Metadata Standards and Software Tools for Research Data Management and Sharing

Selected publications

For a complete list, see: https://orcid.org/0000-0002-1069-1816

The crucial role of bioimage analysts in scientific research and publication

Cimini BA, Bankhead P, D’Antuono R, Fazeli E, Fernandez-Rodriguez J, Fuster-Barceló C, [...], Strambio-De-Castillia, C., [...], et al.  J Cell Sci. 2024; 137(20). Available from: https://doi.org/10.1242/jcs.262322.

Enabling data interpretability and reuse in light microscopy through consensus building, community engagement, and a next-generation metadata framework

Grunwald D, Moore J, Strambio-De-Castillia C.  Zenodo [Internet]. 2024; Available from: https://doi.org/10.5281/zenodo.11639719.

Building momentum through networks: Bioimaging across the Americas

De Niz M, Escobedo García R, Terán Ramirez C, Pakowski Y, Abonza Y, Bialy N, [...], Strambio-De-Castillia, C., [...], et al.  J Microsc. John Wiley & Sons, Ltd; 2024; 294 (special issue)(3):420–39. Available from: https://doi.org/10.1111/jmi.13318.

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, [...], Strambio-De-Castillia, C., [...], et al. Mol Cell. 2023; 83(15):2624-2640. Available from: http://dx.doi.org/10.1016/j.molcel.2023.06.018.

Toward a common standard for data and specimen provenance in life sciences.   

Wittner R, Holub P, Mascia C, Frexia F, Müller H, Plass M, [...], Strambio-De-Castillia, C., [...], et al. Learn Health Syst [Internet]. Wiley; 2023; 8(1):e10365. Available from: https://doi.org/10.5281/zenodo.11639719

Community-developed checklists for publishing images and image analyses

Schmied C, Nelson MS, Avilov S, Bakker G-J, Bertocchi C, Bischof J, [...], Strambio-De-Castillia, C., [...], et al. Nat Methods 2023. Available from: https://doi.org/10.1038/s41592-023-01987-9.

SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data 

Lee L, Yu H, Jia BB, Jussila A, Zhu C, Chen J, [...], Strambio-De-Castillia, C., [...], et al. Nat Commun 2023 [cited 2023 May 14]; 14(1):4873. Available from: https://doi.org/10.1038/s41467-023-40658-3.

Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.  

Rigano A, Ehmsen S, Ozturk SU, Ryan J, Balashov A, Hammer M, [...] Strambio-De-Castillia C. Nature Methods 2021; 18:1489–95. Available from: https://doi.org/10.1038/s41592-021-01315-z

Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.  

Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, [...] Strambio-De-Castillia C. Nature Methods 2021; 18:1427–40. Available from: https://doi.org/10.1038/s41592-021-01327-9.

MethodsJ2: A Software Tool to Capture and Generate Comprehensive Microscopy Methods Text and Improve Reproducibility.

Ryan J, Pengo T, Rigano A, Montero Llopis P, Itano MS, Cameron LC, [...], Strambio-De-Castillia, C., [...], et al. Nature Methods 2021; 18:1414–5. Available from: https://doi.org/10.1038/s41592-021-01290-5.

MDEmic: a metadata annotation tool to facilitate FAIR image data management in the bioimaging community.  

Kunis S, Hänsch S, Schmidt C, Wong F, Strambio-De-Castillia C., Weidtkamp-Peters S. Nature Methods 2021; 18:1415–6. Available from: https://doi.org/10.1038/s41592-021-01288-z.

REMBI: Recommended Metadata for Biological Images - realizing the full potential of the bioimaging revolution by enabling data reuse.  

Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, [...], Strambio-De-Castillia, C., [...], et al.  Nature Methods 2021; 18:1418–22. Available from: https://doi.org/10.1038/s41592-021-01166-8.

QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy.

Boehm U, Nelson G, Brown CM, Bagley S, Bajcsy P, Bischof J, [...], Strambio-De-Castillia, C., [...], et al.  Nature Methods 2021; 18:1423–6. Available from: https://doi.org/10.1038/s41592-021-01162-y.

OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control.

Rigano A, Galli V, Clark JM, Pereira LE, Grossi L, Luban J, [...] Strambio-De-Castillia C.  bioRxiv 2018. Available from: http://dx.doi.org/10.1101/251850.

An algorithm-centric Monte Carlo method to empirically quantify motion-type estimation uncertainty in single-particle tracking.  

Rigano A, Galli V, Gonciarz K, Sbalzarini IF, Strambio-De-Castillia C.  bioRxiv 2018. Available from: http://dx.doi.org/10.1101/379255.

Proposal for minimum information guidelines to report and reproduce results of particle tracking and motion analysis.  

Rigano A, Strambio-De-Castillia C. bioRxiv 2017. Available from: http://dx.doi.org/10.1101/155036.