How to Install Mars

1. Install Fiji on your computer and check the presence of javafx

Mars consists of a collection of scijava commands and user interface that runs in Fiji. Therefore an updated version of Fiji is required to run Mars on your computer.

  1. Download and install Fiji. This should take up to a couple of minutes to be completed.
  2. Open Fiji and make sure you are up-to-date by running Help>Update. Click accept changes to update to the newest versions of all components. After the update, restart Fiji.
  3. Mac: Verify that javafx is installed in your Fiji. Previously, javafx was bundled with the download but the newest versions of Fiji do not come with javafx. To check this, show the package contents of the Fiji folder by right-mouse clicking on the Fiji folder and selecting ‘Show Package Contents’. Check inside the java folder and macosx subfolder. If you see ‘adoptopenjdk-8.jdk’ in the folder then you do not have javafx installed. In this case you will need to replace this jdk file with a ‘zulu_8.jre’ for the Mars interface to work. You can download the jre file here. Unzip the downloaded file and replace ‘adoptopenjdk-8.jdk’ with ‘zulu_8.jre’. Once you have replaced the file, you can go back and double-click Fiji to open it. Javafx is now installed and you can now continue with the installation of Mars.

2. Install the Mars project in your local Fiji

An imagej update site has been created to help with maintenance and distribution of Mars and all necessary dependencies. Follow the directions below to install Mars in your local copy of Fiji:

  1. Run Help>Update in the Fiji menu and click ‘manage update sites’. Then click ‘Add update site’ to create a new entry. For Name put Mars and for URL put http://sites.imagej.net/Mars/ and then check the box to activate the update site. Now mars-core and mars-fx (the gui for Tables, Plots and MoleculeArchives) files should show up as well as the necessary dependencies (there a lot of dependencies for mars-fx related to the markdown editor and charting library). Install them all and restart Fiji. If you don’t see the new jars restart the Updater. Downloading the jars for mars from the update site is very fast and only requires a couple seconds.
  2. If the plugins have been installed correctly, the submenu “Mars” should show up under Plugins.
  3. From now on all you need to do is run the updater to ensure you have the current version of Mars installed. Please update frequently to ensure you benefit from the most recent bug fixes.

Once you have installed Mars in your Fiji using the update site, the submenu “Mars” will show up under the Plugins containing the Mars commands. Usually in the bottom section. In this submenu are a series of commands for general processing of single-molecule data. There are tools for both the analysis of fluorescence data as well as particle finding, fitting, and tracking. From there a range of other commands allow for filtering, sorting, and classification as outlined in the documentation section.

Don’t be a stranger

If you encounter problems of any kind or have a usage question please create an issue on one of the mars repositories in Github or post your question on the ImageJ forum. If you post in the forum please make sure to tag it with mars and add @karlduderstadt in your comment. We would love to hear back about your experience using mars.

System compatibility

Mars is compatible with Windows, Linux and Mac OS. Mars has been extensively tested on mac and linux systems. However, we have not tested Mars as extensively on windows.