CellTrackingChallenge/CTC-FijiPlugins

[OBSOLETE] A collection of plugins related to the cell/nucleus tracking, motivated by the Cell Tracking Challenge.

Note: This repository is now (Jan 2022) considered obsolete by its autors, and is replaced with the following repos:

• CTC measures - technically a library with the tracking measures,
• CTC Fiji plugins - GUI wrappers to operate the measures from Fiji,
• label fusion - GUI and algorithms to combine multiple segmentation results into (hopefully) a superior one (aka silver GT),
• Mastodon plugins - algorithms to connect the CTC world with the beautiful Mastodon tracking software.

Welcome

This is a repository with Java source codes of the Fiji tools related to the Cell Tracking Challenge, and to the quantitative evaluation of biomedical tracking in general. In particular, one can find here:

• Technical (developer-oriented) tracking and segmentation measures: TRA, SEG, DET
• Biological (user-oriented) measures: CT, TF, BC(i), CCA
• Dataset quality measures: SNR, CR, Hetb, Heti, Res, Sha, Den, Cha, Ove, Mit
• Tracking accuracy evaluation with general Acyclic Oriented Graphs Measure (AOGM)
• A Fiji Tool for Automatic Fusion of Segmentation and Tracking Labels
• Importer and Exporter Mastodon plugins from and to the Challenge format.

The binaries of the measures can be downloaded from the official challenge website. The binary of the fusion tool can be found on this website in the release folder. The recommended method, however, is to install all tools via Fiji update mechanism, see below. The Fiji update system mirrors the most recent versions of the measures and tools, and regularly checks for their newer versions.

All the tools are in the form of a Fiji or Mastodon GUI plugins. However, owing to the Fiji capabilities, it is possible to call the tools also from command line, in a batch mode. Notes on how to install the binaries just follows.

The measures used in the paper An objective comparison of cell-tracking algorithms as well as the detection accuracy measure DET are in the CTC-paper folder. Related tools (AOGM, fusion tool, Mastodon plugins) are in the CTC-related folder.

The ideas, that are implemented in the tools, are product of a collective collaboration between CIMA, CBIA, Erasmus MC, UC3M, CSBD and MPI-CBG groups.

The tools were developed and the page is maintained by Vladimír Ulman. The SEG, TRA/AOGM and DET measures were originally developed in C++ by Martin Maška.

Enabling update site in a new or existing Fiji installation:

1. Open Fiji
2. Click menus: 'Help' -> 'Update...'
3. Click 'Manage update sites' in the opened 'ImageJ Updater' dialog
4. Mark the 'CellTrackingChallenge' checkbox
5. Click 'Close' to close the dialog

OR, Fresh Fiji installation:

1. Download recent version of Fiji from http://fiji.sc/
2. Install it, and pay attention where (which Folder) it got installed into
3. Locate the folder where Fiji got installed, say it is folder FIJIROOT
4. Download binary of the tool, and place it into folder: FIJIROOT/plugins

OR, Upgrading existing Fiji installation:

Proceed only with steps 3 and 4.

License

The tools are licensed with the CC BY-SA 4.0.

Notes

Once installed, one can find the tools in the Fiji, in the Plugins menu (and in the Cell Tracking Challenge, Segmentation and Tracking sub-menus). Contact (ulman při mpi-cbg.de) for help on how to use it, or do batch mode processing, or find hints in the scripts sub[sub*]folder.