About Mastodon and this documentation.¶
Mastodon is a large-scale tracking and track-editing framework for large, multi-view images, such as the ones that are typically generated in the domain Development Biology or Stem-Cell Biology or Cell Biology.
Why using Mastodon?
Modern microscopy technologies such as light sheet microscopy allows live sample in toto 3D imaging with high spatial and temporal resolution. Such images will be 3D over time, possibly multi-channels and multi-view. Computational analysis of these images promises new insights in cellular, developmental and stem cells biology. However, a single image can amount to several terabytes, and in turn, the automated or semi-automated analysis of these large images can generate a vast amount of annotations. The challenges of big data are then met twice: first by dealing with a very large image, and second with generating large annotations from this image. They will make interacting and analyzing the data especially difficult.
Mastodon is our effort to provide a tool that can harness these challenges.
This pages centralize the user and developer documentation for Mastodon. It is divided in four parts, that group sections by interest.
A. The first part, Using mastodon contains tutorials, aimed at end-users and focused on cell tracking. They are meant to guide users with the Mastodon software and cover three applications of cell tracking in Mastodon:
automated cell or particle tracking;
manual curation and correction of tracking results;
manual and semi-automatic tracking.
This also where we introduce all the user-oriented features, such as numerical features, tags, navigation facilities, data export etc. If you are new to Mastodon, it is best starting with this part, and reading the tutorial in order.
B. The second part contains tables that summarize the main keyboard shortcuts of Mastodon. They are put in a separate section to facilitate browsing to them quickly.
C. The third part is aimed at developers, that want to extend Mastodon. Mastodon, like [TrackMate](https://imagej.net/plugins/trackmate/), is a software platform meant to be extended by you so that new features and algorithms can be added to it in a relatively simpler manner. This part detail the plugin interface of Mastodon and the discovery mechanism.
D. The last part is made of technical information that serve as a reference for the specificities of algorithms and features currently implemented in Mastodon.
Table of content.¶
- Getting started with Mastodon. Automated tracking.
- Manually editing tracks in Mastodon. TrackScheme.
- TrackScheme, the lineage view and editor.
- The focus and the spot labels.
- Synchronizing several views together.
- The highlight.
- Deleting individual spots and links.
- Linking spots.
- The selection.
- Editing spots and links with the selection.
- Manually adding spots and linking them.
- Moving spots around.
- The undo/redo mechanism.
- Putting things in practice.
- Inspecting large datasets.
- Numerical features and tags. The table view.
- Semi-automated tracking.
- The selection creator.
- Scripting Mastodon in Fiji.
- Mastodon numerical features.
- The graph data structure of Mastodon.
- Containment in Convex Polytopes using k-D trees.
- Scripting functions
- Static methods