⚠️ This organization refers to Mastodon: the open-source scientific software for tracking cells and lineaging in large microscopy images generated in Life-Sciences. It does not refer to Mastodon: the decentralized social network. For the latter, please refer to https://github.com/mastodon
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. You can find the user and developer documentation here.
This page describes the repositories of this organization and list maintainers and responsibilities.
Mastodon tries to offer at the same time
- A Java library for manipulating collections and mathematical graphs containing a very large number of objects.
- A scientific application ('Mastodon') that uses this library to offer Researchers of Life-Sciences a user-friendly tool to perform cell tracking and lineaging in large movies.
- Several optional modules and contributions that extend the features of the Mastodon application.
This results in having about 10 repositories in this organization, that we list and describe briefly in the below.
| Repository | Description | Maintainer | Distribution |
|---|---|---|---|
mastodon-collection |
Core Mastodon repository containing the library to manipulate collections containing a large number of objects efficiently. Offers data locality and garbage-collection free programming. Based on the Trove library. |
TP, JYT, MA | In the Fiji update site "Mastodon" |
mastodon-graph |
A Java library to create and manipulate (mathematical) graphs containing a large number of vertices and edges. Based on mastodon-collection. |
TP, JYT, MA | In the Fiji update site "Mastodon" |
mastodon |
The main repository for the Mastodon application. Based on mastodon-collection and mastodon-graph. |
TP, JYT, MA, VU, KS | In the Fiji update site "Mastodon" |
mastodon-tracking |
Automated tracking algorithms for Mastodon. | TP, JYT | In the Fiji update site "Mastodon" |
mastodon-selection-creator |
Mastodon plugin to create selections from mathematical expressions. | JYT | In the Fiji update site "Mastodon" |
mastodon-ellipsoid-fitting |
Mastodon plugin that can robustly fit a 3D ellipsoid on noisy data of e.g. nuclei images. | TP, JYT | In the Fiji update site "Mastodon" |
mastodon-pasteur |
Small collection of plugins developed for the research led in the Institut Pasteur, Paris, but of general utility. | JYT | In the Fiji update site "Mastodon" |
mastodon-tomancak |
Collection of plugins for editing and analyzing tracking data. Developed for the research in the lab of Pavel Tomancak, MPI-CBG, Dresden, but of general utility. | MA, VU, TP, SH | In the Fiji update site "Mastodon-Tomancak"/ |
mastodon-app |
Scripting interface for Mastodon in the script editor of Fiji. Depends on all the repos above. | JYT | In the Fiji update site "Mastodon" |
mastodon-documentation |
Source files for the online documentation. | JYT | On ReadTheDocs, here. |
mastodon-git |
Versioning and collaborative editing of a Mastodon projection. (Currently under developement. Uses git for data vesioning and data exchange) | MA | In the Fiji update site "Maarzt" |
mastodon-blender-view |
A Mastodon plugin that allows vizualizing cell tracking data interactively in 3D in Blender | MA, SH | In the Fiji update site "Mastodon-Tomancak" |
mastodon-ctc |
Plugins into Mastodon and Fiji related to the Cell Tracking Challenge. | VU | In the Fiji update site "CellTrackingChallenge" |
mastodon-collaborative |
A suite of Mastodon plugins originally developed to foster collaborative distributed tracking, including a counterpart collaborative server. | VU | In the Fiji update site "TomancakLab" |
mastodon-ext-viewers |
Collection of Mastodon plugins that are enabling online transfers of the tracking data (mostly lineage trees) outside Mastodon (usually into sciview or Blender). | VU | In the Fiji update site "TomancakLab" |
mastodon-sciview |
Mastodon plugin that starts sciview in the same session, and shares and displays image and tracking data directly in it. | VU | Download from repo. |
matlab-mastodon-importer |
Several MATLAB functions to import Mastodon files into MATLAB. | JYT | Download from repo. |
mastodon-example-data |
Example data set to demonstrate the Mastodon functionality. | TP | Download from repo. |
mastodon-deep-lineage |
Collection of plugins to analyse tracking data and some import / export tools. | SH | In the Fiji update site "Mastodon-DeepLineage". |
Maintainers:
- TP: Tobias Pietzsch
- JYT: Jean-Yves Tinevez
- MA: Matthias Arzt
- VU: Vladimír Ulman
- KS: Ko Sugawara
- SH: Stefan Hahmann
- If you have questions regarding usage of Mastodon, we invite you to use
the forum on imagesc. You may search for Mastodon related topics using the
hashtag
#mastodonor create a new topic.
- For questions related to Mastodon development, please use the zulip chat.
All contributions like will fall under the "BSD 2-Clause (Simplified) License" as described in the LICENSE file.
We use the Eclipse code formatter. You can find the configuration file here . Please use this formatter for your pull requests.
Users of IntelliJ IDEA can use the Eclipse Code Formatter Plugin to automatically format your code.
We recommend to use Auto-Format on Save in your IDE, preferably only on changed lines.