# Micro-Manager

## Netbeans Installation

DATE: 2017-03-25

sudo aptitude install openjdk-8-jdk


Use aptitude instead of apt-get because apt-get gives up too easily. You may need to force aptitude to install a new certificate by not accepting its original solution, which is to do nothing.

List the available JDK's on your system with

sudo update-java-alternatives --list


and select the OpenJDK 8 as the default with

sudo update-java-alternatives --set java-1.8.0-openjdk-amd64


Finally, add the following lines to the end of /etc/profile

JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64
PATH=$PATH:$HOME/bin:$JAVA_HOME/bin export JAVA_HOME export JAVA_BIN export PATH  and run the command . /etc/profile  ### Install Netbeans 1. Download the Netbeans Java SE package from https://netbeans.org/downloads/ 2. Navigate to the folder where the file downloaded and make it executable: chmod +x netbeans-8.2-javase-linux.sh 3. Run the install script. 4. Follow the prompts. When prompted for the JDK directory, set it to /usr/lib/jvm/java-8-openjdk-amd64 5. Finish with the rest of the prompts. ### Setup a project in Netbeans I followed the instructions here and reproduced below: 1. Download and install the latest Micro-Manager nightly build. We will refer to the installed Micro-Manager directory as$INSTALLDIR below.
2. Download, install and run NetBeans. The Java SE Bundle is sufficient if you already have the JDK (Java Development Kit) installed on your computer. Otherwise, you can install the JDK and NetBeans at the same time from Oracle's JDK download page.
3. Choose File > New Project… > [Categories] Java > [Projects] Java Project with Existing Sources. Press Next.
4. Give your project a name. The Project Folder is best saved outside of the Micro-Manager source directory. Press Next.
5. Under Source Package Folders, click Add Folder at right and browse to $SRCDIR/mmstudio/src/main/resources. Also add$SRCDIR/mmstudio/src/main/java. If you want to develop a plugin, you can also add $SRCDIR/plugins/*/src at this time. Press Next. 6. Right-click your project in the Projects tab (probably at left) and select Properties. 7. Select Libraries under Categories. Make sure the Java Platform matches the version of Micro-Manager you are using (e.g., 64-bit JDK 1.6 - but using a newer Java Platform in NetBeans than the one shipped with Micro-Manager is usually okay). 8. Under Compile > Compile-time Libraries, click Add Jar/Folder and add$INSTALLDIR/ij.jar, as well as all jars in $INSTALLDIR/plugins/Micro-Manager except for MMJ_.jar. 9. Select Run under Categories. For the <default config>, set the following parameters: • Main Class: type in ij.ImageJ • Working Directory: type in your$INSTALLDIR
• VM options: for 64 bit systems, type in -Xmx3000M, otherwise use -Xmx600M. This sets the maximum memory (megabytes) used by Java.
10. Click OK, and then right-click your project and choose Debug. If all is well, then Micro-Manager should launch inside ImageJ.

NOTE: When running Micro-Manager from within Netbeans, I had to navigate to Plugins > Micro-Manager > Micro-Manager Studio to start Micro-Manager.

## The "Hello World!" Plugin

To compile and run the Hello World! plugin, first add the source code to your project.

1. Right click the Netbeans project and select Properties.
2. Select Source in the Categories pane on the left if it's not already selected.
4. Navigate to your plugin source code inside SRCDIR/plugins/*/src where SRCDIR is the Micro-Manager source directory and * represents the name of the folder holding your plugin.
5. Click OK to close the properties dialog.
6. Click the Clean and Build Project button (Shift+F11) to compile the project.
7. Copy the jar file that is generated in project folder to the INSTALLDIR/mmplugins directory, where INSTALLDIR is the directory where Micro-Manager is installed.
8. Alternatively, to avoid copying the jar file manually, follow the directions in step 9 under "Using Netbeans" at https://micro-manager.org/wiki/Writing_plugins_for_Micro-Manager
• Go to the Project Files tab in Netbeans.
• Find the folder with the same name as the plugin (in my case HelloWorld).
• Expand the folder and open build.xml.
• Add the following to the end of the file, before the project closing tag.
<property name="pluginsDir"  location="/home/kmdouglass/programs/ImageJ.app.Testing/mmplugins" />
<target name="-post-jar">
<echo message="--Copied MM plugin JAR to basedir: ${basedir}" /> <copy file="${basedir}/${dist.jar}" toDir="${pluginsDir}" />
</target>


## Micro-Manager 1.4 (OLD)

### Matlab control of Micro-Manager

#### Accessing MMCore Java wrappers in Matlab

I want to access the Java wrappers to easily read image file stack metadata in Matlab. Unfortunately, it appears like the Micro-Manager documentation on this is not too clear. The documentation I am currently looking at on May 7, 2015 is here: https://www.micro-manager.org/wiki/Micro-Manager_File_Formats

• Location of the .jar files

I used the Matlab script for identifying all the .jar files in the MM directory that is mentioned at this link and included below:

function [] = MMsetup_javaclasspath(path2MM)
fileList = getAllFiles(path2MM);
fileListJarBool = regexp(fileList,'.jar\$','end');
fileListJarBool = cellfun(@isempty,fileListJarBool);
fileListJar = fileList(~fileListJarBool);
fid = fopen(fullfile(prefdir,'MMjavaclasspath.txt'),'w');
fprintf(fid,'<before>\r\n');
cellfun(@(x) fprintf(fid,'%s\r\n',x), fileListJar);
fclose(fid);
%% nested directory listing ala gnovice from stackoverflow
% inputs and outputs are self-explanatory
function fileList = getAllFiles(dirName)
dirData = dir(dirName);      % Get the data for the current directory
dirIndex = [dirData.isdir];  % Find the index for directories
fileList = {dirData(~dirIndex).name}';  % Get a list of the files
if ~isempty(fileList)
fileList = cellfun(@(x) fullfile(dirName,x),fileList,'UniformOutput',false);
end
subDirs = {dirData(dirIndex).name};  % Get a list of the subdirectories
validIndex = ~ismember(subDirs,{'.','..'});  % Find index of subdirectories
%   that are not '.' or '..'
for iDir = find(validIndex)                  % Loop over valid subdirectories
nextDir = fullfile(dirName,subDirs{iDir});    % Get the subdirectory path
fileList = vertcat(fileList, getAllFiles(nextDir));  % Recursively call getAllFiles
end


