Open ND2 file in Matlab

[Chen, Jianbo (NIH/NCI) [E]]

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Dear All
We are having problem to open Nikon ND2 file in Matlab with Bio-Formats due to recent upgrading of Nikon software. It looks like Nikon modified their ND2 format but the current Bio-Formats does not recognize. I would appreciate if anyone having a solution to share. Thanks


Jianbo Chen
HIV Drug Resistance Program
National Cancer Institute-Frederick
Frederick MD 21702

[Craig Brideau]

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We've had a major issue with this in our own lab.  We used EZC1 on all our
systems and could import the ids/ics file format for that system no
problem, but ND2 is quite different and Nikon won't hand out the file
format to make it easier for people to use.  That said, what they did for
our case was build a macro in the Elements software that allows you to
export ND2 to a form of TIFF with some metadata that is then easy to import
into whatever you want to use.  I'd bug your local Nikon technical person
to see if they will give you a copy of the macro.

Craig


On Mon, Jan 28, 2013 at 3:46 PM, Chen, Jianbo (NIH/NCI) [E] <
[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear All
> We are having problem to open Nikon ND2 file in Matlab with Bio-Formats
> due to recent upgrading of Nikon software. It looks like Nikon modified
> their ND2 format but the current Bio-Formats does not recognize. I would
> appreciate if anyone having a solution to share. Thanks
>
>
> Jianbo Chen
> HIV Drug Resistance Program
> National Cancer Institute-Frederick
> Frederick MD 21702
>

[Unruh, Jay]

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If I remember right, Nikon has an ImageJ importer (http://rsbweb.nih.gov/ij/plugins/nd2-reader.html)  which they keep fairly up to date and provide the source code for (the plugin that is, not the library).  I have a hacked version which I can send you off list that works fairly well for ImageJ.  Given that I'm not a Matlab guy, I don't really know how you would parlay that into a matlab importer, but I think matlab will call class files.  If nothing else, you could use ImageJ to do the tif conversion if you can't get a hold of the macro.

Jay

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Craig Brideau
Sent: Monday, January 28, 2013 4:55 PM
To: [hidden email]
Subject: Re: Open ND2 file in Matlab

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We've had a major issue with this in our own lab.  We used EZC1 on all our systems and could import the ids/ics file format for that system no problem, but ND2 is quite different and Nikon won't hand out the file format to make it easier for people to use.  That said, what they did for our case was build a macro in the Elements software that allows you to export ND2 to a form of TIFF with some metadata that is then easy to import into whatever you want to use.  I'd bug your local Nikon technical person to see if they will give you a copy of the macro.

Craig


On Mon, Jan 28, 2013 at 3:46 PM, Chen, Jianbo (NIH/NCI) [E] < [hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear All
> We are having problem to open Nikon ND2 file in Matlab with
> Bio-Formats due to recent upgrading of Nikon software. It looks like
> Nikon modified their ND2 format but the current Bio-Formats does not
> recognize. I would appreciate if anyone having a solution to share.
> Thanks
>
>
> Jianbo Chen
> HIV Drug Resistance Program
> National Cancer Institute-Frederick
> Frederick MD 21702
>

[Melissa Linkert-2]

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Hi Jianbo,

> We are having problem to open Nikon ND2 file in Matlab with Bio-Formats due to recent upgrading of Nikon software. It looks like Nikon modified their ND2 format but the current Bio-Formats does not recognize. I would appreciate if anyone having a solution to share. Thanks

If you haven't already, I would suggest first updating to the latest
version (4.4.5, available from http://www.openmicroscopy.org/site/products/bio-formats/downloads).

If that doesn't work, and you are willing to send the error message and
(if possible) an example file, then this is certainly something that could be
fixed in Bio-Formats.

Files can be sent to the Bio-Formats team here:

http://qa.openmicroscopy.org.uk/qa/upload/

Anything uploaded there is used for testing purposes only, and is never
shared with the outside world.

Regards,
-Melissa

On Mon, Jan 28, 2013 at 10:46:46PM +0000, Chen, Jianbo (NIH/NCI) [E] wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear All
> We are having problem to open Nikon ND2 file in Matlab with Bio-Formats due to recent upgrading of Nikon software. It looks like Nikon modified their ND2 format but the current Bio-Formats does not recognize. I would appreciate if anyone having a solution to share. Thanks
>
>
> Jianbo Chen
> HIV Drug Resistance Program
> National Cancer Institute-Frederick
> Frederick MD 21702