2015 at 9:03 AM, mohamed kenawy <
[hidden email]> wrote:

> Hello all,
> I am new with ImageJ. Can someone help me how can I count the number and
> sizes of the air bubbles in this slide ?
> Is there a way to extrapolate the results on an Excel sheet ?
> Regards,
> Kenawy.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

Hi Kenawy,

the following macro may serve as a starting point (beware of line breaks that may be introduced by the mailer; all lines should be indented by two spaces)

  run("32-bit");
  run("Subtract Background...", "rolling=200 light sliding");
  run("Enhance Contrast", "saturated=0.35");
  run("8-bit");
  setOption("BlackBackground", false);
  setAutoThreshold("Triangle dark");

  //the following assumes that the op and bottom of the image is not of interest and deletes it
  doWand(0,0, 0.0, "8-connected");
  run("Set...", "value=0");
  doWand(0, getHeight()-1, 0.0, "8-connected");
  run("Set...", "value=0");

  run("Select None");
  run("Analyze Particles...", "size=3-Infinity show=Masks display clear include");

You may try to vary the parameters, e.g. the size range of "Analyze Particles" and the rolling radius of "Subtract Background".

You may also try the Trainable Weka Segmentation (if you have Fiji, not plain ImageJ).

Michael
________________________________________________________________
On Mar 27, 2015, at 14:03, mohamed kenawy wrote:

> Hello all,
> I am new with ImageJ. Can someone help me how can I count the number and sizes of the air bubbles in this slide ?
> Is there a way to extrapolate the results on an Excel sheet ?
> Regards,
> Kenawy.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html<Nanozoomer PTK.tif>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html