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Software

LoCal - An advanced instrumentation reservation system for equipment calendaring and user management
PHP
1.1.2
SLIM Plotter - A tool for interactive visualization and inspection of combined spectral lifetime (SLIM) data
Java
2009 Apr 27
WiscScan Flow Cytometry - A standalone tool for flow cytometry analysis
Java
2009 Aug 24
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
Java
4.3.3 (2011 October 18)
Data Browser - An ImageJ plugin that facilitates quick browsing of multichannel 4D datasets (such as those produced by WiscScan)
Java
4.1.0 (2009 October 21)
Fiji plugins
Java
Jar2Lib - A command line tool for generating C++ proxy classes corresponding to a Java library.
Java
1.0
SLIM Plugin
4D Software Suite - Development has ceased; see recommendations
OME Metadata Editor - Quickly browse and edit your data's textual and numerical metadata.
Java
2007 Feb 2
JVMLink - A library for communicating between a Java Virtual Machine and other programs (e.g., C++ applications) via sockets
Java, Visual C++
2008 Mar 17
OME Notes - A template-driven, embeddable component for OME metadata editing
Java
4.1.0 (2009 October 21)
Curvelet-Based Alignment Analysis - Standalone MATLAB package allows users to quickly and automatically quantify the alignment of periodic structures (e.g. collagen fibers) in an image.
MATLAB
January 2012
Fusion Event Locator & Classifier - ImageJ macro & MATLAB function to identify fusion events in image stack & classify as proliferating or unchanging.
Intensity Macro for Background Subtraction - Background subtraction customized for Ogle Lab microscopy images
ImageJ Macro Language
VisBio - A biological visualization tool designed for easy visualization and analysis of multidimensional image data.
Java
3.40rc1 (2009 Mar 9)
VisBio Fiji plugins
Java
1.0-SNAPSHOT
WiscScan - Acquisition software for laser scanning microscopy

Research

Metabolic Mapping

Eukaryotic cells depend upon the mitochondrial electron transport chain to produce energy in the form of ATP when oxygen is present.  The first complex of this chain oxidizes NADH to NAD+.  Conveniently, NADH is an intrinsically fluorescent molecule, while NAD+ is not.  Time-resolved studies of NADH fluorescence using fluorescence lifetime imaging (FLIM) can be used to obtain information about NADH and metabolic states in non-malignant and malignant cells. 

Spectral and Lifetime Imaging

Spectral imaging is the collection and display of the spectral components of a fluorescence image. LOCI is currently developing a combined spectral/lifetime detector that is optimized for low-light level multiphoton imaging. The detector works in photon counting mode and essentially sorts detected photons into spectral and temporal bins. This detector is being developed primarily for the Optical Workstation but will also be used with the high-speed multiphoton imaging system currently under development.

High Speed Multiphoton Imaging

Several research projects currently being pursued at LOCI require fast, multiphoton imaging. On the basis of the rationale outlined below we are currently developing a high-speed, single beam laser-scanning MP system. The scanning system will be used in conjunction with the spectral/lifetime detector and will be tightly integrated with this device.

Multiphoton Imaging System

In 1994, we commissioned a multiphoton imaging system that featured an all solid-state excitation source, a 1047nm Nd:YLF laser.  The laser was developed to our specifications by Prof. Allister Ferguson's group at the University of Strathclyde, Scotland, and by Microlase Ltd., a company founded by Prof. Ferguson. This was the first all-solid-state multiphoton system to be developed (Wokosin et al., 1996. Proc.SPIE 2678, 38).

Image Informatics

Bioimage informatics is an interdisciplinary field of research encompassing biology, information science, computer science, statistics, and engineering. Bioimage informatics strives to automate, simplify, and otherwise improve and reinvent techniques for the description, management, analysis, and preservation of biological image data.

Collagen and Breast Cancer

While diagnosis of human breast cancers is advancing, current biomarkers cannot predict outcome for all patients.  Endogenous optical properties of cells and tissues could potentially be used as biomarkers in the clinic.  Collagen can be detected, without staining or labeling of tissue, using second harmonic generation (SHG) imaging, a multiphoton technique.  Collagen signatures, see in mouse models, could be used in breast cancer patients to predict outcomes. 

Multiphoton Flow Cytometry

Traditional flow cytometers are unable to accommodate cell aggregates and often require extrinsic fluorescent labeling for data analysis.  In an effort to analyze larger cell aggregates, a multiphoton flow cytometry (MPFC) instrument has been constructed.  The system is comprised of a flow cell through which large particles and aggregates travel, an optics system with multiphoton excitation capabilities, and data acquisition software.  The flow cell is mounted on an adjustable stage insert compatible with most microscope stages. 

Collagen Signatures

Collagen organization and density can have a profound effect on the behavior of breast cancer cells.  Using second harmonic generation (SHG), the structure of collagen in intact mammary mouse mammary glands can be visualized.  In collaboration with the Keely Lab, a metatstatic collagen signature (TACS3) has been identified leading to useful characterization of breast tissue and tumors.

National Center for Research Resources
National Institute of Biomedical Imaging and Bioengineering
National Institute of Health
National Science Foundation