Welcome to the Laboratory for Optical and Computational Instrumentation!
We are a biophotonics instrumentation laboratory developing advanced optical and computational techniques for imaging living specimens.

Recent News

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Melissa Skala: Follow the light to better cancer treatment

Fri, 02/05/2016

Biomedical engineer Melissa Skala would be happy to chat about some of the whiz-bang features of her medical imaging technology, such as resolution, speed, throughput, signal-to-noise ratio and the like.

But she’d much rather talk about the problems her technologies attack.

Marvin Minsky (1927-2016)

Tue, 01/26/2016

American cognitive scientist and open source advocate Marvin Minsky describes his invention of the confocal microscope in 1955 at Harvard University in video below from Web of Stories.

Creating new workflows for single molecule imaging with ThunderSTORM

Tue, 01/26/2016









FORUM—New open source code written by Christophe Leterrier of the Axonal Domains Architecture (ADA) team at the Center for Research in Neurobiology and Neurophysiology at Marseille complements the ImageJ/Fiji ThunderSTORM plugin for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM.  

Visualizing in 3D with ClearVolume in ImageJ

Wed, 01/20/2016

FORUMImageJ and SciJava developers, including LOCI's Software Developer Mark Hiner and Software Architect Curtis Rueden are in the midst of a hackathon in Konstanz, Germany focusing on ImageJ OpsKNIME Image Processing and related technologies.  Future 3D efforts for ImageJ and SciJava will use the volume rendering ClearVolume plugin developed by members of the Myers Lab at the Max Planck Institute of Molecular Cell Biology and Genetics.  ClearVolume is a Java library and ImageJ plugin that performs 3D rendering and more on the GPU with open sources that can be cloned from GitHub.

Continuing the conversation: New discussion board for ImageJ users and developers

Tue, 01/19/2016










FORUM—In November 2015, ImageJ released a new discussion board, the ImageJ Forum to offer a central place for questions and discussions regarding ImageJ and include the full breadth of the ImageJ community, from basic users to advanced developers.  The community is diverse, helpful, attentive, and aims to facilitate ease of communication.

The new ImageJ Forum was built using Discourse, a modern, open-source interface that serves as mailing list, discussion forum, and long-form chat room. 

Integrating KNIME with ImageJ2

Fri, 01/15/2016













LOCI Collaborator Series: "KNIME with Gabriel Einsdorf" 11:00-12:00 Animal Science Building Room 236 

The KNIME Image Processing Plugin allows you to read in more than 120 different kinds of images (thanks to the Bio-Formats API) and to apply well known methods on images, like preprocessing. segmentation, feature extraction, tracking and classification in KNIME. In general these nodes operate on multi-dimensional image data (e.g. videos, 3D images, multi-channel images or even a combination of them), which is made possible by the internally used ImgLib2-API.

What's your Eigenvector, Victor? Understanding Eigenvectors in BoneJ

Fri, 01/15/2016




FORUMBoneJ is a plugin for bone image analysis in ImageJ, created by Dr. Michael Doube that provides free, open source tools for trabecular geometry and whole bone shape. The anistropy function in BoneJ analyzes the degree of orientation in substructures within bone volume.  

Developing ImageJ Ops with Mark Hiner

Thu, 01/14/2016


LOCI Collaborator Series: "Using ImageJ Ops with Mark Hiner" Thursday, March 24th 11:00-12:00 Animal Science Building Room 236

ImageJ Ops is a framework for reusable image processing operations. Ops extends Java's mantra of "write once, run anywhere" to image processing algorithms.  The central goal is to enable programmers to code an image processing algorithm in the Ops framework, which is then usable as-is from any SciJava-compatible software project.

Correlating pixel intensity: New directions for ImageJ Coloc2 plugin with Ellen Arena

Thu, 01/14/2016


LOCI Collaborator Series: "New Directions with Coloc2 in ImageJ" with Ellen Arena Thursday, May 19th 11:00 am-12:00 pm Animal Sciences Building Room 236

MADISON—Coloc2 is Fiji's plugin for colocalization analysis. It implements and performs the pixel intensity correlation over space methods for scatterplots, analysis, automatic thresholding and statistical significance testing.

