Scientific Volume Imaging b.v.

Scientific Volume Imaging b.v.
Laapersveld 63
1213 VB Hilversum, The Netherlands
http://www.svi.nl
http://support.svi.nl/wiki

ICS file format

The main File Format used by the Huygens Software is the open source Image Cytometry Standard (ICS and ICS2). It stores not only the image data, but also the Microscopic Parameters.

• The original ICS file format actually uses two separate files: a text header file with .ics extension and other, much bigger and with the actual image data, with .ids extension.
• On the other hand the newer ICS2 file format uses only one single .ics file with both the header and the data together.

The .ics in the two-file format is a text file with fields separated by Tabs, and lines ending with a 'newline' character. In the newer ICS2 format this text header file precedes the binary data.

Capabilities

The ICS format is capable to store:

• multidimensional data
  • ...this includes multiple channels,
• basic 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

The sources for an ICS file reader/writer library called libics can be found at http://libics.sourceforge.net/. See also there for more information on the ICS file format.

SIDB

The Scientific Image Data Base uses a special form to upload the two files in the ICS format, but files in ICS2 format must be uploaded as any other 3D image single file (filetype = 3-D).

Also downloading ICS files from the SIDB requires that you download the two separate files one by one. You have different links for that purpose.

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)