This .m file should be run as a function whose argument is a string of the Micro-Manager install directory. On my Debian Linux system, the install directory is usr/local/ImageJ/plugins/Micro-Manager, NOT the directory containing the source code. The function will create a .txt file in Matlab's prefdir directory (which is ~/.matlab/R2014a/ on my system) called MMjavaclasspath.txt. I copied all the lines except for the first one, which was the word before' in angle brackets, into the file javaclasspath.txt. I also inserted /usr/local/ImageJ/ij.jar into this file as the first line.

Next, I restarted Matlab since it requires a restart to access .jar files added to the static class path.

• Test that Matlab can access the MM .jar files

Once the static class path has been updated and Matlab restarted, test that Matlab can see the .jar files using this code:

import mmcorej.*
mmc = CMMCore;


• Don't use ~ to reference the home directory

I discovered after a while that directories in javaclasspath.txt won't work if you use the tilde (~) to reference your home directory. Use the full path instead in directory names instead.

#### Opening a Micro-Manager tagged image

Micro-Manager inserts two kinds of metadata into the images it saves; one follows the OME-TIFF specification and the other includes metadata about the aquisition. I often want the Micro-Manager specific metadata, which is saved in JSON format.

First, ensure that Matlab's javaclasspath can find the Micro-Manager and ImageJ jar files as detailed above. Once this is done, you can easily create instances of classes defined in the jar files with Matlab's javaObjectEDT() command. The key here is to ensure that you pass Java datatypes as arguments into class constructors. For translating between Matlab and Java datatypes, see the documentation here: http://www.mathworks.com/help/matlab/matlab_external/passing-data-to-a-java-method.html.

To open an image stack, you will need to create a class instance of org.micromanager.acquisition.TaggedImageStorageMultipageTiff. If the image stacks are located in a directory called data_dir, we would type:

img = javaObjectEDT('org.micromanager.acquisition.TaggedImageStorageMultipageTiff', 'data_dir/', false, [], false, false, false)


Note that Matlab's empty array [] is the same as a NULL return in Java.

### MMCoreJ: The Micro-Manager Java wrapper

Most of the support one finds for Micro-Manager is for the Java wrapper around the MMCore class (which is written in C++). Because of this, it is useful to try to understand how Micro-Manager works in Java, rather than in Python or C++. Once a particular aspect of MM is understood in Java, I have found that it is easier to use it in another language.

#### Compiling against the MMCoreJ.jar library

For some unknown reason, specifying the location of MMCoreJ.jar in bash's CLASSPATH environment variable just does not work for me. To ensure that a Java program can find the Java wrappers, I pass the full directory and name of the MMCoreJ.jar file to the compiler with the -cp flag:

javac -cp "/home/kmdouglass/mm/micro-manager1.4/MMCoreJ_wrap/MMCoreJ.jar" TestMM.java


(Note that TestMM.java is the file containing the code that I wish to compile.) Doing this successfully allows Java to find the libraries in the .jar when the import mmcorej.CMMCore; line is encountered.

#### Specifying the mmcorej.library.path

In my opinion, the MM documentation on search paths is not very clear. Much of the confusion comes from the fact that the proper library required by the JVM linker is named and located differently on Windows, Linux, and Mac. To get around this, the documentation uses MMCoreJ_wrap to refer to this library independently of the system, which is unfortunate since there is also a folder named MMCoreJ_wrap.

Once a .java file has been compiled with the appropriate classpath flag described above, executing the java class file needs both a classpath and information on where the generic MMCoreJ_wrap library is located.

First, on Linux, the MMCoreJ_wrap library is actually inside a hidden directory. (This fact alone caused me a good deal of grief). On my system it's in (MM SOURCE DIR)/micro-manager1.4/MMCoreJ_wrap/.libs, where (MM SOURCE DIR) is the location of the MM source files. The appropriate library in this folder seems to be libMMCoreJ_wrap.so. In Windows, I think you will need a .dll file instead.

I specify the location of this library to the JVM using the -Dmmcorej.library.path flag. Finally, note that I have to include the current directory containing the .class file in addition to the directory of the MMCoreJ.jar file. (This is what the .: is doing in the argument of the -cp flag below.) The full command line argument to run a class file named TestMM.class that utilizes mmcorej.CMMCore is

java -cp ".:/home/kmdouglass/mm/micro-manager1.4/MMCoreJ_wrap/MMCoreJ.jar" -Dmmcorej.library.path=/home/kmdouglass/mm/micro-manager1.4/MMCoreJ_wrap/.libs TestMM


Say that three times fast.

#### Testing the Java environment

I can test that I have specified the classpath and library path correctly by compiling and running the following simple Java program that creates a CMMCore instance and prints the version to the terminal window.

import mmcorej.CMMCore;

public class TestMM {

public static void main(String[] args) {

CMMCore core = new CMMCore();
String info = core.getVersionInfo();
System.out.println(info);
}
}
`