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FAQ

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Camera issues

I get the error that a core property is read-only?

Please make sure to run an up-to-date installation (you can call the updater via Help>Update Fiji). There was a bug in the HamamatsuHam driver that has been fixed in the meantime (many thanks to Patrick Gregorio of Hamamatsu who helped us a lot to resolve this issue).

Community

How to share images?

We use BitTorrent Sync to have a shared directory of images and stuff. After installing BitTorrent Sync, you will need to add a folder using this "secret": fUS9i4Ps/g+MLohUPun1rEfK8b0A+ABQitckZiONwPZK5BPm1N/wYg==

How to share scripts/macros?

The ideal way, of course, is to add a Wiki page to this Wiki. However, if you want to work on a macro together with somebody else, the easiest way is to use kind of a shared clipboard.

How to report bugs

We have a ticket system. If you add new tickets, please make sure to

  • the category is OpenSPIM
  • assign the ticket to yourself if you intend to solve it
  • add a target version if you want the ticket to show up in the roadmap
  • add a concise summary and additional useful information in the description
  • if you need this ticket to be visible only to the core developers of OpenSPIM, mark it as 'private'

Once you added a ticket, you might want to go back to it and make it a child of a goal ticket in the Relationship box.

Are there similar Open Access projects for life sciences?

Yes!

Software

How do I autostart µManager when Fiji starts?

In Fiji, run the command Plugins>Macros>Startup Macros... and add the following lines to the end:

macro AutoRun {
       run("Micro-Manager Studio");
}

How do I autostart the OpenSPIM plugin when µManager starts up?

If you want the SPIM plugin to be called everytime when Micro-Manager starts, add the following lines to the Fiji.app/MMStartup.bsh file:

setAccessibility(true);

import org.micromanager.MMStudioMainFrame.PluginItem;
for (PluginItem plugin : gui.plugins_)
        if (plugin.className.equals("SPIMAcquisition")) {
                plugin.instantiate();
                plugin.plugin.show();
        }

How do I start µManager from the command-line?

There are two ways, really. The Fiji way:

fiji-win32 --run Micro-Manager_Studio

Call the Studio directly, without first starting ImageJ:

fiji-win32 --main-class=org.micromanager.MMStudioMainFrame

Can I run OpenSPIM with Windows 7 or 8?

At the time of writing, we know that the Hammamatsu camera works with both Windows XP and Windows 7 using the DCAM driver.

How can I build the OpenSPIM software myself?

Please have a look at this page.

Micro-Manager runs and loads my configuration, but the OpenSPIM plugin won't start, what should I do?

Try zeroing the positions of all the stages, especially the twister. You can do this either by opening the Picard software (USB 4D-Stage Version 1.0) and clicking "All Home" and also "Set Zero" for the twister, or you can do it in Micro-Manager by doing the following:

- Launch Micro-Manager. - Click Tools -> Script Panel. - Type or copy/paste the following (If you did not use the default twister name, be sure to replace the text in the line below with the correct name.):

mmc.setPosition("Picard Twister", 0);

- Press enter.

If this doesn't correct the problem, repeat for the X, Y, and Z stages.

Debugging

Look at the CoreLog

Whatever you do, first have a look at the file CoreLog<date>.txt, located in Fiji.app/ or whatever directory Micro-Manager was started in.

When Micro-Manager does not list the driver

  1. Make sure the .dll is present in bin_Win32/mm/Win32/
  2. If you copied the driver from an independent micro-manager installation, make sure the micromanager version the driver comes from corresponds to version embedded into OpenSpim.
  3. Use the Dependency Walker to detect missing dependencies

The driver for my hardware is not listed in OpenSPIM, but it supported by micro-manager

In theory any hardware supported by micro-manager should work in OpenSPIM. If the driver for your hardware is not listed in OpenSPIM, you can add it to the OpenSPIM driver list by copying the .dll to the /mm/Win32/ folder. Watch out that the versions of micro-manager from which the drivers originates and the version of OpenSPIM your are using are compatible. For instance, OpenSPIM-20130131 is built on micro-manager v1.4.9

Micro-Manager just crashes when I connect <device>

Micro-Manager's memory management is not very safe on the driver side. Try to start Fiji with less memory reserved for Java, e.g. --mem=512m.

