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My scientific career has been focused on developing computational tools and methods to advance microscopy image analysis, with a particular emphasis on bacterial cell biology. Education and Early Career: - MSc in Biochemistry (2014) from University of Aveiro, where I gained a strong foundation in molecular and cellular biology. - Joined the Bacterial Cell Biology Lab at ITQB NOVA as a research technician in 2015, where I was first exposed to advanced microscopy techniques and image analysis for studying bacterial cells. PhD Research (2018-2022): - Completed PhD in Molecular Biosciences at ITQB NOVA under supervision of Dr. Mariana Pinho. - Developed novel computational methods for analyzing super-resolution microscopy data of bacterial cells, particularly Staphylococcus aureus. - Key achievement: Created eHooke, an automated image analysis pipeline for spherical bacteria that can segment cells and classify their cell cycle stage using machine learning. This tool has been widely adopted in the field. - Published 4 peer-reviewed papers during PhD, including 2 as first author in high-impact journals like Nature Communications Postdoctoral Research (2022-present): - Joined the Optical Cell Biology Lab at IGC led by Dr. Ricardo Henriques. - Leading the development of NanoPyx, a high-performance bioimage analysis framework. - Integrating machine learning and GPU acceleration techniques to dramatically speed up microscopy image processing workflows. Key Skills and Expertise: - Advanced programming in Python, C, and OpenCL for scientific computing and image analysis - Machine learning and deep learning, particularly applied to microscopy image segmentation and classification - High-performance computing and GPU acceleration of image processing algorithms - Super-resolution microscopy techniques and analysis - Bacterial cell biology, with focus on cell division and antibiotic resistance mechanisms - Open-source software development and community building
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Identification

Personal identification

Full name
Bruno Saraiva

Citation names

  • M. Saraiva, Bruno

Author identifiers

Ciência ID
B61E-2513-7A8B
ORCID iD
0000-0002-9151-5477

Knowledge fields

  • Natural sciences - Biological Sciences - Microbiology
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Engineering and Technology - Electrotechnical Engineering, Electronics and Informatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2022/05/04
Concluded
 Biociências Moleculares (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
"Studies of Staphylococcus aureus’ cell cycle: New approaches for automated analysis" (THESIS/DISSERTATION)
2014
Concluded
 Mestrado em Bioquímica, ramo de Métodos Biomoleculares (Mestrado)
Universidade de Aveiro, Portugal
"Identificação de Bactérias por Espectrometria de Massa" (THESIS/DISSERTATION)
 16
2013
Concluded
 Licenciatura em Bioquímica (Licenciatura)
Universidade de Aveiro, Portugal
"Síntese e Análise da Atividade Antibacteriana de Tetraarilporfirinas catiónicas" (THESIS/DISSERTATION)
 12
Affiliation

Science

Category
Host institution 		Employer
2024/10/01 - Current Postdoc (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Universidade Nova de Lisboa Microbiologia Molecular Estrutural e Celular, Portugal
2022/05/16 - Current Postdoc (Research) Gulbenkian Institute for Molecular Medicine, Portugal

Others

Category
Host institution 		Employer
2018/02/01 - 2022/05/04 PhD Student Universidade Nova de Lisboa Microbiologia Molecular Estrutural e Celular, Portugal
2015 - 2018 Bolseiro de Investigação Universidade Nova de Lisboa Microbiologia Molecular Estrutural e Celular, Portugal
Projects

Grant

Designation Funders
2018/03 - 2023/02 Exploring the bacterial cell cycle to re-sensitize antibiotic-resistant bacteria
ERC-2017-CoG-771709
Research Fellow
2013/03 - 2018/02 Finding New Mechanisms for Protein Localization in Bacteria
ERC-2012-StG-310987
Research Fellow

Contract

Designation Funders
2023/01 - 2023/10/31 Cutting-edge super-resolution image analysis in Napari through NanoJ
2022-311154
Post-doc
Instituto Gulbenkian de Ciência, Portugal
 The Chan Zuckerberg Initiative
Concluded
Outputs

