Ultrack Datasets

Available data

• multi-color-cytoplasm.tif: Metastatic breast cancer cells with RGB lentiviral marking, data from Lammerding lab.
• multi-color-cytoplasm-sparse-tracks.csv: Sparse manually curated annotations of cell lineages of multi-color-cytoplasm.tif.
• a549_virtual_staining.ome.zarr: A549 cells with virtual staining from VisCy.
• a549_virtual_staining_ome_tiff: The same as a549_virtual_staining.ome.zarr but in TIFF format, each frame corresponds to a 3D volume with multiple channels.
• zebrafish_embryo.ome.zarr: Dense nuclear labeled zebrafish embryo.
• zebrafish_neuromast.ome.zarr: Nuclear and membrane labeled zebrafish neuromast.
• zebrafish_neuromast_ome_tiff: The same as zebrafish_neuromast.ome.zarr but in TIFF format, each frame corresponds to a 3D volume of both channels.
• zebrafish_neuromast_tracks.csv: Manually curated tracks of zebrafish_neuromast.ome.zarr.
• network weights: Neural network weights compiled as torch script for foreground and contour prediction.

See ultrack's GitHub repository for the software and ultrack's preprint for additional details.

Citing

@article{bragantini2025ultrack,
  title={Ultrack: pushing the limits of cell tracking across biological scales},
  author={Bragantini, Jord{\~a}o and Theodoro, Ilan and Zhao, Xiang and Huijben, Teun APM and Hirata-Miyasaki, Eduardo and VijayKumar, Shruthi and Balasubramanian, Akilandeswari and Lao, Tiger and Agrawal, Richa and Xiao, Sheng and others},
  journal={Nature Methods},
  pages={1--14},
  year={2025},
  publisher={Nature Publishing Group US New York}
}