Upcoming Events

LOCI Collaborator Meeting: Matt Conklin and Ruth Sullivan

05/17/2012 - 10:00

LOCI Collaborator Meeting
May 17th 10:00am-11:00am

Room 236 Animal Sciences

Matt Conklin, Research Scientist
Keely lab and LOCI

Special BME Seminar: Ben Cosgrove

05/24/2012 - 14:00

"A more youthful self-renewal: Bioengineering approaches to rejuvenate dysfunctional muscle stem cells in aging"

2pm, Forum, Wisconsin Institutes for Discovery

Ben Cosgrove
Postdoctoral Fellow
Baxter Laboratory for Stem Cel Biology
Stanford University School of Medicine

MathBio4: SCALE

10/18/2012 (All day)

MATHBIO4: SCALE Symposium

October 18-19, 2012

Software

Bio-Formats

Bio-Formats is 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.

Curvelet-Based Alignment Analysis (CurveAlign and CurvePrep)

CurveAlign is a standalone MATLAB package that allows users to quickly and automatically quantify the alignment of periodic structures (e.g. collagen fibers) in an image.

Data Browser

The Data Browser is an ImageJ plugin that facilitates quick browsing of multichannel, multi-focal plane time course datasets. It is integrated with the Bio-Formats importer plugin—as well as ImageJ's built-in hyperstack and virtual stack support—to provide multidimensional visualization capabilities across space, time and channels.

Fiji plugins

The LOCI Fiji plugins are a collection of plugins for Fiji, available from our Fiji update site.

Fusion Event Locator & Classifier

The Fusion Event Locator & Classifier is an ImageJ macro & MATLAB function to identify fusion events in image stack & classify as proliferating or unchanging.

Intensity Macro for Background Subtraction

The Intensity Macro for Background Subtraction is customized for the image processing and analysis done by the Ogle Lab. It prompts the user to choose a background region of interest, a percentage of background to retain and a region of interest to which the subtraction should be applied. The intensity level to subtract from the fluorescent regions of interest is calculated by computing the level at which the background intensity histogram corresponds to the amount of background the user desires to retain.

Jar2Lib

Jar2Lib is a command line tool for generating C++ proxy classes corresponding to a Java library. We use it to generate the BF-CPP bindings for our Bio-Formats library.

SLIM Curve

SLIM Curve is an exponential curve fitting library used for Fluorescent Lifetime Imaging or FLIM and Spectral Lifetime Imaging or SLIM. It is based on code developed by Paul Barber and his group at the Gray Institute for Radiation Oncology & Biology and used for FLIM functionality in his TRI2 (Time Resolved Imaging) software. It is also used in the LOCI SLIM Plugin project.

SLIM Plotter

The SLIM Plotter is a tool for interactive visualization and inspection of combined spectral lifetime (SLIM) data. It was originally developed for internal use within LOCI and the White and Keely labs, but has grown into an application that may be useful to others as well.

SLIM Plugin

Threshold and Calculate Average Intensity with Brush Tools for IHC Macro

Threshold and Calculate Average Intensity with Brush tools Macro is customized for immunohistochemistry image analysis done in the Ogle Lab. It is especially suited for stained tissue sections that have large areas of background interspersed between areas of signal.

VisBio

VisBio is a biological visualization tool designed for easy visualization and analysis of multidimensional image data.

VisBio Fiji plugins

As part of the development of ImageJ2, we are reworking VisBio as a collection of ImageJ plugins. There is an initial version of one such plugin, VisBio Ortho Stack, available as part of the LOCI Fiji plugins.

WiscScan

WiscScan is acquisition software for laser scanning microscopy, used by LOCI and our collaborators for much of our scientific research.

WiscScan Flow Cytometry

WiscScan Flow Cytometry is a standalone tool for flow cytometry analysis. It works as a plugin for ImageJ that enables post-acquisition analysis of flow cytometry data.

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.

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).

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.

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.

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.

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.

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.