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The CellTrackingChallenge Mastodon Baseline

In order to link existing segmentation images, both 2D and 3D and stored according to the CellTrackingChallenge standard, with Mastodon one can use the Fiji plugin Baseline Mastodon CTC tracking.

Baseline Mastodon CTC tracking plugin and its parameters

Obtaining the plugin (into new or existing Fiji installation):

This plugin is freely available from Fiji update sites:

  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
  7. After Fiji restart, one can find the plugin in the Fiji menus:

Baseline Mastodon CTC tracking plugin in the Fiji menus

About

This is a repository with Java source codes of the Fiji tools related to the Cell Tracking Challenge and to Mastodon. The original source codes are available from Mastodon github sites.

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

Contact < vladimir.ulman při vsb.cz > for help on how to use it.

License

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

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:

general instance segmentation importer dialog window

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:

CTC import main dialog window

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

CTC own files import dialog window

...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.