
Hi Daniel,

 

I don't really think that it is a BioC related question, nevertheless here are my comments.

 

Have you tried ImageJ?

There is a version with many plugins in MacBiophotonics. Just for free:

 

http://www.macbiophotonics.ca/downloads.htm

 

If you are using an automatic slide in your microscope, in my case a Leica microscope, you can take many photos of all an area, an the Leica program puts one next to the other automatically. If you want take a photo of all the slide (23x76mm), you should take photos at 10x. If you are taking photos from a core (2mm diameter) you can take them at 40x.

 

If you have big images [100-300 Mb] (as the one obtained after taking 56 photos at 40x from a core of 2mm diameter and joined together to form a unique image), I would recommend to work under a 64bits platform and get a minimun of 4Gb of RAM. If it is not the case, you can work under a 32bits system, with quite less RAM.

 

Good luck!

 

Jordi Altirriba

Hospital Clinic

Barcelona

Spain

 

Message: 4
Date: Wed, 22 Jul 2009 14:48:10 +0100
From: Daniel Brewer <daniel.brewer@icr.ac.uk>
Subject: [BioC] Software to find the area of a shape in an image
To: Bioconductor mailing list <bioconductor@stat.math.ethz.ch>
Message-ID: <4A67189A.2050304@icr.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1
 
Hi,
 
We have a series of tissue slices that have tumour within them and we
would like to quantify the area within each slice that is occupied by
tumour. Is there a cheap or free program that will assist in this?
either by automatically looking for colours or for a user to manual draw
round a shape and it give you the area?
 
Not exactly bioconductor related but the idea is to quantify this and
then do various bioinformatics on it. Hope you forgive me.
 
Thanks
 
 
Dan
 
-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer@icr.ac.uk
**************************************************************

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