Re: Segmentation and analysis of silver grains in TEM image

Posted by Jacqueline Ross on Apr 12, 2011; 3:10am
URL: http://imagej.273.s1.nabble.com/Segmentation-and-analysis-of-silver-grains-in-TEM-image-tp3685041p3685045.html

Dear Gabriel, Michael and Chris,

Thanks very much to you all for your suggestions. I have run the 2
macros written by Chris and Gabriel and they both work quite well so I
will send them off to the researcher who sent me the data. It's always
interesting to see different approaches to the same problem.

I've also had a play with the Versatile Wand as per Michael's suggestion
but this isn't working quite as well as I would like, since it's a bit
fiddly to get the right selection, however I can see it will be really
useful for other tasks.

I also had a look at other Top Hat filters as suggested by Gabriel and
Michael and came across the Lipschitz filter
(http://rsbweb.nih.gov/ij/plugins/lipschitz/) that also seems to work
very well for this data with the default setting (Slope 10.00, Top Down
and Top Hat) selected.

We don't have the Soille book but I managed to find a paper by Soille,
which covers the grayscale reconstruction mentioned by Gabriel.

Thanks very much to anyone/everyone who put effort into looking into
this analysis problem. As usual, the responses have been very helpful
and I have learnt more myself in the process...!

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Gabriel Landini
Sent: Saturday, 9 April 2011 2:34 a.m.
To: [hidden email]
Subject: Re: Segmentation and analysis of silver grains in TEM image

On Friday 08 Apr 2011 14:35:46 you wrote:
> just to give you one more pointer: You can get a top-hat filter by
> Process>Math>Min and then Max, both with the same radius (or other
> way around, first Max, then Min, if your foreground objects have lower

> pixel values than the background as in the sample images).

What is described above is closing and opening in greyscale. One more
step gives you the traditional top hat: subtract from the original the
result of the above.

> Nevertheless, I could not get a decent removal of the fiber background

> with any of these.

I attached the result of:

1. Applied gaussian blur of size 1
2. Greyscale black top hat by reconstruction (see below, following
Soille's
book)
3. Stretched the greyscale so the result can be seen

Step 2 is the following (and requires the Morphology collection
installed)

// GreyBlackTopHatByReconstruction
// G. Landini at bham. ac. uk.
// 1/Oct/2010
setBatchMode(true);
a=getTitle();
run("Duplicate...", "title=_seed");
run("Maximum...", "radius=2");
run("Invert");
selectWindow(a);
run("Invert");
run("GreyscaleReconstruct ", "mask="+a+" seed=_seed create");
selectWindow(a); run("Invert"); selectWindow("Reconstructed");
run("Invert"); rename("BlackTopHatReconstructed");
imageCalculator("Subtract", "BlackTopHatReconstructed",a);
setBatchMode(false);
//------

Cheers

Gabriel