[ome-users] .nd file from Metamorph timelapse

[Melissa Linkert]

Hi Sho,

Thank you for uploading the dataset.

We are testing a fix for this now:

https://github.com/openmicroscopy/bioformats/pull/1843

and I would expect the upcoming 5.1.3 release of Bio-Formats to resolve
the problem.

Regards,
-Melissa

On Tue, Jun 16, 2015 at 02:32:05PM +0000, Sebastien Besson (Staff) wrote:
> Dear Sho,
> 
> thanks for reporting this issue. From your description it looks like this is a bug
> in Bio-Formats. Can you confirm the Bio-Formats version you are using is 5.1.2
> from the 'Help > About Plugins > Bio-Formats Plugins....' menu in Fiji?
> 
> Uploading sample files would be ideal for us to assess the nature of the error.
> If your files are smaller than 2GB, you can try to upload them at
> https://www.openmicroscopy.org/qa2/qa/upload/. If this is too big, uploading
> the .nd file and the list of the TIFF file names would definitely be a good start.
> Alternatively,  we can provide the details of an FTP server to upload larger
> datasets. Let us know which solution is the most adapted to you.
> 
> Best regards,
> Sebastien
> 
> On 15 Jun 2015, at 20:37, fujisaws at mskcc.org<mailto:fujisaws at mskcc.org> wrote:
> 
> There might be a bug in opening .nd files in FIJI.
> 
> My user took a multi-channel, multi-position z-stack timelapse using a widefield system controlled by Metamorph software. You get an ".nd" file that compiles all the individual tif files.
> 
> When I open the .nd file in FIJI, one of 3 channels acquired is always from the wrong xy position, except for the first position. The images, obviously open fine in Metamorph.
> 
> Has anybody seen something like this and know a work around? I will be happy to upload the files, but they are rather big.
> 
> 
> Sho Fujisawa
> Sr. Digital Microscopist
> Molecular Cytology Core Facility
> Memorial Sloan-Kettering Cancer Center
> 417 E. 68th St.
> Zuckerman Room 1834
> New York NY 10065
> (212) 639-6667
> (646) 888-2186
> 
> 
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