Caterina Strambio De Castillia:

ORCID: https://orcid.org/my-orcid?orcid=0000-0002-1069-1816

Biosketch:

• Trained at The Rockefeller University with Nobel Prize Gunter Blobel one of the pioneers of modern molecular cell biology.
• Ongoing interest in the fundamental principles governing intracellular trafficking and the interaction between the nuclear pore complex, nucleocytoplasmic transport, chromatin maintenance, and gene regulation.
• Broad expertise spanning from molecular cell biology, virology, mass-spectrometry, and proteomics, to advanced electron, and light microscopy.
• Spearheaded several collaborative efforts involving individuals with diverse expertise to develop, bio-image informatics technology aimed at promoting rigor, quality, reproducibility, and Findable Accessible Interoperable Reproducible (FAIR) sharing value in quantitative light microscopy through the standardization of metadata models and quality control (QC) procedures, and the development of shared Research Data Management software infrastructure for imaging pipelines.
• Faculty Member at the Program of Molecular Medicine at the University of Massachusetts Chan Medical School (UMass Chan).

Major Open-Science Efforts:

• 2008-present: Active participation and contribution to the Open Microscopy Environment community. Highlights:
  • Participant at 2008, 2009, 2010, 2013, 2014, 2015 OME Users’ Meetings.
  • Speaker at OME Community Meeting in 2011 and 2018.
  • Invited speaker at 2020 OME Community Meeting
  • Tutorial presented 2021 OME Community Meeting
• 2009-2019: Leader of the Open Microscopy Environment inteGrated Analysis (OMEGA) project.
• 2012-present: Member of the Biomedical Imaging Group interdisciplinary team developing integrated light microscopy pipelines for cell biology and biophysics.
• 2018-present: Member of the NIH-Funded 4D Nucleome (4DN) Initiative with the specific goal of developing metadata specifications, formats for data exchange, and software tools to promote the integration of imaging and omics and advance the understanding of the role of chromatin organization in health and disease. Highlights:
  • 2018-2019: Associate member recruited specifically to develop exchange data formats for Particle Tracking experiments on the basis of the MIAPTE specifications.
  • 2020-present: Funded member of the 4DN Data Coordination and Integration Center (4DN-DCIC).
  • 2020-present: Chair of 4DN Imaging Working Group (IWG).
  • 2021-present: Organizer of Common Coordinate Framework (CCF) sub-Group of the Integrating Imaging and Omics Working Group (IOWG).
• 2019-present: Chan Zuckerberg Initiative Imaging Scientist – Project title: Bridging the gap between quantitative bioimaging and bench side scientists. Project goals: Development and dissemination of community efforts, metadata specifications, and software tools to democratize access to advanced quantitative bioimaging by biomedical scientists, regardless of their expertise.
• 2019-present: Chair of the Bioimaging North America Quality Control and Data Management Working Group (QC-DM-WG). Highlights:
  • Nature Methods Focus Issue on Reporting and Reproducibility in Light Microscopy.
  • Community Conversations to assess the microscopy reporting and reproducibility needs of the bioimaging community.
  • Metrology Suitcase program.

• 2019-present: Invited contributor to strategic community workshops to define shared best practices, metadata specifications, and tools to advance and democratize quantitative microscopy:
  • 2019 European Molecular Biology Laboratory – European Bioinformatics Institute workshop to define recently published minimal metadata recommendation to enable the reuse of microscopy data to be deposited to the BioImage Archive.
    • REMBI: Recommended Metadata for Biological Images
  • Allen Institute 2022 Workshops on Changing the World of Light Microscopy. Invited participants included community experts, funders, publishers, industrial partners, and institutional leadership. The workshops were convened to follow up on a recent Molecular Cell article identifying key challenges in transforming microscopy into a robust, reproducible, and quantitative tool to explore biological processes in health and disease. Two workshops were organized:
    • Data Generation (September 13th, 2022)
    • Data Management (September 20th, 2022)

• 2020-present: Co-founding member of QUality Assessment and REProducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi; https://quarep.org). Highlights:
  • Co-chair of the Working-Group-7 (WG7) on Metadata.
  • Lead organizer of the series of community-feedback sessions aimed at developing broad consensus microscopy camera metadata specifications in collaboration with QUAREP-LiMi WG2, and with representatives of all major global camera manufacturers (Andor, Hamamatsu, Leica, Nikon, Olympus, Pico-QUANT, PCO, Teledyne Photometrics, and Zeiss).

