Grant Harris

Scientific Informatics Analyst at the Marine Biological Laboratory, 2002-2015

in the Laboratory of Rudolf Oldenbourg, Cellular Dynamics Program

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 until 2015.  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.

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)
See  Overview of Software Projects

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

Bioimage Informatics

ImageJ2, Architect and Developer

I was an active participant in the ImageJ open source community.

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).

LC-PolScope Birefringence Imaging Components

PSj/LC-PolScope is now

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

Microscopy & Optics

References and Resources

[Image Informatics]

[Image Informatics and Microscopy Resources]

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

Java Resources

[On Java Programming, Imaging, NetBeans, and Software Design]

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.