[ome-users] Problems with SCN files

[Balaji Ramalingam (Staff)]

Hi,

Thank you for reporting your bug.

We were able to reproduce the same locally with a few SCN files.
I have filed a ticket for the same,
https://trac.openmicroscopy.org/ome/ticket/12680

And have added you to the CC list.

Notifications will be sent to your email id, when there is a status change
on the ticket.

In future cases, it would be helpful if you could submit your raw files
(.SCN) to our QA server,
https://www.openmicroscopy.org/qa2/qa/upload/

This will help us troubleshoot your issues in better detail.

Best,
Balaji

__________________
Mr Balaji Ramalingam
Software Developer

OME Team
College of Life Sciences
University of Dundee






On 06/12/2014 15:00, "Joseph Jacobs" <j.jacobs at cs.ucl.ac.uk> wrote:

>Hey all,
>
>I am having some problems opening Leica SCN files with Bio-Formats. So I
>have quite a few SCN files that I want to convert to TIFF/BigTIFF files.
>Each SCN file has 6 series which are basically the same image at
>different magnifications.
>
>The first problem seems to be with reading the file. A lot of noise is
>introduced into the image when I read it with showinf. Tried reading the
>files on the demo server and I get the same results
>(https://dl.dropboxusercontent.com/u/15317306/noise%20sample.png). Has
>any one seen this problem before? The noise seems to be most common in
>background regions and only sometimes occurs on the tissue itself.
>Perhaps it¹s an issue with decompression?
>
>The second problem I have been having is with the actual saving of
>TIFF/BigTIFF files. When I try to save the 6 different series to TIFF
>files, the two series with the highest magnifications are saved wrong.
>Here are samples of high
>(https://dl.dropboxusercontent.com/u/15317306/high.tiff) and low
>(https://dl.dropboxusercontent.com/u/15317306/low.tiff) magnification.
>You can still see the noise on the low magnification but it is largely
>correct. Whereas with the high magnification image, there seems to be
>some information on the blue channel and noise on the red channel. Anyone
>know what I am doing wrong here? The command I am using to convert the
>images is as follows:
>
>bfconvert -series 3 filename.scn filename.tiff
>
>Any help/pointers would be greatly appreciated.
>
>Best,
>Joe
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