Building MM on Windows

Before you start

First make sure you have enough hard disk space. 15 GB is probably enough.

Setting up the required tools

Subversion client

You will need a Subversion client. GUI clients such as TortoiseSVN also work well.

Microsoft Visual Studio 2010 SP1 Express

Micro-Manager's C++ components (Core, MMCoreJ, MMCorePy, and device adapters) are currently built using Visual Studio 2010 Express. To install a complete build environment, follow these instructions (all are free downloads):

1. Open Control Panel > "Uninstall a program". If there are any items named Microsoft Visual C++ 2010 Redistributable with version number greater than 10.0.30319, uninstall them (see the note below for why).
2. Install Microsoft Windows SDK 7.1 (http://www.microsoft.com/en-us/download/details.aspx?id=8279). If the installer complains that .NET Framework 4 is required, cancel the SDK install and first install the .NET Framework (from http://www.microsoft.com/en-us/download/details.aspx?id=17851). If installation of the SDK fails, see the notes below.
3. Install Visual C++ 2010 Express from http://www.visualstudio.com/products/visual-studio-express-vs.
4. Upgrade to Visual Studio 2010 SP1 (http://www.microsoft.com/en-us/download/details.aspx?id=23691).
5. Repair the compilers that come with Windows SDK 7.1 by installing this package: http://www.microsoft.com/en-us/download/details.aspx?id=4422

Java Development Kit (JDK) for Java Standard Edition (Java SE)

Download and install from Oracle. Version 6 or later is required. The official Micro-Manager build currently uses JDK 6.

You do not need the JDK if you are only building device adapters or other C++ components.

Apache Ant

Apache Ant is the build tool used to automate the full Windows build of Micro-Manager. Version 1.8.1 or later is required (tested with 1.9.2).

Download the binary package.

You do not need Ant if you are only building device adapters of other C++ components.

Environment variables

For building the Java and Clojure components using Ant, the following environment variables need to be set correctly. They can be added in Control Panel > System and Security > System > "Advanced system settings" > "Environment variables...".

• JAVA_HOME: set to the path to your JDK installation, e.g. C:\Program Files\Java\jdk1.6.0_45. Do not add quotes to the value, even if it contains spaces.
• ANT_HOME: set to the path to your Ant installation (whereever you placed the extracted binary package), e.g. C:\apache-ant-1.9.1. Do not add quotes to the value, even if it contains spaces.
• PATH: It is convenient to add Ant to the command search path. You can append ;%ANT_HOME%\bin to the end of the System PATH varialbe, or add a User variable named PATH and set its value to %PATH%;%ANT_HOME%\bin.

Preparing the source code

Directory layout

Create a directory named projects (the name is not important, but we will refer to this name below). The projects directory may reside anywhere you like and will contain the subdirectories micromanager, 3rdpartypublic, and (optionally) 3rdparty.

All directories mentioned below that don't start with project are relative to projects\micromanager.

Obtaining the source code

Checkout the Micro-Manager Source Code inside the projects directory, using your Subversion client. This should result in the following directories:

projects\micromanager
projects\3rdpartypublic

Vendor SDKs and libraries

If you have third-party libraries (e.g. from device vendors), create the directory projects\3rdparty and place them in an appropriately named subdirectory.

If you are building a device adapter included in the Micro-Manager Subversion repository, and it requires third-party libraries, you will need to place them in the correct directory within projects\3rdparty, as determined by the settings in the Visual Studio project file for the adapter. Alternatively, you can locally edit the build settings in the project file.

(There are cases where the location of a header file is hard-coded (relative to the 3rdparty directory) in the source (.h and .cpp) files. This practice is discouraged, but if you encounter it, you might have to edit the path.)

Building Micro-Manager

Building single device adapters

Open the project file (.vcxproj) for the device adapter in Visual Studio.

Right-click on the Solution, and select Add > Existing Project.... Choose MMDevice/MMDevice-SharedRuntime.vcxproj. (There are a few device adapters that require MMDevice/MMDevice-StaticRuntime.vcxproj instead. If you get an LNK1104 error asking for it, add it and then right-click the device adapter project and select "Rescan Solution".)

At this point, close the solution file (File > Close Solution, or just quit Visual Studio). It will prompt you to save a solution file (.sln). Save it in the default location (next to the device adapter project). Then, reopen either the device adapter project or the newly saved solution (either will have the same result). (This extra step is necessary because Visual Studio does not correctly update its internal state when you add projects that theoretically know their interdependencies.)

