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(Micro-Manager Documentation)
 
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In addition to the [http://micro-manager.org/documentation.php main Micro-Manager manual], we maintain here documentation for those aspects of Micro-Manager that are still in flux and/or rapidly changing.   
 
In addition to the [http://micro-manager.org/documentation.php 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''
+
* ''[[Files and Metadata]]''
  [[Autofocus setup]] - Making Micro-Manager use image-based autofocus
+
  [[Autofocus manual]] - Configure the image-based autofocus
+
  
''Scripting in Micro-Manager''
+
* ''[[Device_Support|Device Adapters]]''
  [[Script Panel GUI]] - Introduction to the Script Panel GUI
+
  [http://micro-manager.org/content/doc/mmstudio/org/micromanager/api/ScriptInterface.html gui object] - Documentation of the GUI scripting object
+
  [http://micro-manager.org/content/doc/mmcore_api/html/class_c_m_m_core.html mmc object] - Documentation of the mmc Micro-Manager core object
+
  [[example Beanshell scripts]] - A few example scripts with minimal annotation
+
  
''Matlab and Micro-Manager''
+
* ''[[Plugins]]''
  [[Matlab Configuration]] - Setting up Matlab to run Micro-Manager
+
  [[Roboscope project]] - Roy Wollman's Roboscope project
+
  
''Communicating through serial ports using a terminal application''
+
* ''[[High Speed Acquisition]]''
  [[Windows]] - Configuring HyperTerminal
+
  
''Coordinates and Directionality in Micro-Manager''
+
* ''[[Display troubleshooting]]''
  [[Overview]] -
+
  
 +
* ''Autofocus configuration''
 +
** [[Autofocus setup]] - Making Micro-Manager use image-based autofocus
 +
** [[Autofocus manual]] - Configure the image-based autofocus implemented in Java
 +
** [[Autofocus Device Adapter|SimpleAutofocus Device Adapter]] - Configure the image-based autofocus 'device' implemented in C++
  
''User contributed adapters and notes''
+
* ''Scripting in Micro-Manager''
 +
** [[Script Panel GUI]] - Introduction to the Script Panel GUI
 +
** [http://micro-manager.org/content/doc/mmstudio/org/micromanager/api/ScriptInterface.html gui object] - Documentation of the GUI scripting object
 +
** [http://micro-manager.org/content/doc/mmcore_api/html/class_c_m_m_core.html mmc object] - Documentation of the mmc Micro-Manager core object
 +
** [http://micro-manager.org/content/doc/mmstudio/org/micromanager/api/AcquisitionEngine.html acq object] - Documentation on the Multi-Dimensional Acquisition object
 +
** [[example Beanshell scripts]] - A few example scripts with minimal annotation
  
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.
+
* ''Matlab and Micro-Manager''
 +
** [[Matlab Configuration|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
  
''Building the software (for developers)''
+
* ''Python and Micro-Manager''
  [[Building ACE on the Mac]] - How to build ACE on the Mac
+
** [[Using the Micro-Manager python library]]  
  [[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]]
+
  
''Papers citing and/or acknowledging the use of Micro-Manager''
+
* ''Communicating through serial ports using a terminal application''
  [[Papers citing Micro-Manager]] - Add your own paper to the list!
+
** [[Windows]] - Configuring HyperTerminal
 +
** [[Useful terminal applications for Windows and Mac]]
 +
 
 +
* ''Coordinates and Directionality in Micro-Manager''
 +
** [[Overview]] -
 +
 
 +
 
 +
* ''User contributed adapters and notes'' <br> 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.
 +
** [http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=alex:projects:fluorescent_imaging:start 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.<br>Takes only one image, can be useful as a control before starting a whole acquisition with main beanshell above (J. Husson).
 +
[[Image:MultiROI_MultiD_Acquisition_V1.7_10122010_(2).bsh]] - Beanshell script for acquiring stacks in 3 different channels and at 4 different fields of view. COntributed by Saumya Saurabh[[http://valelab.ucsf.edu/~nico/MMwiki/index.php/User:Saumya]]
 +
 
 +
* ''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]]
 +
** [[(Windows) 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!
 +
 
 +
 
 +
{{Documentation_Sidebar}}

Latest revision as of 10:31, 26 September 2013

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.

  • Coordinates and Directionality in Micro-Manager


  • 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.

File:MultiROI MultiD Acquisition V1.7 10122010 (2).bsh - Beanshell script for acquiring stacks in 3 different channels and at 4 different fields of view. COntributed by Saumya Saurabh[[1]]


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