Upcoming Events

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LOCI Collaborator Series: Focusing through a multimode fiber with a spatial light modulator with Zach Poskin

02/18/2016 - 11:00

"Focusing through a multimode fiber with a spatial light modulator" with Zach Poskin
February 18th 11:00 AM Animal Sciences Building Room 236

LOCI Collaborator Series: Computational imaging with active light fields with Andreas Velten

02/18/2016 - 11:00

"Computational imaging with active light fields" with Andreas Velten
11:00-12:00 Animal Science Building Room 236 

LOCI Collaborator Series: KNIME with Gabriel Einsdorf

02/25/2016 - 11:00


KNIME with Gabriel Einsdorf; 11:00-12:00 Animal Science Building Room 236 

LOCI Collaborator Series: Emergent second harmonic generation of tungsten diselenide nanostructures with Melinda Shearer and Leith Samad

02/25/2016 - 11:00


"Emergent second harmonic generation of tungsten diselenide nanostructures" with Melinda Shearer and Leith Samad; The Jin Group, Department of Chemistry. 11 am-12 pm Room 236 Animal Sciences Building.

LOCI Collaborator Series: Development of an integrated collagen quantification platform for cancer research with Yuming Liu

03/10/2016 - 11:00

"Development of an integrated collagen quantification platform for cancer research" with LOCI Associate Scientist Yuming Liu
11:00-12:00 Animal Science Building Room 236

LOCI Collaborator Series: Development of an integrated collagen quantification platform for cancer research with Corinne Esquibel

03/10/2016 - 11:00


















"Development of an integrated collagen quantification platform for cancer research" with LOCI Post Doctoral Fellow Corinne Esquibel, Neural Interfaces Technology Research and Optimization Laboratory, Department of Biomedical Engineering, PI Justin Williams; 11:00-12:00 Animal Science Building Room 236

LOCI Collaborator Series: Mapping the collagen ECM landscape using high throughput SHG imaging and computational analysis to predict and diagnose breast cancer with Matt Conklin

03/24/2016 - 11:00

"Mapping the collagen ECM landscape using high throughput SHG imaging and computational analysis to predict and diagnose breast cancer" with Scientist Matt Conklin, Paul Campagnola Laboratory. 11:00-12:00 Animal Science Building Room 236

LOCI Collaborator Series: Using ImageJ Ops with Mark Hiner

03/24/2016 - 11:00


Using ImageJ Ops with Mark Hiner 11:00-12:00 Animal Science Building Room 236

ImageJ Ops is a framework for reusable image processing operations. Ops extends Java's mantra of "write once, run anywhere" to image processing algorithms.  The central goal is to enable programmers to code an image processing algorithm in the Ops framework, which is then usable as-is from any SciJava-compatible software project, such as ImageJCellProfilerKNIMEOMERO and Alida.

LOCI Collaborator Series: LINK multiscale imaging platform for quantitative analysis of collagen organization with Lauren Woods

03/31/2016 - 11:00

"LINK Multiscale Imaging Platform for Quantitative Analysis of Collagen Organization" with Lauren Woods, Paul Campagnola Laboratory
11:00-12:00 Animal Science Building Room 236

Software at LOCI

LOCI is an active partner in the SciJava and Open Microscopy Environment consortiums, and participates in many related software projects, including:

ImageJ
Fiji
SCIFIO
Bio-Formats
WiscScan
ImgLib2
SciJava Common
SLIM Curve
KNIME
OMERO
Insight Toolkit

Browse all LOCI software

Software Highlight

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.

When do I use CurveAlign and when  do I use CT-FIRE?

These two programs were developed with complementary but slightly different main goals. CurveAlign was developed first and had the main goal of quantifying all fiber angles within a region of interest relative to a user defined boundary be it a straight line or a tumor boundary. As our research grew in investigating the role of collagen in cancer progression and invasion we wanted to investigate how individual fiber parameters could influence cancer and other diseases. Out of this need came the development of CT-FIRE to analyze individual fiber metrics such as length, width, angle, and curvature.  Besides the relative angle quantification, the newest version of CurveAlign can be used to extract other collagen fiber features, such as localized fiber density, fiber alignment, and the spatial relationship between fiber and the defined boundary. In addition, the extracted individual fibers extracted by CT-FIRE can be imported into the CurveAlign for the feature extraction mentioned above. We have future plans to integrate these programs further. For now CurveAlign should be used for bulk assessment of collagen features including angles/density and CT-FIRE for individual fiber quantification.

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 is an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

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

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

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

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.

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 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.

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).

SCientific Image Format 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 is an exponential curve fitting library used for Fluorescent Lifetime Imaging (FLIM) and Spectral Lifetime Imaging (SLIM).

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. 

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.

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

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

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.

Instrumentation at LOCI

To benefit the scientific community in an accessible way, LOCI develops new and improved imaging instrumentation and optical-based experimental techniques:

SETI
OpenSPIM
CAMM
MPFC
Spectral Confocal
FLIM
Intravital
Photoactivation
Ultra
SLM
Optical Work Station
Beam-Shaping

Browse all LOCI instrumentation

Research Highlight

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. 

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.

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. 

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.

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).

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.

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