The CellTrackingChallenge Mastodon Baseline

...one can find here

Welcome

This is a repository with Java source codes of the Fiji tools related to the Cell Tracking Challenges and to Mastodon.

The tools were developed and the page is maintained by Vladimír Ulman.

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 'Mastodon' and 'CellTrackingChallenge' checkboxes
5. Click 'Apply and Close' to close the dialog
6. Click "Apply" to finish the Updater, and restart Fiji

License

The tools are licensed with the BSD 2-Clause License.

Notes

Once installed, one can find the tools in the Mastodon, in the File and Plugins menus. Contact (ulman při fi.muni.cz) for help on how to use it.

Instance segmentation importers

Generic segmentation-only importer

This importer was designed to extract spots from images showing instance segmentation, and on-demand create links between segments (spots) that overlap significantly in consecutive time points.

One can find the dialog in Mastodon -> Plugins -> Cell Tracking Challenge -> Import from instance segmentation:

CTC-formatted segmentation and tracking importer

This importer was designed to extract spots from images with instance segmentation, and create links between segments (spots) of the same label.

One can find the dialog in Mastodon -> File -> Import -> Import from CellTrackingChallenge:

There, one could choose a folder and format of the filenames in that folder:

...the res_track.txt file is an auxiliary file that informs which instance label existed in what time points range and, especially, provides the parental relationship information. If one holds only a segmentation and not also the tracking, it should also suffice to provide an empty res_track.txt file. But this is not a supported mode of operation.