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Instrument Control and Image Acquisition Using Micromanager

Abstract

This is a proposal for workshop consisting of two parts: Using Micromanager (for general users) and Extending Micromanager (for advanced users/developers). This material could be presented in one workshop (with 2/3 of the time on Using Micromanager and 1/3 of the time on Extending Micromanager, or if desirable expanded into two workshops – one general, one advanced.)

Using Micromanager : This section is a general overview of configuring and using Micromanager for controlling devices and acquiring images. It will include exercizes covering the following:

- Setup and configuration

- Devices and Properties

- Defining Channels and Groups

- Performing Multidimensional Acquisitions

- Storing Data and Metadata

- Scripting with Beanshell

Extending Micromanager: This section will begin with an overview of the options available for extending Micromanager, including:

- Micromanager’s Architecture

- Using MMCore directly (e.g. from Python or Matlab)

- Using AttachedRunnables and DataProcessors

- Adding ImageProcessors (in C++)

An Example of a Customized Acquisition: Following the overview, this section we will review how we developed a plugin written in Java that performs a custom multichannel acquisition process. We will demonstate how images can be processed as they are acquired using a combination of AttachedRunnables and DataProcessors to produce calculated images in ‘virtual’ channels. We will demonstrate the use of some classes we have designed to make this process easier.

Authors:

Grant B. Harris,

Amitabh Verma, averma@mbl.edu

Grant is a Scientific Informatics Analyst who as worked with ImageJ and Java for more than a decade. He worked for the last two years on design of ImageJ2.

He has a mechanical engineering degree from MIT.

Amitabh is working as a Scientific Informatics Analyst with experience in MATLAB, C# .Net and Java in the field of algorithm development, signal processing, and instrumentation. He has a M.S. in Biomedical Engineering from Drexel University.

Both Amit and Grant work in the Laboratory of Rudolf Oldenbourg, in the Cellular Dynamics Program at the Marine Biological Laboratory, Woods Hole, Massachusetts. The lab specializes in instrument development for live-cell imaging using polarized light and other techniques.

Keywords

micromanager acquisition processing

Administrative data

Presenting author: Grant Harris
Organisation: Marine Biological Laboratory

co-authors: Amitabh Verma

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