Max Planck Institute of Molecular Cell Biology and Genetics

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Published December 12, 2025 | Version mastodon-deep-lineage-0.5.0
Software Open

Mastodon Deep-Lineage

Authors/Creators

Description

What's Changed

  • Enable Detection with Cellpose3, Cellpose4 and StarDist by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/132
  • Modify label image utils by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/131
  • Use appose-java 0.9.0 and appose-python 0.7.2 by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/133
  • Region of Interest and Channel Priority by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/135
  • Search for Lineage motifs by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/136
  • Search for Lineage motifs accross multiple projects by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/139
  • Update pom to beta 35 and scijava 42 by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/141
  • Add Linking using Trackastra Linker by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/142
  • Add Cancelation support for deep learning detectors by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/144
  • Fix appose processes hanging on windows by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/145
  • Add Appose Python Environment Manager UI by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/146
  • Re-use already loaded python environments by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/149
  • Fix trackastra and stardist get stuck on windows by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/151
  • Enable Stardist 3D with GPU support by @stefanhahmann in https://github.com/mastodon-sc/mastodon-deep-lineage/pull/152

Full Changelog: https://github.com/mastodon-sc/mastodon-deep-lineage/compare/mastodon-deep-lineage-0.4.7...mastodon-deep-lineage-0.5.0

Notes

If you use this software, please cite it as below.

Files

mastodon-sc/mastodon-deep-lineage-mastodon-deep-lineage-0.5.0.zip

Files (22.2 MB)

Additional details

Related works

Is supplement to
Software: https://github.com/mastodon-sc/mastodon-deep-lineage/tree/mastodon-deep-lineage-0.5.0 (URL)

Funding

Deutsche Forschungsgemeinschaft
Verstehen, wie sich Zellvielfalt in Tieren entwickelt und regeneriert Integration von Live-Imaging, Zell-Tracking, Deep Learning und Visualisierung großer Bilddaten 490966236
Agence Nationale de la Recherche
Understanding how animals generate and regenerate cell diversity: integrating live imaging, lineage tracking, deep learning and big image data visualization – DeepLineage ANR-21-CE13-0044

Software

Repository URL
https://github.com/mastodon-sc/mastodon-deep-lineage