.nd2 playing well with others

[Feinstein, Timothy]

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Hello all,

Does anyone have occasional trouble opening .nd2 files in third party software?  We use Bio-Formats (OMERO, Fiji, CellProfiler etc), Imaris and Huygens Professional for our work, all of which ostensibly should open the format and normally do (the Huygens option is officially experimental).  Sometimes a given file will not open in any of the three for reasons that we cannot figure out.  Huygens will fail to open it and both Imaris and Bio-Formats will get confused by its metadata.  Bio-Formats gives the clearest sign of what is going on, apparently thinking that each Z plane is an experiment and each channel is a Z plane.  Elements opens these files with no problem.

This seems to happen most often (maybe ~20% of the time) when we split an XY multipoint into single files using the Elements ‘File' menu.  When it happens we kludge it by manually saving each XY file in the older .ics format; that just gets ridiculous when someone brings a 96-well dish.   I guess we could write a macro.

Do other folks see this?  Any workarounds would be appreciated.

Thanks,


TF

- No commercial interests -

Timothy Feinstein, Ph.D. | Manager, Core for Confocal Microscopy and Quantitative Imaging
333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
Phone: [phone] | Email: [hidden email]<mailto:[hidden email]>

[Straatman, Kees (Dr.)]

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Dear Timothy,

There is a imageJ plugin from Nikon which you can find at http://rsb.info.nih.gov/ij/plugins/nd2-reader.html. We have used it with success where other options failed. Limitation is that it is only for Windows.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Feinstein, Timothy
Sent: 05 August 2014 17:34
To: [hidden email]
Subject: .nd2 playing well with others

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*****

Hello all,

Does anyone have occasional trouble opening .nd2 files in third party software?  We use Bio-Formats (OMERO, Fiji, CellProfiler etc), Imaris and Huygens Professional for our work, all of which ostensibly should open the format and normally do (the Huygens option is officially experimental).  Sometimes a given file will not open in any of the three for reasons that we cannot figure out.  Huygens will fail to open it and both Imaris and Bio-Formats will get confused by its metadata.  Bio-Formats gives the clearest sign of what is going on, apparently thinking that each Z plane is an experiment and each channel is a Z plane.  Elements opens these files with no problem.

This seems to happen most often (maybe ~20% of the time) when we split an XY multipoint into single files using the Elements 'File' menu.  When it happens we kludge it by manually saving each XY file in the older .ics format; that just gets ridiculous when someone brings a 96-well dish.   I guess we could write a macro.

Do other folks see this?  Any workarounds would be appreciated.

Thanks,


TF

- No commercial interests -

Timothy Feinstein, Ph.D. | Manager, Core for Confocal Microscopy and Quantitative Imaging
333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
Phone: [phone] | Email: [hidden email]<mailto:[hidden email]>