LOCI Bio-Formats package

[ctrueden]

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

[Michael Schell]

Hi Curtis,

Many thanks for your work on LOCI Bio-formats package.  I am trying  
to find a way to export Improvision Volocity files with their  
metatdata into ImageJ.  Volocity offers the option of exporting as  
a .liff file (OpenLab), so I think that will be the best way forward  
via LOCI bio-formats.

However, when I use the LOCI Bio-formats plugin in ImageJ (on a Mac),  
the plugin seems operate fine until the end part of the import, when  
it returns the error messge:  "expected iPic comment block not found."

Is this a bug in Bio-formats, or is it due to some glich in the way  
the Volocity exports into the .liff format?

I'll happily work with you to develop a way to get Volocity data +  
metadata into ImageJ.  Improvision  claims that the metadata  from  
Volocity is also contained in the header of their exported .tiff  
files, but I am unable check this or confirm this.  If you wish I can  
provide test datasets or else try out beta versions of your plugins  
in order to make this work.

Best regards,

Michael


Michael J. Schell
Dept. Pharmacology
USUHS
4301 Jones Bridge Rd.
Bethesda, MD  20814
Tel: [phone]
[hidden email]
http://www.usuhs.mil/pha/mschell.html


On Mar 31, 2006, at 6:31 PM, Curtis Rueden wrote:

> 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