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Micro-Manager FAQ

Revision as of 08:56, 20 January 2012 by Nico (Talk | contribs)

Micro-Manager, Frequently Asked Questions

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

Check the list of supported hardware. 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.

Why are my images being displayed incorrectly on screen?

Sometimes ImageJ and Micro-Manager images show strange blocky artifacts on Windows XP. You may be able to fix this problem by turning off Direct3D for Java. To do so, set the following environment variable in your system:

Variable: J2D_D3D
Value: false

(To edit environment variables, right click on My Computer, select Properties > Advanced > Environment Variables)

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 Micro-Manager Device Developer's Kit for Windows, 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.

Does Micro-Manager work with my Axiocam camera?

No. Despite many requests from us and Micro-Manager users, Zeiss does not make available the documentation and programming interface needed to operate AxioCam cameras. If you have one of these cameras and would like to operate it with Micro-Manager, please ask your local Zeiss contact person to make available the AxioCam SDK to the Micro-Manager team. If you are considering to buy one of these cameras, be aware that it will lock you into using Zeiss software with that camera. If you have one of these cameras and want to upgrade your system, it might be cheaper to buy a decent Micro-Manager compatible camera (for instance from "The Imaging Source" or "Scion") than to buy a new copy of AxioVision.

Something does not work. What do I do?

Download and install the latest Nightly Build and check if the problem still persists. Send an email describing your problem to the Micro-Manager mailing list. Describe your system (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). Please do not send screenshots!

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 entire 'CoreLog.txt' file (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-Manager1.3
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-Manager1.3"
3. Start Micro-Manager by typing: jre\bin\java -cp ij.jar ij.ImageJ
4. Copy relevant output from the terminal into your email.

Some problems are only due to missing .dll files required by Micro-Manager's device drivers. To find out whether that is the case, use Dependency Walker on Windows, otool -L on MacOSX or ldd on Linux to determine the status of the dependencies of the Micro-Manager driver (i.e. a file whose name starts with mmgr_dal_ in the Micro-Manager directory).

Citing Micro-Manager

You can cite either:

  • Arthur Edelstein, Nenad Amodaj, Karl Hoover, Ron Vale, and Nico Stuurman (2010) Computer Control of Microscopes Using μManager. Current Protocols in Molecular Biology 14.20.1-14.20.17
  • 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:

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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