Frequently Asked Questions

On this page, we try to list common questions and the solution. It can very well be that you experience a bug that is not listed here. In this case, please let us know (‘How do I report an issue or bug I got while using Mars?’).

How do I install Mars?

We created a detailed installation guide on this website as well as a video guide on YouTube.

Where do I find the files for the tutorials and examples?

Most of the tutorial files can be found on our Mars tutorial GitHub page.

For the FMT example, you can find the scripts on the FMT tutorial github including the archive and a truncated video. The full dataset is saved on zenodo.

How can I contact you?

The contact details you can find on our lab website or on our institute website

Why didn’t anything open when I ran the command to create a Molecule Archive?

Always check the console for more information (Windows->Console). If you had the wrong settings for a command it will display ‘failure’ and usually, an error message will pop up. In the console, error messages from Fiji will be displayed.

If you are a Mac user please verify if JavaFX is installed in your Fiji. 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’. Re-open Fiji after making this change. Alternatively, you can download a new copy of Fiji, which now comes with the zulu jdk with JavaFX.

Why do I get the error ‘statement cannot begin with ‘<’ in line 8:’ when trying to run the ActionBar and scripts from mars-tutorials?

This error is caused by unrecognized syntax in the scripts or ActionBar layout files. This error occurs when the files from mars-tutorials are downloaded from GitHub in html format. See this post on the forum for further details.

We recommend using git clone https://github.com/duderstadt-lab/mars-tutorials.git on your local machine to download the mars-tutorials repository. This method ensures all the files are downloaded in the correct format. Downloading the larger Molecule Archives will require installing git lfs. Otherwise, the mars-tutorials can be downloaded directly from the GitHub website in zip format to avoid this problem.

How do I report an issue or bug I got while using Mars?

In this case, you can create an issue on one of the Mars GitHub repositories or post your question on the ImageJ forum (do not forget to tag it with ‘mars’ and/or @karlduderstadt). We are happy to help!