Documentation

Micro-Manager Documentation

In addition to the main Micro-Manager manual, we maintain here documentation for those aspects of Micro-Manager that are still in flux and/or rapidly changing.

• Files and Metadata

• Device Adapters

• Plugins

• High Speed Acquisition

• Display troubleshooting

• Autofocus configuration
  • Autofocus setup - Making Micro-Manager use image-based autofocus
  • Autofocus manual - Configure the image-based autofocus implemented in Java
  • SimpleAutofocus Device Adapter - Configure the image-based autofocus ‘device’ implemented in C++

• Scripting in Micro-Manager
  • Script Panel GUI - Introduction to the Script Panel GUI
  • gui object - Documentation of the GUI scripting object
  • mmc object - Documentation of the mmc Micro-Manager core object
  • acq object - Documentation on the Multi-Dimensional Acquisition object
  • example Beanshell scripts - A few example scripts with minimal annotation

• Matlab and Micro-Manager
  • Matlab and the Micro-Manager core - Setting up Matlab to control hardware through the Micro-Manager core.
  • Matlab and the Micro-Manager GUI - Controlling the Micro-Manager graphical user interface with Matlab.
  • Roboscope project - Roy Wollman’s Roboscope project

• Python and Micro-Manager
  • Using the Micro-Manager python library

• Communicating through serial ports using a terminal application
  • Windows - Configuring HyperTerminal
  • Useful terminal applications for Windows and Mac

• Coordinates and Directionality in Micro-Manager
  • Overview

• User contributed adapters and notes
  Some of the Micro-Manager users have written adapters that have not (yet) been incorporated into the Micro-Manager distribution. We’ll keep information on these adapters right here.
  • Firewire camera/LED synchronization - A Micro-Manager plugin by Alex Hodge synchronizing multi-color LED illumination with a Firewire camera
  • RatiometricImaging_main.bsh - Beanshell for ratiometric Imaging (J. Husson).
  • RatiometricImaging_singleImage.bsh - Beanshell for ratiometric Imaging.
    Takes only one image, can be useful as a control before starting a whole acquisition with main beanshell above (J. Husson).

MultiROI_MultiD_Acquisition

• Beanshell script for acquiring stacks in 3 different channels and at 4 different fields of view. Contributed by Saumya Saurabh

• Building and Coding Micro-Manager (for developers)

  • Building Boost on MacOS X
  • Full Build on MacOS X Leopard - How to install and build Micromanager 1.2 and dependencies (tested on MacOS X 10.5.2)
  • Building Universal Binaries on Mac OS X
  • Configuration options - Build options on Mac OS X and Linux
  • Building ACE on the Mac - How to build ACE on the Mac (only for MicroManager versions before 1.3.42)
  • Linux installation from source (Ubuntu)
  • Building Firewire camera support on Linux
  • Building MM on Windows - Different environments and options
  • Compiling MM and creating deb files on 64-bit Ubuntu - A log of things I needed to do to build 64-bit version of MM.
  • Using Eclipse - How to configure Eclipse to compile and debug the Micro-Manager GUI.
  • Using Netbeans - How to configure Netbeans to compile and debug the Micro-Manager GUI.
  • Debugging MM on MacOSX and Unix - How to use gdb or Netbeans to debug the Micro-Manager C++ core.
  • Micro-Manager Coding Style and Conventions
  • Writing plugins for Micro-Manager
  • Tools useful for Device Adapter Developers

• Papers citing and/or acknowledging the use of Micro-Manager
  • Papers citing Micro-Manager - Add your own paper to the list!