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ICS file format

The open source Image Cytometry Standard (ICS and ICS2) is capable to store not only the image data, but also the Microscopic Parameters of all microscope types supported by the HuygensSoftware. See also: File Format.

The original ICS file format actually uses two separate files: a text file with .ics extension containing the meta data and a second much larger file with extension .ids containing the image pixel data. The newer ICS2 file format uses only one single .ics file containing both the header and the pixel data.

In the two-file format, the .ics is a plain text file with keywords and values separated by tabs, and lines ending with a 'newline' character. In the newer ICS2 format this text header file precedes the binary pixel data.

Capabilities

Currently, the ICS format is capable to store:
  • multidimensional data
    • ...this includes multiple channels and detectors,
  • basic pixel or voxel data can be both 8 or 16 bit integer, floating point and floating point complex data.
  • all microscopic parameters directly relevant to the image formation

ICS converter

The Huygens Software can read ICS and ICS2 files and export it to other File Formats, even in FreeWare mode. You can download the Huygens Suite and use the Huygens Essential for that purpose.

There is also an ICS_opener plugin for ImageJ, programmed by Nico Stuurman.

Open Source ICS library

Scientific Volume Imaging maintains the open source libary libics for reading and writing ICS files. The sources for libics can be found on GitHub. A manual for the libics library can be found here.


Compression of .ids files

When the two-file format is used, large .ids files may be compressed with the
well known gzip program. Since typically this increases access times, compression is recommended after an image has not been used for some time.
Compression with gzip changes the extention into .ids.gz. The Huygens Software automatically decompresses it on the fly when the file is opened.

Reference

ICS was first proposed in: P. Dean, L. Mascio, D. Ow, D. Sudar, J. Mullikin, Proposed standard for image cytometry data files, Cytometry, n. 11, pp. 561-569, 1990. (ref)

Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands


Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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