Open Microscopy Environment
Laboratory for Optical and Computational Instrumentation
OME at LOCI – Software – Overview

This page provides an overview of software projects in active development at LOCI. For questions regarding the software, feel free to email the mailing list or the Bio-Formats developers, or contact Curtis Rueden and Kevin Eliceiri directly.


Mailing list

There is a low-traffic mailing list for announcements, questions, bug reports and discussion about LOCI software.

Subscribing: You can sign up through the web. Be sure to specify "science0" as the "New Subscriber Password."

Posting: Once you are subscribed, you can either post messages through the web, or email the list at locisoftware@lists.wisc.edu.

Archives: All messages to the list are archived and searchable through the web.

Unsubscribing: If you wish to unsubscribe from the list, send an email to leave-locisoftware@lists.wisc.edu.


Accessing source code

If you are interested in the latest Java source code from our Subversion repository, you can check it out using the repository path:

https://skyking.microscopy.wisc.edu/svn/java/trunk

You will find each package in the corresponding "SVN path" listed below. We also have a Trac server for project management, including tasks, milestones and known issues.

If you are unfamiliar with Subversion, read the Initial Checkout and Basic Work Cycle sections of the online Subversion book for a primer. If you use Windows and want a graphical Subversion client, try TortoiseSVN.

If you use the Eclipse SDK for development, you can use the Subclipse plugin to import the LOCI Software project by choosing File > Import... from the menu and selecting "Checkout Projects from SVN" under the "Other" heading. After doing so, the project should build successfully with no further configuration (though please note that seeing hundreds of non-fatal warnings is normal). Alternately, if you check out the code with an external tool such as TortoiseSVN, you can import the project into Eclipse afterward using the "Existing Projects into Workspace" import option under the "General" heading.

If you have Ant installed, you can make use of our Ant build script—try "ant -p" for a list of targets.

Lastly, you can browse the online Javadocs for all our Java software, or generate them yourself using the "docs" Ant target.


Applications

VisBio
A biological visualization tool designed for easy visualization and analysis of multidimensional image data.
Latest version 3.40rc1 (2009 Mar 9)
Language Java
Main developer Curtis Rueden
Download visbio340rc1_win32.zip
visbio340rc1_macosx.tar.gz
visbio340rc1_linux.tar.gz
Screenshot VisBio
Trac path components/visbio
SVN path components/visbio
Web sites VisBio web site
OME at LOCI – VisBio
WiscScan
A DSP-based acquisition system for laser scanning microscopes.
Latest version 4.0
Language Visual C++
Main developers Mike Smith
Screenshot WiscScan
Trac path WiscScan (authorized only)
SVN path WiscScan (authorized only)
Web sites OME at LOCI – WiscScan
WiscScan web site
SLIM Plotter
A tool for visualization and analysis of spectral lifetime data.
Latest version 2009 Apr 27
Language Java
Main developers Curtis Rueden, Eric Kjellman
Download slim.zip
Screenshot SLIM Plotter
Trac path components/slim-plotter
SVN path components/slim-plotter
Web site OME at LOCI – SLIM Plotter
LoCal Calendar System
An advanced instrumentation reservation system for equipment calendaring and user management.
Latest version 1.1
Language PHP
Main developer Sachin Bavishi
Download LoCal-1.1.tar.gz
Screenshot LoCal
Web site LoCal web site



Components and Plugins

Bio-Formats
A library (and collection of ImageJ plugins) for reading and writing popular microscopy file formats, including processing and conversion of metadata into standard OME-XML structures.
Latest version 4.0.1 (2009 June 1)
Language Java
Main developer Melissa Linkert
Download loci_tools.jar
(place in ImageJ plugins folder)
Trac path components/bio-formats
SVN path components/bio-formats
Web site OME at LOCI – Bio-Formats
Data Browser
An ImageJ plugin that facilitates quick browsing of multichannel 4D datasets (such as those produced by WiscScan).
Latest version 4.0.1 (2009 June 1)
Language Java
Main developer Curtis Rueden
Download loci_tools.jar
(place in ImageJ plugins folder)
Screenshot Data Browser
Trac path components/loci-plugins
SVN path components/loci-plugins
Web site OME at LOCI – Data Browser
OME Plugins for ImageJ
ImageJ plugins for interacting with OME and OMERO databases, including image search, browse, and download, as well as upload of images into the database.
Latest version 4.0.1 (2009 June 1)
Language Java
Main developers Melissa Linkert
Download loci_tools.jar
(place in ImageJ plugins folder)
Screenshot OME Plugins
Trac path components/loci-plugins
SVN path components/loci-plugins
Web site OME at LOCI – OME plugins for ImageJ
OME-XML Java library
An API for reading, writing and editing OME-XML metadata.
Latest version 2008 May 30
Language Java
Main developers Curtis Rueden, Chris Allan
Download ome-xml.jar
Trac path components/ome-xml
SVN path components/ome-xml
Web site OME at LOCI – OME-XML Java library



Legacy Software

4D Software Suite
A suite of tools for working with 4D microscopy datasets.
Main developer Charles Thomas
Download Legacy software archive
Web site OME at LOCI – 4D software suite
JVMLink
A library for communicating between a Java Virtual Machine and other programs (e.g., C++ applications) via sockets.
Latest version 2008 Mar 17
Languages Java, Visual C++
Main developer Hidayath Ansari
Download jvmlink.jar
Trac path components/legacy/jvmlink
SVN path components/legacy/jvmlink
Web site OME at LOCI – JVMLink
OME Notes
A template-driven, embeddable component for OME metadata editing.
Latest version 4.0.1 (2009 June 1)
Language Java
Main developer Melissa Linkert
Download loci_tools.jar (save to disk, then double-click to launch)
Trac path components/legacy/ome-notes
SVN path components/legacy/ome-notes
Web site OME at LOCI – OME Notes
OME Metadata Editor
Quickly browse and edit your data's textual and numerical metadata.
Latest version 2007 Feb 2
Language Java
Main developer Chris Peterson
Download Build from Subversion
Screenshot OME Metadata Editor
Trac path components/legacy/ome-editor
SVN path components/legacy/ome-editor
Web site OME at LOCI – OME Metadata Editor



Last update: Monday, June 1, 2009