[BioC] Software to find the area of a shape in an image

[Oleg Sklyar]

Well, it is not a bioconductor question, but depending on data analyzed it can be a
very relevant question. If you work in R and want to integrate image analysis and object
detection into your R-script workflow, then the above mentioned EBImage is something you
should try. It contains numerous examples, on object detection and feature extraction as 
well.

It incorporates pretty much everything of CellProfiler and many functions found in ImageJ
adding a bunch of its own. The best side of it is that you can actually script any
of the analysis and image processing so that you can apply it to thousands of images
objectively. Well, this can also be seen as its worst part -- apart from image display
and browser there is no GUI, it is all scripting ;) Runs on any platform tested so far,
MS Windows, Linux 32/64bit, MacOS both from source and as binary.

We developed it to analyze full genome microscopy assays with more than 500K images.

The memory point is valid: you will probably need a 64bit Linux system to run any large-scale
image analysis due to memory requirements, but this is up to you, this is not a problem
of any particular software.

Best of luck,
Oleg 

Jordi Altirriba Gutiérrez wrote:

> 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.
>
>  
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> Good luck!
>
>  
>
> Jordi Altirriba
>
> Hospital Clinic
>
> Barcelona
>
> Spain
>
>  
>
> Message: 4
> Date: Wed, 22 Jul 2009 14:48:10 +0100
> From: Daniel Brewer <daniel.brewer at icr.ac.uk>
> Subject: [BioC] Software to find the area of a shape in an image
> To: Bioconductor mailing list <bioconductor at stat.math.ethz.ch>
> Message-ID: <4A67189A.2050304 at 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
>  
>