Documentation

From Micro-Manager

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.

Autofocus configuration

  Autofocus setup - Making Micro-Manager use image-based autofocus
  Autofocus manual - Configure the image-based autofocus

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 Configuration - Setting up Matlab to run Micro-Manager
  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

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
  Media:RatiometricImaging_main.bsh - Beanshell for ratiometric Imaging (J. Husson).
  Media: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).

Building the software (for developers)

  Building ACE on the Mac - How to build ACE on the Mac
  Full Build on MacOS X Leopard - How to install and build Micromanager 1.2 and dependencies (tested on MacOS X 10.5.2)
  Using Eclipse - How to configure Eclipse to compile and debug Micro-Manager
  Configuration options - Build options on Mac OS X and Linux
  Building MM on Windows - Different environments and options
  Debugging MM on MacOSX and Unix - How to use gdb with Micro-Manager
  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.
  Linux installation from source (Ubuntu)

Papers citing and/or acknowledging the use of Micro-Manager

  Papers citing Micro-Manager - Add your own paper to the list!