Re: Segmentation and analysis of silver grains in TEM image

Posted by Jacqueline Ross on Apr 08, 2011; 12:28am
URL: http://imagej.273.s1.nabble.com/Segmentation-and-analysis-of-silver-grains-in-TEM-image-tp3685041p3685047.html

Hi All,

Sorry all. I am unable to send to the listserver the PDF which
demonstrates the approach I have taken so far. If anyone is interested,
please contact me offlist.

Thanks!

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
Jacqui Ross
Sent: Friday, 8 April 2011 12:02 p.m.
To: [hidden email]
Subject: Segmentation and analysis of silver grains in TEM image

Dear All,

 

I recently had an enquiry from a researcher outside my institution
regarding analysis of silver grains in a transmission electron
micrograph.

 

I have attempted to assist this person but have not been able to obtain
the information that they are looking for although it's been interesting
trying!

 

The original bmp image sent to me by the researcher is attached
(Fig1.bmp). They want to analyse the dense black spots, which are silver
grains and find out the following;

 

How many grains/spots are there?

What size is each grain/spot?

 

They also want to define regions of interest (ROIs) and count the number
and size of the spots in specific locations within the image. You will
note that there are areas where the grains/spots are larger and in
higher density.

 

I found it impossible to segment out the spots using thresholding based
on grayscale because there are some ER fibres running behind the spots
in some places, which are of similar gray value to some of the smaller
grains/spots. I have attached a JPG image with a region drawn on it to
indicate where the problem lies. Also, some of the smaller less dense
grains are similar in intensity to these fibres.

 

I haven't managed to confirm the source of the image, e.g. film, etc.

 

All of the files that were sent to me are .bmp not TIFF.

 

So far, I have managed to count the number of grains/spots by using the
Find Maxima option. But I can't get any information on the size of each
spot using this method. I have attached some instructions showing my
approach.

 

I hope that someone will be able to provide a better solution....

 

Any assistance would be much appreciated.

 

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/