ICS file format

The open source Image Cytometry Standard (ICS and ICS2) was the main File Format used by the HuygensSoftware is before version 3.5. It stores not only the image data, but also the Microscopic Parameters. Since version 3.5, HDF5 is the preferred format.

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. 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.


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

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.


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)