ICS file format

The Image Cytometry Standard (ICS and ICS2) file format is an open source image format that offers a few big advantages over file formats such as Tiff.

First of all, this format is supported by ImageJ/FIJI and nearly all professional image processing software packages ensuring easy portability between different image processing software packages. The ICS format is also capable of preserving the image dimensions and relevant metadata, important for the proper restoration and analysis of the image data. Furthermore, the Microscopic Parameters of all microscope types supported by the HuygensSoftware is maintained. See also: File Format.

We encourage microscopists to use the newer ICS2 file format, which only uses a single .ics file containing both the meta data and the pixel data. This is in contrast to the original ICS file format actually uses two separate files: a text file with extension .ics containing meta data and a second much larger file with extension .ids containing 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 can store:

• multidimensional data
  • ...this includes multiple channels and detectors
• basic pixel or voxel data as 8 or 16 bit integer values, floating point values or floating point complex values
• all microscopic parameters related to image formation

ICS (batch) file converter

The Huygens Software can read ICS and ICS2 files and then export them as other File Formats, even in FreeWare mode. Other image formats, supported by Huygens can be read and converted to the ICS and ICS2 file format. Batch conversion of files can be easily done with the Workflow Processor.

To use the Workflow Processor, you can download the Huygens Suite and use Huygens Essential or Huygens Professional

There is also an ICS_opener plugin for ImageJ, written 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 this typically increases access times, compression is only recommended for images that are not going to be used for a while. Compression with gzip changes the extension to .ids.gz. The Huygens Software automatically decompresses these files on the fly when 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)