[ome-users] Image coordinate reference

[Ghislain Bonamy]

Melissa,

Thanks a lot for the info. 

From, your email, I understand that although no standard has been
defined, so far the default has been 0,0=top-left.

My reason for thinking that 0,0 is at the bottom left is due to the old
habits of math (geometry, calculus etc.), but it does not matter to me
as long as some sort of convention is adopted in the OME standard. 

In addition, perhaps this questions points out a greater need to allow
users to provide a place where they can define non standard coordinate
systems.

Best,

Ghislain Bonamy, PhD
__________________________________________
Research Investigator

Genomic Institute of the
Novartis Research
Foundation
Department of Molecular & Cell Biology, room G214
10675 John Jay Hopkins Drive
San Diego CA 92121
USA

+1 (858) 812-1534 (W & F)
+1 (757) 941-4194 (H)
+1 (858) 354-7388 (M)
www.gnf.org

Hudson-Alpha Institute for Biotechnology
www.hudsonalpha.org


-----Original Message-----
From: Melissa Linkert [mailto:melissa at glencoesoftware.com] 
Sent: Wednesday, June 10, 2009 1:49 PM
To: Ghislain Bonamy
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Image coordinate reference

Hi Ghislain,

As far as I know, the (0, 0) coordinate corresponds to the top left
corner.  All 
of the file formats that I've seen so far use (0, 0) as the top left, so
that's 
how Bio-Formats populates ROIs.

The SVG specification (on which OME-XML ROIs are based) does say that
(0, 0) 
corresponds to the top left corner - see 
http://www.w3.org/TR/SVG11/coords.html#InitialCoordinateSystem.
However, this 
isn't explicitly documented in the OME-XML schema, so it may be that you
are 
correct and (0, 0) should correspond to the bottom left.

Regards,
-Melissa

Ghislain Bonamy wrote:
> Hello everyone,
> 
>  
> 
> I wanted to verify what was frame of reference that OME uses to map
ROI to a picture. I assume that the image coordinate x=0,y=0 corresponds
to the bottom left corner and that Y increases going up and X increases
going right, but perhaps this is not correct.
> 
>  
> 
> Acapella which I use to generate my ROI coordinate list uses 0,0 as
the top left corner with increasing Y values going down and increasing X
values going left (most likely due to the way the image is read). I want
to make sure that I am not missing anything when I create a ROI set to
use in conjunction with OME.
> 
>  
> 
> Thanks for the info,
> 
>  
> 
> Ghislain Bonamy, PhD 
> _______________________________
> Genomic Institute of the
> Novartis Research
> Foundation
> Functional Genomics, G214
> +1 (858) 812-1534 (W & F)
> +1 (858) 354-7388 (C)
> www.gnf.org <http://www.gnf.org/> 
>  
> HudsonAlpha Instiute for Biotechnology
> www.hudsonalpha.org
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
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