LOCI utilizes and develops several types of light microscopy techniques, including 4D Nomarski video-microscopy (3D timelapse), confocal laser scanning, multiphoton laser scanning, harmonic, spectral and fluorescence lifetime imaging. As our technology becomes more complex, our multidimensional data management needs also increase. We have joined the Open Microscopy Environment (OME) consortium of developers to pursue the use of OME as a practical, effective data management system for multidimensional images.

Accessibility is our guiding software design principle. We strive for compatibility between different software packages, putting a wide variety of visualization and analysis options at the biologist's fingertips. A multitude of useful software already exists, and it makes sense to ensure that our data works with that software. For this reason, we have chosen to take advantage of open standards within the microscopy community whenever possible.

1. Acquisition and storage – Establish an OME system as our lab's main repository, automatically storing both acquired images and corresponding metadata within the database.
   Related projects: OME-TIFF, Bio-Formats, WiscScan.


2. Visualization and analysis – Create flexible, biologist-friendly tools to visualize and analyze our data.
   Related projects: Bio-Formats, VisBio, Slim Plotter, Data Browser, OME plugins for ImageJ, OME Notes, OME-Java library.

1. Roadmap and future directions – A discussion of LOCI's software goals for the next year and beyond.


2. Frequently asked questions – A list of common issues and questions relating to both LOCI's involvement in the Open Microscopy Environment (OME), and the OME project as a whole.

See the software overview for a summary of LOCI software technologies. A brief list follows:

1. OME-TIFF – A file format standard for the exchange of rich microscopy image data. OME-TIFF combines the power and flexibility of the OME-XML schema for microscopy metadata with the mature, efficient and widely supported multi-page TIFF format for image pixels.


2. Bio-Formats – A standalone Java library for parsing popular microscopy file formats, including both pixels and metadata, and converting them to OME-TIFF format. It is intended for use within any application wishing to support microscopy formats, including OME, VisBio, ImageJ and MATLAB.


3. OME Notes – An application to browse and edit data's textual and numerical metadata.


4. JVMlink – A micro client/server architecture for communicating between a Java Virtual Machine and other programs (e.g., C++ applications) via IP over localhost (or remotely).


5. Data Browser – An ImageJ plugin that facilitates quick browsing of multichannel 4D datasets, such as those produced by WiscScan.


6. OME plugins for ImageJ – Plugins for ImageJ capable of interacting with an OME database.


7. OME-Java library – An API for reading, writing and editing OME-XML metadata. Currently used by VisBio and the OME plugins for ImageJ to support the OME-TIFF format.


8. VisBio – An open-source program for visualization and analysis of multidimensional biological image data.


9. WiscScan – Acquisition software for collecting a rich set of information from our light microscopes, and storing it in OME-TIFF format.


10. Slim Plotter – A tool for interactive inspection of spectral lifetime data.