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Micro-Manager FAQ

Revision as of 15:27, 12 September 2009 by Nico (Talk | contribs)

Micro-Manager, Frequently Asked Questions

Does Micro-Manager work with ... camera/microscope/etc?

Check the list of supported hardware here. If you are unsure, post your question to the Mailing List

There is an ImageJ driver for my camera. Can I use the camera with Micro-Manager?

Not necessarily. Micro-Manager provides an identical interface to all cameras, which means that scripts and applications written using Micro-Manager will work with all supported cameras. ImageJ camera drivers do not work that way (i.e., they are all different, and Micro-Manager has no way of operating with them), so whether or not there is an ImageJ driver for a device has no bearing on it working with Micro-Manager. In technical terms, to make a camera work in Micro-Manager, you will need a Micro-Manager device adapter (written in C++), which is very different from an ImageJ camera driver. Check the list of supported hardware to see if there is a Micro-Manager device adapter for your camera.

I have some hardware that is not supported by Micro-Manager. How do I make it work?

First, contact the manufacturer of the hardware and express your interest in a Micro-Manager adapter. We simply do not have the resources to work on every piece of hardware out there and we made an open interface so that everyone can write support for any piece of hardware. We strongly encourage companies producing hardware to take care of Micro-Manager support themselves (and quite a few have already done so). The company might be persuaded if they hear from enough customers. Alternatively, you can write the adapter yourself, or find a friend with experience writing code in C++ (there are quite a few examples so it will not be extremely difficult). There is a device developer's kit, and providing support to people writing device adapters is one of our top priorities. Lastly, post your request to the Micro-Manager mailing list. We or others might be persuaded to work on this if we hear that people need it.

Something does not work. What do I do?

Send an email describing your problem to the Micro-Manager mailing list. Describe your system in as much detail as possible (OS, attached hardware), and describe the steps that lead to the problem you encounter as well as the error message you see. Include the configuration file that you are using (the *.cfg file you select on startup).

If the problem is not resolvable through the email list, you will need to send more debug information. To do so, go to the 'Tools' menu in Micro-Manager and select 'Options...'. Click the 'Clear log file' button and make sure that the 'Debug log enabled' checkbox is checked. Now repeat the steps that cause the error and then email the file 'CoreLog.txt' (in your Micro-Manager directory) to together with your config file and a description of the problem (include the error message on the screen). We will likely need your help to test some code modifications to deal with your problem.

In some cases, even more debug output can be obtained by running Micro-Manager from a command terminal. On the Mac:
1. open a terminal (Applications/Utilities/Terminal)
2. Type: cd /Applications/Micro-Manager1.2
3. Start Micro-Manager by typing: java -cp ij.jar ij.ImageJ
4. Copy relevant output from the terminal into your email.

On Windows:
1. open a terminal (Start->Run..., type 'cmd', click 'OK')
2. Type: cd "C:\Program Files\Micro-Manager1.2"
3. Start Micro-Manager by typing: jre\bin\java -cp ij.jar ij.ImageJ
4. Copy relevant output from the terminal into your email.

Citing Micro-Manager

You can cite either:
Stuurman, N., Amodaj N., Vale, R.D. (2007). Micro-Manager: Open Source software for light microscope imaging. Microscopy Today. 15(3):42-43.
and/or the website:
µManager (

Also, please update "Papers citing Micro-Manager" with a reference to your paper. We will need this information to secure future funding.

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