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Mastodon Blender View - An easy to use interactive 3D viewer for the Mastodon cell tracking software

The Mastodon Blender View is a plugin for the Mastodon cell tracking software. The plugin visualizes Mastodon cell tracking data in the Blender 3d modeling software. It adds a new menu entry Plugins > New Blender Window to Mastodon. Upon clicking it a Blender window will opens. After a few seconds the cell tracking data will be visible. This visualization is far more than static, not only can the data be rotated and shown from all angles. Blender & Mastodon are linked together. You may use Blender to select objects, just as if it's a part of Mastodon.

mastodon_blender_3d_view_v0.1.1.mov

(This is a plugin for the Mastodon cell tracking software used in biological research. Please don't confuse it for the social network called Mastodon.)

Installation

  1. Install Fiji and Blender on your computer. Make sure to install Blender as a "portable" installation.
  2. Next step is to activate the "TomancakLab" update site in Fiji.
  3. In Mastodon's main menu, you will find an entry Plugins > Setup Blender Addon ..., click it and follow the instructions.

That's it, the Mastodon Blender View is ready to be used. Simply click: Window > New Blender Window.

Usage

Quick Start

In the Mastodon main menu click Window > New Blender Window ... wait for 20 seconds, for the data to load in Blender. And play around! Finally make sure to find the "Mastodon 3D View" panel in Blender, it's useful.

"Mastodon 3D View" panel in Blender

Click on the 3D view in Blender. Press N, This makes a few tabs appear on the right edge of the 3D view. One of the tabs is called "Mastodon 3D View". Click it and you will be able to:

  • Select a Mastodon synchronization group
  • Change sphere sizes
  • Select a "tag set" (The colors will be visualized in the 3d view.)
  • Update the "tag set" (If you made changes in tags in Mastodon.)

Synchronize Mastodon and Blender

In the Mastodon TrackScheme window click one of the lock symbols 1, 2 or 3. In Blender go to the "Mastodon 3D View" panel, and under "Synchronization Group" choose the same number 1, 2 or 3.

image image

Now the active time points and the active spot are synchronized between Blender and Mastodon.

Project Details

Status

The project is currently under development and at a prototype stage. That said, the plugin can already be easily installed and used.

I'm open to suggestions on how to improve the tool.

Known Limitations

  • The plugin assumes that the tracking data doesn't change. Changing the tracking data while using the 3D view, might lead to some unexpected behaviour.
  • Tag sets are not automatically updated. You need to click Update Tags in Blender "Mastodon 3D View" tab.

License

The source code of this project is published under BSD 2 license.

Development

Maven is used as a build tool. It is therefore possible to open the project with Eclipse, IntelliJ or any other java IDE. The class StartMastodonLauncher may be used as an entry point to execute the code.

The project can be fully compiled with just one command:

mvn package

Once compiled, it can be launched with this command:

mvn -Dexec.mainClass=org.mastodon.blender.StartMastodonLauncher -Dexec.classpathScope=test clean test-compile exec:java

The Mastodon Blender View is an open source project. You are welcome to contact me, if you would like to contribute.

How does it work?

Mastodon Blender View consists of two components. An add-on for Blender that is written in Python and a plugin for Mastodon. Both components communicate using google RPC library.