Scripting Micro-Manager

Nico Stuurman and Henry Pinkard, late 20202...

Program:

  1. Introductions (30 s each;)
  2. Intro to Core APIs(Nico)
  3. Intro to pycro-manager(Henry)
  4. Breakout session on Core
  5. Intro to MM 2.0 API(Nico)
  6. Intro to pycro-manager APIs(Henry)
  7. Breakout on higher level APIs
  8. Plugins: Micro-Magellan (plugins)
  9. (optional) Breakout on plugins, freeform, etc..
  10. Evaluation/Summary

Micro-Manager, Key Points:

Open Source

> 150 code contributors

Community driven

Cross-platform

Mac, Windows

Extensible:
Script, Plugins, APIs
Python, Matlab, Labview, C/C++, etc..

FREELY AVAILABLE!

Software architecture overview, 2005

Nenad Amodaj

Supported by the Sandler Foundation

Bottom (device adapter) API

All Devices

Cameras

Compiled Binaries

Software architecture overview, 2005

Nenad Amodaj

Software architecture overview, 2005

Nenad Amodaj
Swig
MMCoreJ_wrap.jnilib
MMCoreJ.jar
MMCorePy.Pi
μManager UI
Matlab
Python aps

https://micro-manager.org/wiki/Micro-Manager_Programming_Guide

Many ways to interact with APIs

Java Icon Images #201788

Micro-Manager Beanshell scripting

Script-Button Panel Editor Pane Immediate Pane (REPL)

Startup Script

Thanks!

Ron Vale
Multiple generations of Vale Lab members
μManagers:
Nenad Amodaj
Arthur Edelstein
Oleksiy Danikhno
Karl Hoover
Henry Pinkard
Ziah Dean
Mark Tuschida
Chris Weisiger
Many, many code and documenation contributions from scientists, enthusiasts, and companies.
μManager Community
Supported by grants from the Sandler Foundation and NIH (NIBI) R01EB007187