Tutorials

Tutorials for learning how to use Mars. For exploring the software and its most commonly used features please follow the Let’s make a Molecule Archive tutorial first.

The files accompanying the tutorials, such as an example dataset, can be found in the git tutorials repository.

Working with Mars

• Let’s make a Molecule Archive
  Skill level: Beginner. Learn the basic elements of Mars by creating and working with a Molecule Archive.
• Let’s calculate the Variance
  Skill level: Intermediate. Learn how to calculate the variance from the traces in the Molecule Archive. Note: it is advised to do the Let’s make a Molecule Archive tutorial before doing this tutorial.
• How to use Scriptable Widgets
  Skill level: Advanced. Learn how to create customised widgets for fast initial data analysis on the Rover Dashboard.
• Kinetic Changepoint Analysis
  Skill level: Intermediate. Learn how to do a kinetic changepoint analysis.
• How to Find Tracked Molecules in the Video
  Skill level: Advanced. Learn how to visualise an Molecule Archive entry in the original video. This enables the user to look back at the molecule in the original video.
• How to Copy Drift Between Archives
  Skill level: Advanced. Learn how to create an archive with drift information and copy that information to other archives. This shows how to correct for drift when manually tracking molecules using the BDV in the mars rover.

Python

• How to open a Molecule Archive in python
  Skill level: Intermediate. Learn how to load and work with Molecule Archives in Jupyter notebooks running Python 3 and work with mars together with all the wonderful packages available in the python environment.

TrackMate

• How to convert TrackMate Results to Mars
  Skill level: Intermediate. Learn how to import tracking results from TrackMate to Mars.

Scripting

• Introduction to groovy scripting
  Skill level: Intermediate. Learn how to access and perform basic operations with Molecule Archives.
• Advanced groovy scripting
  Skill level: Advanced. Learn advanced approaches to filter, collect, and report characteristics of Molecule Archive records.
• MarsTable tutorial
  Skill level: Intermediate. Learn how to use scripts to build and edit a fully customizable MarsTable.

Affine2D Transformation

• How to calculate Affine2D transformation coordinates
  Skill level: Intermediate. Learn how to calculate an Affine2D transformation matrix using the Descriptor-based registration plugin that comes standard with Fiji. Use this transformation to align multiple videos concerning the same field of view.

FRET Power Tools ActionBar

• FRET Power Tools ActionBar
  Learn how to use the awesome Fiji ActionBar plugin to add all FRET example workflow scripts to a custom button window for faster processing.