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Pylibics - Python wrapper for libics (Image Cytometry Standard).

The Image Cytometry Standard (ICS) is a file format for images, primarily in microscopy imaging. The file format has been described by [Dean1990][#literature]. ICS files allow to store further information on the imaging system along with the actual image (e.g aperture, light setting, microscope, and camera). Moreover, the file format allows to store several integer format, floating point images as well as complex valued images.

Installing and Using pylibics

Introduction

The library libics is a C library to read an write ICS image files. This module wraps the functions provided by libics to Python. Actual image data are returned as numpy arrays. Numpy array in turn can be written to ICS image files.

Literature

  • Dean1990: Dean, P.; Mascio, L.; Ow, D.; Sudar, D. & Mullikin, J.

    ‘Proposed standard for image cytometry data files’ Cytometry, Part A, 1990, 11, (5), 561-569 doi: 10.1002/cyto.990110502

Limitations and known bugs

  • Ics data written as version 2.0 is broken
  • Accessing ics history entries with the iterator interface seems not to work properly
  • Compression appears to be not working

Installation instructions

These installation instructions currently do not work. Please download the source from the Github Repository.

You can download the source code package_ to compile everything yourself or you can use easy_install to install the precompiled package (py2.6, win32 and linux, x86_64). To compile the package please follow the instructions provided in the README file.

Windows

Installing with easy_install is done by calling from the windows command prompt (C:>):

C:> easy_install pylibics

Linux

Installing with easy_install is done by calling from the command prompt:

easy_install pylibics

.. _source code package: http://www.andre-bell.de/projects/pylibics/downloads

Usage

Please see the project homepage_ for usage examples. Also refer to the examples provided in the source package.

.. _project homepage: http://www.andre-bell.de/projects/pylibics

Release Changes

1.5.2b1, Released 2010-11-23

  • Basic support for libics
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