jordão bragantini

I’m senior research scientist at Biohub working at the intersection of AI and biology.

Multi-terabyte 3D video of developing zebrafish embryo cells tracked with ultrack;

Publications

Nature Methods Cover

Ultrack featured on the cover of Nature Methods

  1. J. Bragantini, I. Theodoro, X. Zhao, T. A. Huijben, E. Hirata-Miyasaki, S. VijayKumar, A. Balasubramanian, and others. "Ultrack: pushing the limits of cell tracking across biological scales," Nature Methods, 2025. | link | github
  2. T. A. Huijben, A. G. Anderson III, A. Sweet, E. Hoops, C. Larsen, K. Awayan, J. Bragantini, and others, "intracktive: a web-based tool for interactive cell tracking visualization," Nature Methods, 2025. | link
  3. M. Lange, A. Granados, S. VijayKumar, J. Bragantini, S. Ancheta, Y.-J. Kim, S. Santhosh, and others, "A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors," Cell, 2024. | website | link
  4. J. Bragantini, M. Lange, and L. A. Royer, "Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps," European Conference on Computer Vision (ECCV), 2024. | link | pdf
  5. E. Eck, B. Moretti, B. H. Schlomann, J. Bragantini, M. Lange, X. Zhao, and others, "Single-cell transcriptional dynamics in a living vertebrate," bioRxiv, 2024.
  6. J. Moore, D. Basurto-Lozada, S. Besson, J. Bogovic, J. Bragantini, E. M. Brown, J.-M. Burel, and others, “OME-Zarr: a cloud-optimized bioimaging file format with international community support,” Histochemistry and Cell Biology, 2023. | pdf
  7. I. F. Silva, A. M. Sousa, A. X. Falcão, and J. Bragantini, "Differential Dynamic Trees for Interactive Image Segmentation," International Conference on Pattern Recognition (ICPR), pp. 4328-4334, 2022.
  8. B. Yang, M. Lange, A. Millett-Sikking, X. Zhao, J. Bragantini, S. VijayKumar, M. Kamb, R. Gómez-Sjöberg, A. C. Solak, W. Wang, and others, “DaXi—high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy,” Nature methods, vol. 19, no. 4, pp. 461–469, 2022. | link | pdf
  9. J. Bragantini, A. Falcão, and L. Najman, “Rethinking Interactive Image Segmentation: Feature Space Annotation,” Pattern Recognition, vol. 131, p. 108882, 2022. | link | pdf | github
  10. J. Bragantini, “Interactive Image Segmentation: From Graph-based Algorithms to Feature-Space Annotation,” Master's thesis, Universidade Estadual de Campinas, Instituto de Computação, 2021. | pdf
  11. J. Bragantini, B. Moura, A. X. Falcão, and F. A. M. Cappabianco, “Grabber: A tool to improve convergence in interactive image segmentation,” Pattern Recognition Letters, vol. 140, pp. 267–273, 2020. | link | pdf | github
  12. S. B. Martins, J. Bragantini, A. X. Falcão, and C. L. Yasuda, “An adaptive probabilistic atlas for anomalous brain segmentation in MR images,” Medical Physics, vol. 46, no. 11, pp. 4940–4950, 2019. | link
  13. A. X. Falcão and J. Bragantini, “The Role of Optimum Connectivity in Image Segmentation: Can the Algorithm Learn Object Information During the Process?,” Int. Conf. on Discrete Geometry for Computer Imagery, pp. 180–194, 2019. | link
  14. J. Bragantini, S. B. Martins, C. Castelo-Fernandez, and A. X. Falcão, “Graph-based image segmentation using dynamic trees,” Iberoamerican Congress on Pattern Recognition, pp. 470–478, 2018. | link | github