Ics Opener

Ics Opener

Author: Nico Stuurman (nico@cmp.ucsf.edu)

Date: 2003/02/06
2003/07/23: Fixed problem with multichannel images. Moved files into directory InputOutput.
2003/07/25: Improved ICS2 import. Actually tested two!
2003/08/05: Now also imports time series (4D might be problematic)
2004/09/20: Added error checking code by Wayne Rasband
2006/02/15: Added deinterleaving code by Rudolf Oldenbourg, packaged plugin into a jar
2007/02/28: Based on example files provided by Gerald Baron and Jon Harman bugs were fixed that caused interleaved z-stacks (and probably time-lapses) not to be imported correctly, and that made endiannes detection fail. Also, capitalization of the filename extension is now allowed (.ICS and .IDS pairs are now recognized).

Requirements: ImageJ

Limitations: Not tested extensively on different ics files. Let me know how it works. This goes especially for the newly added support for Nikon Ics files. Import of interleaved 8-bit images is likely to fail (I need examples of such files to fix this). If ics files are not opened correctly, please send me a (small) example file and a short description. The plugin does not interface with Image5D (a nice way to display multi-dimensional images in ImageJ). The plugin opens multiple channels in individual stacks, however, when more than 4 channels are found in interleaved data (as in spectral images) it opens all data in a single stack. Import of interleaved data is quite slow.

License: By downloading this software you agree to the terms of the license.

Source: Ics_Opener.jar

Installation: Copy Ics_Opener.jar to the plugins folder and restart ImageJ.

Description: This plugin opens files in the ics format. Ics stands for Image Cytometry Standard and provides for a very flexible way to store multi-dimensional image data (see: libics). Both version 1.0 and 2.0 ics files can be read. Each channel contained in the ics file is opened in a separate stackin ImageJ. Calibration data are also imported. Current version fixes (hopefully) a problem with the byteorder, and it allows for time series to be read in. There are still some assumptions made that are not explicit in the ics format, so it may fail on some files. The latest version (2007) adds code contributed by Rudolf Oldenbourg to deinterleave Nikon C1 ICS files.

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Author:	Nico Stuurman (nico@cmp.ucsf.edu)
Date:	2003/02/06 2003/07/23: Fixed problem with multichannel images. Moved files into directory InputOutput. 2003/07/25: Improved ICS2 import. Actually tested two! 2003/08/05: Now also imports time series (4D might be problematic) 2004/09/20: Added error checking code by Wayne Rasband 2006/02/15: Added deinterleaving code by Rudolf Oldenbourg, packaged plugin into a jar 2007/02/28: Based on example files provided by Gerald Baron and Jon Harman bugs were fixed that caused interleaved z-stacks (and probably time-lapses) not to be imported correctly, and that made endiannes detection fail. Also, capitalization of the filename extension is now allowed (.ICS and .IDS pairs are now recognized).
Requirements:	ImageJ
Limitations:	Not tested extensively on different ics files. Let me know how it works. This goes especially for the newly added support for Nikon Ics files. Import of interleaved 8-bit images is likely to fail (I need examples of such files to fix this). If ics files are not opened correctly, please send me a (small) example file and a short description. The plugin does not interface with Image5D (a nice way to display multi-dimensional images in ImageJ). The plugin opens multiple channels in individual stacks, however, when more than 4 channels are found in interleaved data (as in spectral images) it opens all data in a single stack. Import of interleaved data is quite slow.
License:	By downloading this software you agree to the terms of the license.
Source:	Ics_Opener.jar
Installation:	Copy Ics_Opener.jar to the plugins folder and restart ImageJ.
Description:	This plugin opens files in the ics format. Ics stands for Image Cytometry Standard and provides for a very flexible way to store multi-dimensional image data (see: libics). Both version 1.0 and 2.0 ics files can be read. Each channel contained in the ics file is opened in a separate stackin ImageJ. Calibration data are also imported. Current version fixes (hopefully) a problem with the byteorder, and it allows for time series to be read in. There are still some assumptions made that are not explicit in the ics format, so it may fail on some files. The latest version (2007) adds code contributed by Rudolf Oldenbourg to deinterleave Nikon C1 ICS files.