Micro-Manager
Introduction
A Meiji Techno EMZ5-TR stereo zoom microscope with
focus drive.
Micro-Manager is an open-source software package for microscopes. It provides an all-in-one solution to automate tasks such as time-lapse photography, z-stacks or even autofocus.
This document describes how to configure Micro-Manager on a Meiji Techno stereo microscope with focus drive and a camera in four steps:
- Installing Micro-Manager
- Configuring the Focus Drive
- Configuring the Camera
- Taking pictures
Installing Micro-Manager
Micro-Manager Main Window
- Download the latest version of Micro-Manager from
the Micro-Manager
web
site.
- Execute MMSetup to install the Micro-Manager program.
Focus Drive
The focus drive (or z-stage) allows precise, computer-controlled, vertical positioning of your Meiji Techno microscope. For installation instructions, please refer to the Micro-Manager wiki.
Focus Drive Settings
A graphical interface is available to configure the Focus Drive. From the Micro-Manager main window, open the Tools menu and select Device/Property Browser to access the Focus Drive settings. The following settings are available:
StepperSpeed
Sets the speed of the focus drive. Various settings are available from 1 revolution per minute (1 rpm) to 2 revolutions per second (2 rps). The default value is 1 rps.StepperIdleTimerS
Sets the focus drive idle timer. Units are seconds. If no positioning command has been received for more than StepperIdleTimerS seconds, the focus drive releases the fine focus knob. A value of 0 disables the idle timer; the focus drive never releases the fine focus knob. The default value is 0.StageTravelUm
Sets the vertical travel. Units are µm. The focus drive will refuse positioning more than StageTravelUm above or less than StageTravelUm below the initial position at power up. The default value is 33000µm, or 33mm.StageStepSizeUm
Sets
the focus drive step size.
Units are µm. One revolution of the focus drive equals 200 steps.
The default value is 19.25µm.StagePositioningTimeOutS
Sets the focus drive positioning timeout. Units are seconds. The focus drive will halt the motor if a positioning command takes more than StagePositioningTimeOutS seconds. You may have to increase this value if you wish to move large distances (e.g. 33mm) at very low speeds (e.g. 1 rpm). The default value is 60s.PortTimeoutMs
Sets the
focus drive port timeout.
Units are milliseconds. The focus drive drive will report an error if
the focus drive takes more than PortTimeoutMs
milliseconds to
begin execution of a command. If this error occurs, check the cable
between focus drive and PC. Check the focus drive power supply is
plugged in. The default value is 1000ms, or 1 second. Tethered Camera
The Tethered Camera driver allows using off-the-shelf Canon and Nikon digital reflex cameras for microphotography. For installation instructions, please refer to the Micro-Manager wiki.
A graphical interface is available to configure the camera. From the Micro-Manager main window, open the Tools menu and select Device/Property Browser. You can:
- set exposure times
- choose color or grayscale images
- scale the image down
- mirror or rotate the camera image. This is useful if camera and eyepiece produce images with a different orientation.
Taking Pictures Using Micro-Manager
Micro-Manager: z-stack
We have set up Micro-Manager with camera and focus drive. We are ready to take pictures.
As an example, we'll set up Micro-Manager to take pictures every 0.2 mm from the current position to 5 mm down. From the Micro-Manager main window, open the Tools menu and select Multi-Dimensional Acquisition.
Select "relative Z" and introduce 0 µm for Z-start, 5000 µm for Z-end, 200 µm for Z-step. Verify the objective will not bump into anything when the pictures are taken. Click on Acquire. The focus drive should move 5 mm down in steps of 0.2 mm, taking pictures at each step. Once all pictures have been taken the focus drive returns the microscope to its original position.
Micro-Manager has many more functions such as time-lapse, or auto-focus. Auto-focus is especially interesting for trinocular stereo microscopes such as Meiji Techno EMZ8TR and Meiji Techno EMZ13TR, where camera and eyepiece ports can be used simultaneously.
Micro-manager is also available for MacOS X and Linux systems. A full discussion of Micro-Manager is beyond the scope of this document. For further information about Micro-Manager, see Micro-Manager user's guide.
Links
Focus Drive
Tethering Software
- Breeze Systems software for Canon and Nikon.
Back to Focus Drive
