Re: automating segmentation counting of synaptic vessicles in TEM

[dpoburko]

Hi All,

   A collegue has asked for help in automating the counting of synaptic
vesicles in TEM images. I was wondering if anyone had any suggestions
for effective means of going about this. I can get pretty clear outlines
of the vessicles with a simple bandwidth FFT, passing the width of the
vesicle membrane. But from there I'm a little stumped as to who to
segment what effectively is a bunch of dark circles with wholes in the
middle. Any suggestions would be appreciated.

Tx,
Damon

--

Damon Poburko, PhD
Postdoctoral Research Fellow
Stanford University School of Medicine
Dept. of Molecular & Cellular Physiology
279 Campus Dr., Beckman B103, Stanford, CA 94305
Ph: 650 725 7564, fax: [phone]

[Prodanov Dimiter]

Hi,

May be you can try Hough transforms? They are supposed to identify circular shapes.

Best regards,

Dimiter

-----Original Message-----
From: Damon Poburko [mailto:[hidden email]]
Sent: Thursday 10 December 2009 02:22
Subject: Re: automating segmentation counting of synaptic vessicles in TEM

Hi All,

   A collegue has asked for help in automating the counting of synaptic
vesicles in TEM images. I was wondering if anyone had any suggestions
for effective means of going about this. I can get pretty clear outlines
of the vessicles with a simple bandwidth FFT, passing the width of the
vesicle membrane. But from there I'm a little stumped as to who to
segment what effectively is a bunch of dark circles with wholes in the
middle. Any suggestions would be appreciated.

Tx,
Damon

--

Damon Poburko, PhD
Postdoctoral Research Fellow
Stanford University School of Medicine
Dept. of Molecular & Cellular Physiology
279 Campus Dr., Beckman B103, Stanford, CA 94305
Ph: 650 725 7564, fax: [phone]