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 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.


Developers

Most of the software listed below is written in Java (with the exceptions of WiscScan in C++ and LoCal in PHP). If you are a developer 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 v3.31a (2006 Nov 3)
Main developer Curtis Rueden
Download visbio331a_win32.zip
visbio331a_macosx.tar.gz
visbio331a_linux.tar.gz
Screenshot VisBio
Trac path java/loci/visbio
SVN path java/loci/visbio
Web sites VisBio web site
OME at LOCI – VisBio
WiscScan
A DSP-based acquisition system for laser scanning microscopes.
Latest version v4.0
Main developers Mike Smith, Kerry Creeron
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 2007 Sep 19
Main developers Curtis Rueden, Eric Kjellman
Download slim.zip
Screenshot Slim Plotter
Trac path java/loci/apps/slim
SVN path java/loci/apps/slim
Web site OME at LOCI – Slim Plotter
LoCal Calendar System
An advanced instrumentation reservation system for equipment calendaring and user management.
Latest version v1.1
Main developer Sachin Bavishi
Download LoCal-1.1.tar.gz
Screenshot LoCal
Web site LoCal web site
Data Converter
A utility for converting multidimensional image series between formats.
Latest version Not yet released
Main developer Curtis Rueden
Trac path java/loci/formats/gui
SVN path java/loci/formats/gui
OME Metadata Editor
Quickly browse and edit your data's textual and numerical metadata.
Latest version 2007 Feb 2
Main developer Chris Peterson
Download Build from Subversion
Screenshot OME Metadata Editor
Trac path java/loci/ome/editor
SVN path java/loci/ome/editor

Components and Plugins

Bio-Formats
A Java 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 2008 April 17
Main developer Melissa Linkert
Download loci_tools.jar
(place in ImageJ plugins folder)
Trac path java/loci/formats
SVN path java/loci/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 2008 April 17
Main developer Curtis Rueden
Download loci_tools.jar
(place in ImageJ plugins folder)
Screenshot Data Browser
Trac path java/loci/plugins/browser
SVN path java/loci/plugins/browser
Web site OME at LOCI – Data Browser
Java OME-XML library
An API for reading, writing and editing OME-XML metadata.
Latest version 2007 Jul 2
Main developer Curtis Rueden
Download ome-java.jar
CVS path OME-JAVA/src/ome/xml
Web site OME at LOCI – Java OME-XML library
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 2008 April 17
Main developers Melissa Linkert, Allison McArton
Download loci_tools.jar
(place in ImageJ plugins folder)
Screenshot OME Plugins
Trac path java/loci/plugins
SVN path java/loci/plugins
Web site OME at LOCI – OME plugin for ImageJ
OME Notes
A template-driven, embeddable component for OME metadata editing.
Latest version 2008 April 17
Main developer Melissa Linkert
Download loci_tools.jar (save to disk, then double-click to launch)
Trac path java/loci/ome/notes
SVN path java/loci/ome/notes
Web site OME at LOCI – OME Notes
JVMLink
A library for communicating between a Java Virtual Machine and other programs (e.g., C++ applications) via sockets.
Latest version 2008 Mar 17
Main developer Hidayath Ansari
Download jvmlink.jar
Trac path java/loci/jvmlink
SVN path java/loci/jvmlink
Web site OME at LOCI – JVMLink

Legacy Tools

Older LOCI applications can be found in our legacy software archive.



Last update: Thursday, April 17, 2008