jordão bragantini

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

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

Publications

  1. J. Bragantini, I. Theodoro, X. Zhao, T. APM H., E. Hirata-Miyasaki, S. VijayKumar, A. Balasubramanian, and others. “Ultrack: pushing the limits of cell tracking across biological scales,” bioRxiv, 2024. | pdf | github
  2. M. Lange, A. Granados, S. VijayKumar, J. Bragantini, S. Ancheta, S. Santhosh, and others, “Zebrahub–Multimodal Zebrafish Developmental Atlas Reveal the State-Transition Dynamics of Late-Vertebrate Pluripotent Axial Progenitors,” Cell, 2024. | website | pdf
  3. J. Bragantini, M. Lange, and L. A. Royer, “Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps,” ECCV, 2024. | pdf
  4. E., Elizabeth, B. Moretti, B. H. Schlomann, J. Bragantini, M. Lange, X. Zhao, and others, “Single-cell transcriptional dynamics in a living vertebrate,” bioRxiv, 2024.
  5. 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
  6. 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.
  7. 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
  8. J. Bragantini, A. Falcão, and L. Najman, “Rethinking Interactive Image Segmentation: Feature Space Annotation,” Pattern Recognition, vol. 131, p. 108882, 2022. | link | pdf | github
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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