Major Contribution to Open-Science:

1. Open Microscopy Environment inteGrated Analysis (OMEGA) project
   1. OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and QC.
   2. Minimum Information for Particle Tracking Experiments (MIAPTE).
   3. Monte Carlo QC methods for motion-type estimation in particle tracking.
2. Community data formats for capturing and exchanging results of imaging experiments conducted in the context of the 4D Nucleome Initiative:
   1. 4DN Single Particle Tracking format.
   2. 4DN FISH Omics Format – Chromatin Tracing (FOF-CT).
   3. 4DN FISH Omics Format – Chromatin Tracing datasets.
   4. 4DN FOF – Genomic Single Molecule Localization IN PROGRESS
3. 4DN-BINA-OME Microscopy Metadata specifications that scale with experimental, instrumentation, and analytical complexity and extend the OME Data Model.
   1. GitHub repository
   2. Nature Methods article
   3. Global Bioimaging Training Module
4. Interoperable microscopy metadata collection tools that facilitate the adoption of microscopy quality-control, reporting, and reproducibility practices on the basis of community specifications. These tools extract available metadata from microscope configuration and image-data files, collect missing information and produce well-documented datasets:
   1. Micro-Meta App –
      1. GitHub release
      2. Nature Methods article
      3. Website
      4. ReadTheDocs documentation
      5. Protocols.io tutorial
      6. Global Bioimaging Training Module
   2. MethodJ2 –
      • GitHub repository
      • Nature Methods article
   3. MDEmic –
      • Nature Methods article
5. Research Data Management tools to automate the automatic import, metadata annotation, and analysis of microscopy image datasets into OMERO repositories:
   1. OMEGA-App – GitHub release
   2. OMERO Importer – GitHub repository
   3. OMERO Data Writer – GitHub repository
6. Advocacy efforts to improve institutional support for the use of the OMERO image data repository at core facilities as the ideal keystone for integrated research data management, imaging experiments reporting and QC, and image analysis pipelines:
   1. University of Massachusetts Medical School, Program in Molecular Medicine, Biomedical Imaging Group, OMERO UmassMed Repository
      
   2. University of North Carolina, Michelle Itano, Neuroscience Center, Neuro-Microscopy Facility.
   3. The Rockefeller University, Alison North, Bioimaging Resource Center.
   4. McGill University/Canada Bioimaging, Claire Brown, Advanced BioImaging Facility (ABIF).
   5. The Neuro (Montreal Neurological Institute-Hospital), Thomas Stroh, Neuro Microscopy Core Facility.
   6. Canada BioImaging – Digital Research Alliance, National OMERO Image Data Resource
      
7. Educational and Training efforts to improve awareness and adoption of Research Data Management practices to maximize image-data quality, reproducibility, and FAIR sharing value. Recent highlights:
   1. Talks and workshops
      1. Micro-Meta App: live demo. 2021 OME Community Meeting. Available on YouTube. (2021).
      2. QUAREP-LiMi WORKSHOP: WG 7 (Metadata): Micro-Meta App: an interactive software to facilitate the collection of microscopy metadata based on the 4DN-BINA-OME community-driven specifications. Invited speaker and session organizer. 2021 European Light Microscopy Initiative Meeting.  (2021).
      3. QUAREP-LiMi TUTORIAL: WG 7 (Metadata) – Micro-Meta App: an interactive software to facilitate the collection of microscopy metadata based on the 4DN-BINA-OME (NBO) community-driven specifications. Invited speaker and session organizer. The 19th Annual Advanced Imaging Methods Workshop, hosted by the University of California at Berkeley. (2022).
      4. Open microscopy documentation for the real world: interactive tools for quality, reproducibility, and sharing value of imaging experiments based on community specifications. Invited talk. Royal Microscopy Society SIMposium: recent advancements in structured illumination microscopy. FigShare (2022).
      5. Microscopy reproducibility for the real world: building interactive tools to document light microscopy experiments based on community specifications. Invited lecture. Royal Microscopy Society Imaging ONE World Lecture Series. YouTube (2022).
      6. Community Guidelines and Tools for the Collection and Reporting of Microscopy Metadata. Selected talk. Images 2 Knowledge (I2K) Conference. Available on YouTube. (2022).
      7. Collecting and Reporting Microscope Metadata with Micro-Meta App and MethodsJ2. Selected tutorial workshop. Images 2 Knowledge (I2K) Conference (https://www.i2kconference.org/). Available on YouTube. (2022).
      8. Core Facility Day – Sessions on QUAREP-LiMi and  Research Data Management. Session Organizer and Chair, Presenter. 2022 European Light Microscopy Initiative Meeting (2022).
      9. Microscopy reproducibility for the real world: building interactive tools to document light microscopy experiments based on community specifications. Invited lecture. Unidad de Bioimagenologia Avanzada, Institute Pasteur de Montevideo. YouTube (2022).
      10. Reporting and reproducibility in microscopy through rigorous image publication and community-driven tools for research data management. Invited lecture. The University of Chicago, Marine Biology Laboratory, Optical Microscopy & Imaging in the Biomedical Sciences (OMIBS) (2022).
   2. Training Material
      1. Website: Micro-Meta App: Microscopy Metadata for the real world!
      2. ReadTheDocs software documentation: Micro-Meta App: Tutorials and Documentation
      3. Protocols.io: Getting started with Micro-Meta App Tutorial.
      4. Global-BioImaging training modules: Reporting & Reproducibility in Microscopy