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Dear List,
I will try to provide clarification for those on the list who have questions about the .ids file format and its implementation by Nikon.
Image Cytometric Data, the formal name for what is referred to as the .ids format, is a public domain data format. The reason Nikon selected it was that it is by design, a very open data format that can be implemented according to the specific requirements of the imaging device. What makes Nikon's implementation of the format different from others is the structure of the header and the way series data like time series, Z-stack, channel series, and combinations of series is handled and saved.
The .ids file contains the image data in up to four 16-bit channels. Because the Nikon C1 confocal scanner produces 12-bit data, the top four bits are not used. If a series is acquired, all images in the series are saved to the same file. A separate file with the .ics extension contains the header information. The header includes information about the specific configuration of the C1 scanner used to acquire the data and also about conditions of the acquisition, including series information. The .ids and .ics files are linked. Opening the .ids file opens the .ics file. The only place I am aware of that the link breaks is when a file is renamed. Both the .ids and .ics files must be renamed for the link to be preserved.
The Huygens option fits the data to the conventions employed by some image analysis software. For instance the first element or pixel in each dimension must be zero. Also, any scaling, such as the distance between points, must be positive. These conventions are very useful for measuring distances in image analysis. They are less useful for confocal acquisition where a reference plane (the plane to return to after acquiring a stack) may be selected within a specimen. The top will be some positive distance above the reference plane. The bottom will be recorded as a negative distance below it. The Huygens option also provides some additional information useful for deconvolution.
I will be happy to provide any additional information users require off list.
Regards,
Jeffrey Larson
Product Manager, Confocal Systems
Nikon Instruments Inc.
1300 Walt Whitman Road
Melville, NY 11747
(631) 547-8540
-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]] On Behalf Of Glen MacDonald
Sent: Monday, April 18, 2005 8:53 AM
To: [log in to unmask]
Subject: Re: NIKON .ids file/Image J
Search the CONFOCAL archive at
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We ran into the same problem attempting to open the Nikon .ids files in
ImageJ with Nico's plugin and with Huygens software. Nikon's
explanation is that they have a "special" version of the .ids file
format. Your only option is to open the files with the Nikon software.
Then, go into the Nikon software preferences, check the box to save
in a "Huygens compatible" .ids format and re-save the files. The Nikon
software defaults to their proprietary version of the .ids, but once
you've set the prefs, it will save accordance to the published .ids
format. I didn't get an explanation of what benefits Nikon might be
gaining from modifying the .ids format. If the difference is bit
depth, then you may not notice any difference unless you have very
bright images, or extraordinary dynamic range in your samples.
The great thing about file standards is that everyone can have one.
regards,
Glen
On Apr 18, 2005, at 8:16 AM, Barbier, Elisabeth wrote:
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Hello,
>
>
>
> I want to process my data with Image J. But I cannot open my .ids
> files acquired with a NIKON TE 2000.
>
> When I open the files I get a black picture.
>
> Can anyone help?
>
> Thanks
>
>
>
> Elisabeth Barbier Ph.D.
>
> Univ. Maryland-School of Pharmacy
>
> Pharmaceutical Sciences
>
> 20 Penn Street- HSF II Bldg
>
> Room # S 534
>
> Baltimore, MD 21201
>
> Phone: 410-706-7058
>
> Fax: 410-706-5017
>
> E-mail: [log in to unmask]
>
>
>
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923 USA
(206) 616-4156
[log in to unmask]
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