Installation guide

MoMA is available for download in two different ways:

• For new users it is recommended to try out the Fiji plugins which will guide you through the analysis process.
• Advanced users may want to try the command line tools to facilitate automated pre-processing of many data sets, e.g. by exploiting high performance computing capabilities. Advanced users may also profit from direct access to MoMAs open source code.

Installation of Fiji and the MoMA plugin

The first step is to download and install Fiji from http://fiji.sc/Downloads. Afterwards, run Fiji and click its Help > Update... menu entry.

In the ImageJ updater dialog that appears click on the Manage Update Sites button:

The Manage update sites dialog will open. Click the Add update site button and enter "MoMA" in the name column on the left and "http://sites.imagej.net/MoMA/" in the URL column on the right. Click the Close button afterwards.

Close the ImageJ Updater window by clicking the Apply changes button:

After restarting Fiji, a menu entry Plugins > MoMA should appear. If not, please contact us!

Running MoMA for the first time

Check the installation by clicking the menu Plugins > MoMA > MoMA application;

When you run MoMA for the first time, it will ask you to get a license for the Gurobi Solver engine it utilises for optimisation. Visit http://www.gurobi.com/downloads/licenses/license-center to acquire this license. Most academic users may want to click “Obtain a free university license”. Afterwards, copy and paste grbgetkey xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx in the Getting Gurobi License File dialog.

After clicking ok, a console window may appear showing the installation progress. Finally, after installation succeeded, a window titled _MoMA configuration_ will appear. You may download an [example data set](MoMA-Datasets) and follow the instructions in our [Quick user guide](Quick-user-guide) to learn how MoMA can be used.

Installation of command line tools for MoMA

The following procedures are not neccessary for running MoMA inside Fiji. These steps are only recommended to be performed by advanced users requiring command line functionality.

To run MoMAs command line tools, you need either Java 8 Development Kit or Runtime Environment installed on your computer. Download and install it from here:

• Download Java 8 JDK (Development Kit)

• Download Java 8 JRE (Runtime Environment)

• Download the most recent version of MotherMachine_.jar and MMPreprocess_.jar from here: http://sites.imagej.net/MoMA/plugins/

Detailed information on how to apply the preprocessing steps from the command line can be found here:

• Preprocessing From The Command Line