[ome-users] .nd file from Metamorph timelapse

[Sebastien Besson (Staff)]

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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