Now select the Debug or Release configuration and the Win32 or x64 platform from the drop-down menus (for various reasons, the Debug configuration does not work for all device adapters). If everything is configured correctly as described above, you should now be able to simply select Build.

In Visual Studio 2010 and later, the solution is little more than a list of project files to be built together, so our policy is not to include solution files for each project in the repository (but see below about the master micromanager.sln file).

The build binaries are placed under the directory build, within the device adapter directory.

Some device adapters (those made up of more than one project) may not build correctly by this method. In that case, build it from micromanager.sln as described below.

Building multiple device adapters, MMCoreJ, or all C++ components

Open micromanager.sln (in the root of projects\micromanager). Visual Studio will warn you that some projects are missing (they are the closed-source device adapters), but you can ignore that message. Then (after setting the configuration and platform) simply right-click the desired projects and select Build.

Note that the built binaries are placed under the directory build at the root of projects\micromanager.

If you build MMCoreJ, MMCoreJ_wrap.dll will be generated. Additionally, Java source files are generated in build\intermediates\Swig\MMCoreJ\. These files are compiled into MMCoreJ.jar in a separate step by Ant (see below).

You can also build all available projects by right-clicking the Solution and choosing Build.

Building MMCorePy

First, you need to install Python 2.7 and Numpy 1.7 (different versions, such as Python 2.6, may work if the project settings are appropriately edited).

To tell Visual Studio where to find the Python installation, open MMCorePy_wrap\Python.props in a text editor (these settings can be edited in Visual Studio, but it's simpler to explain how to manually edit this file). Find the block that starts with PropertyGroup Label="UserMacros", which contains a line for PythonDir. Set its value to the path to your Python installation. If you installed Python 2.7 in the default location, you probably just need to remove the -$(Platform) part.

Once this is done, you should be able to build MMCorePy from micromanager.sln by the steps described above. Make sure to select the Release configuration and the platform that matches your Python binaries.

The build will generate _MMCorePy.pyd (the extension module) and MMCorePy.py (the Python wrapper module).

Building individual Java components

On Windows, Micro-Manager's Java components are built using Apache Ant.

Each Java (and Clojure) component has a build.xml (an Ant build script):

 MMCoreJ_wrap\build.xml
 mmstudio\build.xml
 acqEngine\build.xml
 plugins\*\build.xml
 autofocus\build.xml

To build one of these components, open the Command Prompt, and change to the directory containing the build script. Then simply type

 ant jar

This should produce the jar file in build\Java. (Ant automatically uses the build.xml file in the current directory.)

For example,

 cd MMCoreJ_wrap
 ant jar

will produce build\Java\MMCoreJ.jar.

Some of the Java components depend on each other. When building the components one by one, you will need to build them in the order listed above (see below for building everything automatically).

To build MMCoreJ.jar (and, by transitive dependency, any of the other Java components), you need to have built the C++ part of MMCoreJ (either in Visual Studio as described above, or using Ant as described below) before running Ant.

Building Clojure components (acqEngine and some of the plugins) requires a loadable MMCoreJ_wrap.dll. "Loadable", in this context, means that it is built for the same architecture (32-bit vs 64-bit) as your Java runtime (on which Ant is running). If you are using a 32-bit JDK but have built MMCoreJ for 64-bit, you will also need to build the 32-bit MMCoreJ_wrap.dll (and vice versa). The MMCoreJ_wrap.dll for the two architectures go in different directories, so there is no harm in building both in the same source tree.

Building all components

The master Ant build script (build.xml at the root of the source tree) can be used to build the whole application. It's usage differs from the individual build scripts for each Java component.

Open the Command Prompt, and change to the projects\micromanager directory. Type

 ant -p

This should list a number of options.

To build all C++ components (similar to building the micromanager.sln Solution in Visual Studio), type

 ant build-cpp -Dmm.build.failonerror=false -Dmm.architecture=Win32

Setting the mm.build.failonerror property to false allows the build to continue even if some of the projects (e.g. device adapters that depend on libraries you don't have) fail to build. (But you will want to check that the ones you want did build. Look in the build directory.)

The architecture (what Visual Studio calls 'platform' - but we reserve that term for Windows vs OS X vs Linux) can be set to Win32 or x64.

The command

 ant build -Dmm.build.failonerror=false -Dmm.architecture=Win32

will build everything (all C++, Java, and Clojure compoenets).

There is also a build-java target that you can use to build just the Java and Clojure components (it will not try to build the C++ components).

The stage, run and package targets are not yet fully implemented for general use (they expect files to be present at specific paths).