LOCI | Laboratory for Optical and Computational Instrumentation

Welcome to the Laboratory for Optical and Computational Instrumentation (LOCI) web site!

Upcoming Events

Bock Labs Research Hour: Cedric Finet

05/24/2013 - 15:30

Title: Recruitment of a partial gene network underlies wing pigmentation novelty in flies

Cedric Finet
Postdoctoral Fellow, Carroll Laboratory
Laboratory for Cell and Molecular Biology
Howards Hughes Medical Institute
University of Wisconsin at Madison

LOCI Collaborator Meeting: Greg Longmore Laboratory

05/30/2013 - 14:30

Callie Corsa
Graduate Student, Greg Longmore Laboratory
Washington University, St. Louis MO

"DDR2 and Breast Cancer"

Room 274 Animal Sciencs

2:30pm-3:30pm
May 30th 2013

LOCI Collaborator Meeting: Suresh Alahari

05/31/2013 - 12:00

Suresh K. Alahari, PhD
Fred G. Brazda Professor
Department of Biochemistry & Molecular Biology
LSU Health Sciences Center
New Orleans, LA

"Nischarin, a novel tumor suppressor of breast cancer, is regulated by microRNA-27b"

Software at LOCI

LOCI is an active partner in the SciJava and Open Microscopy Environment consortiums, and actively develops several related software projects, including:

	ImageJ
	Fiji
	SCIFIO
	Bio-Formats
	SciJava Common

Software Highlight

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.

ctFIRE

The purpose of this standalone MATLAB package is to allow users to automatically extract and quantify the alignment of collagen fibers in an image.

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

Fiji is an image processing package. It can be described as a distribution of ImageJ (and soon ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

Fiji image stitching

The image stitching plugins, written by Stephan Preibisch, provide a means for reconstructing large mosaics from tiled datasets.

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.

ImageJ

ImageJ2 is a new version of ImageJ for the next generation of multidimensional image data. It improves upon ImageJ's core design, enabling support for N-dimensional image data beyond 5D, from sources beyond just hard disks, additional pixel types, more flexible visualization, more modular analysis, and headless capabilities for automated server-side image processing.

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++ wrapper libraries around Java JAR files. We use it to generate the BF-CPP bindings for Bio-Formats, which we use in our WiscScan acquisition software.

Prairie Conversion & Backup Script

A script to help manage Prairie Technologies datasets. It converts Prairie datasets to compressed OME-TIFF, and archives the original files as a ZIP archive (which can then be backed up externally).

SCIFIO

SCientific Imaging Formats Input and Output (SCIFIO) is a framework for developing and accessing image I/O plug-ins. SCIFIO will include support for many open-source formats, and Bio-Formats will become the flagship SCIFIO plug-in.

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 Plugin

Threshold and Calculate Average Intensity with Brush Tools

The 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.

Tracking Movie Script

This script creates an animation from ROIs added to the ROI Manager. It uses the associated image plane of each ROI, adjusted spatially such that the first (X, Y) coordinate of each ROI occupies the same location, as a "poor man's" registration technique. Each plane is then assembled into the final movie.

TumorTrace

The TumorTrace program is an automated image analysis tool, developed in MATLAB (The Mathworks, Inc., Natick, MA), for examining the ECM surrounding cells or tumors in the context of cellular morphology, protein expression and movement. It takes as input multiple image channels, either single images or stacks representing time-series or 3D data. It then finds a metric for the cell/cell cluster morphology and outputs plots representing intensity, morphology, collagen fiber alignment, and cell movement; .csv files containing raw data and image files containing the regions of interest.

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.

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.

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 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 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.

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.

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).

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.

Upcoming Events

Software Highlight

Research Highlight