[ome-users] Open .scn that contains images of different pixel sizes

[LIM Soon Yew John (IMB)]

Dear Dr Roger,

I had uploaded the ".scn" file using the link you gave me. The ID is 7770, url is https://www.openmicroscopy.org/qa2/qa2/qa/feedback/7770/?token=8e0ed29756cf07f2c9207c7fc184f094 
and the filename is "0148-13 1635 12 PSMADZ.scn".

Thank You,
John

________________________________________
From: Roger Leigh [rleigh at dundee.ac.uk]
Sent: Wednesday, December 11, 2013 4:56 PM
To: LIM Soon Yew John (IMB)
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Open .scn that contains images of different pixel sizes

On 11/12/13 07:14, LIM Soon Yew John (IMB) wrote:
> Dear All,
>
> I had a .scn data set from slide scanning that contains 8 images in one
> .scn file. I could not fully open all the images using Bio-format
> importer as two of those images are bigger than what is stated in the
> meta-data. Images 1, 2, 3, 6, 7 & 8 are 1616 pixel width by 4668 pixel
> height but image 4 & 5 arebigger than that. Therefore all the images
> opened as 1616 by 4668, this resulted in image 4 & 5 being only
> partially open.
>
> Can I please find out is there a way for me to open image 4 & 5 fully
> even if they are not of the same pixel dimensions as the other images in
> the series?

If the metadata doesn't match the pixel data and the Leica SCN reader
code isn't handling this properly, this is something we need to take a
closer look at to see if we can handle it in the reader code.

Please could you upload a copy of the file to
https://www.openmicroscopy.org/qa2/qa/upload/ and we will then be able
to take a look at the problem in more detail and then be able to suggest
a workaround if possible, and look at any changes we might be able to
make to handle this data.


Many thanks,
Roger Leigh

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096