Posted by
Allison Hall on
Jan 21, 2007; 11:53pm
URL: http://imagej.273.s1.nabble.com/Segmentation-troubleshooting-tp3700540p3700541.html
Thanks for the response,
We are actually interested in quantifying the amount of perfusion
(viable blood vessels) within the tumour or tissue section, not
specifically looking at the individual structures. Is your suggestion
applicable to this?
Our images were originally saved in bmp format, and the composite image
is also saved as a bmp. You mention never to use mosaics, is this also
the case for quantifying vessels??
Allison Hall
Research Assistant
Cancer Drug Discovery Group
Bionomics Limited
31 Dalgleish Street
Thebarton SA 5031
Phone: +61 8 8354 6190
Fax: +61 8 8354 6199
Email:
[hidden email]
Website: www.bionomics.com.au
ABN 53 075 582 740
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
Karsten Rodenacker
Sent: Friday, 19 January 2007 7:23 PM
To:
[hidden email]
Subject: Re: Segmentation troubleshooting
Hi,
you show interesting examples.
Allow me some remarks:
1. Seemingly you have used images which were originally stored in
jpeg format with relatively low quality. I think you should improve
the quality considerably if the vessel structure is of interest.
2. Vessel structure of the control seems similar to the vessel
structure in the treated case INSIDE some lets call it hot (cold?)
regions or patches.
3. For characterizing structures never use mosaics from beginning!
For differentiation of tumour and non tumor regions it should be
clear which clues should be used or are of importance e.g.: micro-
structure(texture), macro structure and/or isolated events ...:
I recommend math morphology: (see plugin graymorphology)
microstructure: grayscale tophat transformation radius 2, circular):
original minus open(radius 2); threshold
macrostructure: vessel free or vessel rare zones: inversion of
closure (radius 4-5, circular) of the microstructure; threshold
isolated events: difficult in control, bright spots in treated.
Seemingly in control there are spots like in treated, slightly
larger, but with finer vessel structure.
Good luck,
KR
Am 19.01.2007 um 01:10 schrieb Allison Hall:
> Image J to quantify functional fluorescently
Karsten Rodenacker
-------------------------------------------------------------------- :-)
GSF - Forschungszentrum Institute of Biomathematics and Biometry
D-85758 Oberschleissheim Postfach 11 29
Karsten.Rodenacker_AT_gsf.de |
http://ibb.gsf.de/http://ibb.gsf.de/homepage/karsten.rodenacker/Tel: +49 89 31873401 | FAX: ..193401