Publications

Journal article
  1. Bruno M. Saraiva; Inês Cunha; António Brito; Gautier Follain; Raquel Portela; Robert Haase; Pedro M. Pereira; Guillaume Jacquemet; Ricardo Henriques. "Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework". Nature Methods (2025): http://dx.doi.org/10.1038/s41592-024-02562-6.
    10.1038/s41592-024-02562-6
  2. Simon Schäper; António D. Brito; Bruno M. Saraiva; Georgia R. Squyres; Matthew J. Holmes; Ethan C. Garner; Zach Hensel; Ricardo Henriques; Mariana G. Pinho. "Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus". Nature Microbiology (2024): https://doi.org/10.1038/s41564-024-01629-6.
    10.1038/s41564-024-01629-6
  3. Sara F. Costa; Bruno M. Saraiva; Helena Veiga; Leonor B. Marques; Simon Schäper; Marta Sporniak; Daniel E. Vega; et al. "The role of GpsB in Staphylococcus aureus cell morphogenesis". mBio (2024): https://doi.org/10.1128/mbio.03235-23.
    10.1128/mbio.03235-23
  4. Helena Veiga; Ambre Jousselin; Simon Schäper; Bruno M Saraiva; Leonor B Marques; Patricia Reed; Joana Wilton; et al. "Cell division protein FtsK coordinates bacterial chromosome segregation and daughter cell separation in Staphylococcus aureus". The EMBO Journal (2023): https://doi.org/10.15252/embj.2022112140.
    10.15252/embj.2022112140
  5. Joanna W. Pylvänäinen; Romain F. Laine; Bruno M. S. Saraiva; Sujan Ghimire; Gautier Follain; Ricardo Henriques; Guillaume Jacquemet. "Fast4DReg: Fast registration of 4D microscopy datasets". Journal of Cell Science (2023): http://dx.doi.org/10.1242/jcs.260728.
    10.1242/jcs.260728
  6. Joana Figueiredo; Carlos Javier Orihuela; Mafalda Xavier Henriques; Maria João Catalão; Sara Pinheiro; Ana Rita Narciso; Francisco Mesquita; et al. "Encapsulation of the septal cell wall protects Streptococcus pneumoniae from its major peptidoglycan hydrolase and host defenses". PLOS Pathogens (2022): https://doi.org/10.1371/journal.ppat.1010516.
    10.1371/journal.ppat.1010516
  7. Bruno M. Saraiva; Ludwig Krippahl; Sérgio R. Filipe; Ricardo Henriques; Mariana G. Pinho. "eHooke: A tool for automated image analysis of spherical bacteria based on cell cycle progression". Biological Imaging (2021): 1-25. https://doi.org/10.1017/S2633903X21000027.
    10.1017/S2633903X21000027
  8. Bruno M. Saraiva; Moritz Sorg; Ana R. Pereira; Mário J. Ferreira; Léo C. Caulat; Nathalie T. Reichmann; Mariana G. Pinho. "Reassessment of the distinctive geometry of Staphylococcus aureus cell division". Nature Communications 11 1 (2020): https://doi.org/10.1038/s41467-020-17940-9.
    10.1038/s41467-020-17940-9
  9. Nathalie T. Reichmann; Andreia C. Tavares; Bruno M. Saraiva; Ambre Jousselin; Patricia Reed; Ana R. Pereira; João M. Monteiro; et al. "SEDS–bPBP pairs direct lateral and septal peptidoglycan synthesis in Staphylococcus aureus". Nature Microbiology 4 8 (2019): 1368-1377. https://doi.org/10.1038/s41564-019-0437-2.
    10.1038/s41564-019-0437-2
  10. Monteiro, J.M.; Pereira, A.R.; Reichmann, N.T.; Saraiva, B.M.; Fernandes, P.B.; Veiga, H.; Tavares, A.C.; et al. "Peptidoglycan synthesis drives an FtsZ-treadmilling-independent step of cytokinesis". Nature 554 7693 (2018): 528-532. http://www.scopus.com/inward/record.url?eid=2-s2.0-85042553143&partnerID=MN8TOARS.
    10.1038/nature25506
Preprint
  1. Mariana G. Ferreira; Bruno M. Saraiva; António D. Brito; Mariana G. Pinho; Ricardo Henriques; Estibaliz Gómez-de-Mariscal. "ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation". 2025. https://doi.org/10.1101/2025.04.09.647871.
    10.1101/2025.04.09.647871
  2. Afonso Mendes; Bruno M. Saraiva; Guillaume Jacquemet; João I. Mamede; Christophe Leterrier; Ricardo Henriques. "Structural Repetition Detector: multi-scale quantitative mapping of molecular complexes through microscopy". 2024. https://doi.org/10.1101/2024.09.16.613204.
    10.1101/2024.09.16.613204
  3. Bruno M. Saraiva; Inês M. Cunha; António D. Brito; Gautier Follain; Raquel Portela; Robert Haase; Pedro M. Pereira; Guillaume Jacquemet; Ricardo Henriques. "NanoPyx: super-fast bioimage analysis powered by adaptive machine learning". 2023. https://doi.org/10.1101/2023.08.13.553080.
    10.1101/2023.08.13.553080
  4. Giovanni Volpe; Carolina Wählby; Lei Tian; Michael Hecht; Artur Yakimovich; Kristina Monakhova; Laura Waller; et al. "Roadmap on Deep Learning for Microscopy". 2023. https://arxiv.org/abs/2303.03793.
    10.48550/ARXIV.2303.03793

Other

Other output
  1. SEDS-bPBP pairs direct Lateral and Septal Peptidoglycan Synthesis in Staphylococcus aureus. 2019. Nathalie T. Reichmann; Andreia C. Tavares; Bruno M. Saraiva; Ambre Jousselin; Patricia Reed; Ana R. Pereira; João M. Monteiro; et al. https://doi.org/10.1101/552034.
    10.1101/552034
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/08/30 NanoPyx: super-fast bioimage analysis powered by adaptive machine learning SMLMS24
ITQB-NOVA (Lisboa, Portugal)
2024/06/17 Accelerating bioimage analysis throught an adaptive Python framework AI/Smart microscopy workshop (AISMW2024)
University of Lund (Lund, Sweden)
2023/05/11 NanoPyx: a high-performance Python Library for microscopy image analysis NEUBIAS 23
(Porto, Portugal)
2022/10/03 Biological discovery through image analysis EMBO Course: Computational Optical Biology
Instituto Gulbenkian de Ciência (Lisboa, Portugal)
2021/11/26 eHooke: a framework for automated image analysis of Staphylococcus aureus based on cell cycle progression Microbiotec 21
(Portugal)
Distinctions

Award

2018 Pfizer Award
Pfizer Portugal, Portugal