Image Cytometry Standard
Encyclopedia
The Image Cytometry Standard (ICS) is a digital multidimensional image file format
used in life sciences
microscopy
. It stores not only the image data
, but also the microscopic parameters describing the optics during the acquisition.
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 http://dx.doi.org/10.1002/cyto.990110502.
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. This allows the compression of the data while leaving the header file accessible.
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 Tab
s, and lines ending with a newline
character. In the newer ICS2 format this text header precedes the binary data.
The ICS format is capable to store:
File format
A file format is a particular way that information is encoded for storage in a computer file.Since a disk drive, or indeed any computer storage, can store only bits, the computer must have some way of converting information to 0s and 1s and vice-versa. There are different kinds of formats for...
used in life sciences
Life sciences
The life sciences comprise the fields of science that involve the scientific study of living organisms, like plants, animals, and human beings. While biology remains the centerpiece of the life sciences, technological advances in molecular biology and biotechnology have led to a burgeoning of...
microscopy
Microscopy
Microscopy is the technical field of using microscopes to view samples and objects that cannot be seen with the unaided eye...
. It stores not only the image data
Voxel
A voxel is a volume element, representing a value on a regular grid in three dimensional space. This is analogous to a pixel, which represents 2D image data in a bitmap...
, but also the microscopic parameters describing the optics during the acquisition.
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 http://dx.doi.org/10.1002/cyto.990110502.
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. This allows the compression of the data while leaving the header file accessible.
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 Tab
Tab
Tab or tabs may refer to:* Tab, a British Army term for a loaded march* Tab , by Monster Magnet* Tab , a small protective covering for the fingers* Tab , the mechanism for opening a beverage can...
s, and lines ending with a newline
Newline
In computing, a newline, also known as a line break or end-of-line marker, is a special character or sequence of characters signifying the end of a line of text. The name comes from the fact that the next character after the newline will appear on a new line—that is, on the next line below the...
character. In the newer ICS2 format this text header precedes the binary data.
The ICS format is capable to store:
- multidimensional and multichannel data
- images in 8, 16 or 32 bit integer, 32 or 64 bit floating point and floating point complex data
- all microscopic parameters directly relevant to the image formation
- free-form comments
External links
- Sources for an ICS file reader/writer library: http://libics.sourceforge.net/.
- Python interface to libics: pylibics
- ICS converter.
- ICS opener for ImageJImageJImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using...
.