LOCI Bio-Formats package

Posted by ctrueden on
URL: http://imagej.273.s1.nabble.com/LOCI-Bio-Formats-package-tp3703215.html

Hi everyone,

Today I have the pleasure of announcing the LOCI Bio-Formats package, a
Java library for reading and writing popular microscopy image formats,
written by Melissa Linkert and myself. It currently supports reading 24
formats, and writing a few as well (TIFF stacks, JPEG, AVI and QuickTime).

You can find full details, including download links, online at:

    http://www.loci.wisc.edu/ome/formats.html

This work grew out of file format support within VisBio
(http://www.loci.wisc.edu/visbio); a forthcoming major release of VisBio
will utilize the Bio-Formats package directly.

The library provides support for parsing metadata for supported formats,
as well as representation of this metadata in standard OME-XML format,
using our LOCI OME-XML library
(http://www.loci.wisc.edu/ome/loci-ome-xml.html), but the OME-XML
standardization logic should be considered very early (alpha status).

By dropping the loci_formats.jar file into your ImageJ plugins folder, a
new entry called "LOCI Bio-Formats" will appear, capable of opening any
of the supported formats.

For those of you who use Handle Extra File Types
(http://rsb.info.nih.gov/ij/plugins/file-handler.html), it is possible
to add support for LOCI Bio-Formats. Just extract the bio_formats.jar
file and take a look at the loci/formats/LociPlugin.java source file. At
the bottom is a commented-out block of code that when added to
HandleExtraFileTypes.java will enable automatic calling of the
Bio-Formats package.

There is also a simple viewer/converter bundled with the package,
accessible by double-clicking the JAR file (or "java -jar
bio_formats.jar" from the command line).

Please let me know if you have any comments, questions or issues
regarding the package.

Cheers,
-Curtis