If that does not help, try to find out what's in the core log, and if that fails, too, you might have more luck #Using Visual Studio's interactive debugger.

Using Visual Studio's interactive debugger

Start Fiji, and before starting Micro-Manager use Visual Studio's Debug>Attach to Process... to attach to the process. After that, you may set breakpoints (optional) and then start Micro-Manager in Fiji.

Using Eclipse to debug MicroManager/SPIM Acquisition

Option 1: Eclipse-only

  1. Make sure you have Eclipse installed.
  2. Add Fiji's JRE to Eclipse:
    1. Window -> Preferences; under Java, select Installed JREs and click Add...
      1. Use Standard VM.
      2. Set the JRE Home to Fiji.app/java/win32/jdk1.6.0_24 (or similar). Eclipse should fill in the rest.
      3. Click Finish.
    2. Check the checkbox next to the newly-added JRE.
  3. Create a new project for Micro-Manager Studio:
    1. File -> New -> Java Project...
      1. Uncheck "Use Default Location"
      2. Point Location to /src/fiji/3rdparty/micromanager/mmstudio
      3. Eclipse should auto-configure all sorts of useful things.
    2. Click Next.
      1. On the Libraries tab, click Add External JARs...
        1. From /src/fiji/3rdparty/bin_Win32/jars/:
          • bsh.jar
          • commons-math-2.0.jar
          • ij-<version>.jar
          • MMCoreJ.jar
          • MMAcqEngine.jar
          • swing-layout-1.0.4.jar
          • swingx-0.9.5.jar
    3. Click Finish.
  4. Create a project for SPIMAcquisition:
    1. File -> New -> Java Project...
      1. Uncheck "Use Default Location"
      2. Point Location to /src/fiji/3rdparty/micromanager/plugins/SPIMAcquisition/src/main/java
      3. Let Eclipse auto-configure things.
    2. Click Next.
      1. On the Projects tab, click Add... and select the mmstudio project added above.
      2. On the Libraries tab, click Add External JARs...
        1. From /src/fiji/3rdparty/bin_Win32/jars/:
          • ij-<version>.jar
          • MMCoreJ.jar
    3. Click Finish.
  5. Depending on your workspace settings, you may need to reduce the enforced JRE level for both projects:
    1. Right click on each project and go to Properties.
    2. Select Java Compiler.
    3. Enable project-specific settings and set the Compiler Compliance Level to 1.6 (depending on the JDK used by Fiji).
    4. Click Apply then OK.
  6. Set up the debug configuration:
    1. Run -> Debug Configurations...
      1. Create a fresh launch configuration
      2. Use SPIMAcquisition as the project.
      3. For the Main class, click Search... and find ij.ImageJ
      4. On the Arguments tab, under VM arguments, pass the following: -Dplugin.dir=fiji/3rdparty/micromanager/bin_Win32 (modifying as appropriate).
      5. On the Classpath tab, select SPIMAcquisition, then Add External JARs...
        1. From fiji/3rdparty/micromanager/bin_Win32/jars:
          • MMAcqEngine.jar
      6. Click Apply.
    2. Click Debug to make sure everything works.

Option 2: Eclipse and Maven

  1. Follow steps 1-3 above. Additionally install m2e for Maven support in Eclipse .
  2. Import the SPIMAcquisition Maven project
    1. File -> Import...
    2. Select Maven -> Existing Maven projects
    3. Browse to micromanager/plugins/SPIMAcquisition and let m2e work.
    4. Click Finish
  3. Continue on steps 5 and 6 above.