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mDSLM format request

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Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

mDSLM format request

Postby hroque » Thu Jul 25, 2013 2:02 pm

Hi all,

Just started working with a SPIM scope that writes each stack in a separate tiff file. Was wondering if it would be possible to have bioformats recognise the format and read all the stacks as one big movie.
Have uploaded a dataset for you guys with ID 7540.

Cheers,
Helio
hroque
 
Posts: 36
Joined: Thu Nov 04, 2010 6:20 pm

Re: mDSLM format request

Postby ajpatterson » Fri Jul 26, 2013 9:21 am

Hello Helio,

Thanks for the dataset.

Can you answer a few questions about what it came from:

What is the make and model of the scope?
What application (vendor, name, version, website) was used to save the files?

When I get this information I can make a ticket for the work.

I have had a quick looks at some of the individual TIFF files.
They all seem to be totally black, is this expected?

Ta,

Andrew
--
Andrew Patterson
Software Developer, Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression
University of Dundee
ajpatterson
 
Posts: 50
Joined: Fri May 01, 2009 11:18 am

Re: mDSLM format request

Postby hroque » Fri Jul 26, 2013 10:07 am

Hi Andrew,

The microscope is a mDigital Scanning Lightsheet microscope. Its an in-house built by EMBL-Heidelberg and to be honest I don't think they have a website.
I will try and find out the version of the software that created the files.

I realize that this is a very much niche file format so would understand if you guys can't really do much about it.

About the files they should not be black. They in principle are 16bit files with some sort of fluorescence. Maybe it was the compression. Let me know if you need and I can upload the original files.

Cheers,
Helio
hroque
 
Posts: 36
Joined: Thu Nov 04, 2010 6:20 pm

Re: mDSLM format request

Postby ajpatterson » Mon Jul 29, 2013 4:14 pm

Hello Helio,

Thanks, I have made a ticket on trac:

https://trac.openmicroscopy.org.uk/ome/ticket/11318

Ta,

Andrew
--
Andrew Patterson
Software Developer, Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression
University of Dundee
ajpatterson
 
Posts: 50
Joined: Fri May 01, 2009 11:18 am


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