Grant B. Harris

Scientific Informatics Analyst

in the Laboratory of Rudolf Oldenbourg

This is a summary of the work I have been engaged in while working at the Architectural Dynamics in Living Cells Program (now part of the Cellular Dynamics Program) at MBL from 2002 to the present.  The lab engages in interdisciplinary collaborations to conduct research in physical optics for the interpretation of image content and of computational methods for image enhancement and restoration.  These physical and engineering projects are stimulated and guided by biological inquiries into the structural basis of cell function.

In particular, I have been involved in the development of software systems for birefringence imaging of live cells using polarized light microscopy.  I work primarily for Dr. Rudolf Oldenbourg, while also assisting Dr. Shinya Inoué and Dr. Michael Shribak.  My work has involved software design & development, microscopy and optics, engineering, and multimedia production.

(For information on my education and work prior to joining the MBL in 2001, see my CV.)

Software Design & Development

I have performed all aspects of software systems design and development in the Lab, including testing, debugging, documentation and support.

I have primarily used Java in the programming of various projects since 2001.  I have mastered many aspects of this object-oriented programming language, including concurrency / multi-threading, polymorphism, generics,  annotations, etc.  I have extensively incorporated open source libraries in the construction of systems and components.  I have used the Java Native Interface to utilize third-party libraries for hardware control and data interfacing.  This requires the design of  C/C++ wrappers, which I have built for cameras and an X-Y stage controller.  I use the Netbeans integrated development environment, as well as other development tools including ANT, SWIG, etc.  I have also utilized other programming languages, including C++, C#, and  Python.

Technical Expertise:

  • API Design, Refactoring
  • Java Applications Design/Development
  • Application frameworks
  • extensive review of available open source frameworks, SAF, NetBeans Platform
  • Java – generics, annotations
  • Dependency injection, Module systems (OSGI, NetBeans)
  • GUI
  • Swing, EDT, UI Designers, layouts
  • Java/C++: JNI, Swig

Development Tools I Work With:

  • NetBeans IDE & Platform
  • Version control (SVN, Git, GitHub)
  • Build (Ant, Maven),
  • Issue Tracking (Trac)

Microscopy & Optics

Microscopy and Optics Resources

AQLM

I completed the Analytical & Quantitative Light Microscopy course at MBL in 2005 and have subsequently presented workshops on using ImageJ and other open source software for particle tracking with Khuloud  Jaqaman.

Current Projects

I have designed the application architecture, user interface, configuration, data management, and application programming interfaces (API) for a series of projects, including:

Jif: Java Instrumentation Framework

The Java-Instrumentation-Framework is open source  software developed over the last decade for instrument control and image acquisition.

Combined Birefringence and Dichroism Imaging System

We are currently developing a a new system for measuring linear and circular dichroism dispersion for Gus Rosania at the University of Michigan.

LC-PolScope Birefringence Imaging Components

Micro-Manager and ImageJ Plugins for Birefringence and Fluorescence Polarization Imaging.

Link to our  MicroManager Plugins.

Link to LC-PolScope  resources.

ImageJ2 & ImgLib2Imglib2-logo

I worked as an architect and developer on the ImageJ2 project (Sept. 2009 – Sept. 2012) which grew out of a paper I wrote in 2009,  IjX: ImageJ refactored to interfaces for eXtensibility  This NIH-funded project involved the refactoring/reengineering of ImageJ and integration with ImgLib2.  The project lead is  Kevin Eliceiri, along with Curtis Rueden and Johannes Schindelin at the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin, Madison.  Collaborators include Anne Carpenter and Lee Kaminski of the Imaging Platform at the Broad Institute at MIT, Pavel Tomancak at  MPI-CBG, Dresden and others affiliated with Fiji.  I continue as reviewer/contributor as time allows.

Past Projects

For an overview of projects I have worked on while at MBL, see this summary of past projects .

References and Resources

Image Informatics

Image Informatics and Microscopy Resources

On Java Programming, Imaging, NetBeans, and Software Design

ImageJ Conferences (Luxembourg)

2008, I presented a Poster: Instrument Control and Image Acquisition Tools for Live-Cell Imaging,  (received 3rd place award)  This presents the design of modules within the Jif Framework and CamAcqJ.

2012, I presented a Workshop: Instrument Control and Image Acquisition Using Micromanager (90 min).

Multimedia Production

In addition to my software design and engineering work, I provide support for multimedia projects.

  • PowerPoint – Extensive work with PowerPoint, designing templates, embedding  multimedia, and graphical  design work. I trained Dr. Inoue on PowerPoint and have assisted him extensively  on the design of presentations and preparation of images, illustrations  and video materials.
  • Video Production & Editing – Produced video tutorial on Polarized Light Microscopy Demonstration for Dr.  Inoue.  Video codec conversions & testing.
  • DVD Production – Produced a companion DVD for the book The Collected Works of  Shinya Inoue.  Integration of video, PowerPoint presentation,  instructions, DVD/CD auto-run & menu system.
  • Video Archival Project -Supervised the digitization/conversion of 400+ hours of  material from Dr. Shinya Inoue’s library of video microscopy experiments going back to 1980.  Transfers  from UMatic, ED-Beta, VHS, and Hi-8, and optical disk  recorders to DVD;  Time-lapse video converstions  using Sony TVO-9000,  time- lapse UMatic VTR.