bia-binder: A web-native cloud compute service for the bioimage analysis community

Authors: Russell, Craig T., Burel, Jean-Marie, Athar, Awais, Li, Simon, Sarkans, Ugis, Swedlow, Jason, Brazma, Alvis, Hartley, Matthew, Uhlmann, Virginie

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2411.12662

Bringing Open Data to Whole Slide Imaging
Digital pathology (European congress)

Authors: Besson, Sébastien, Leigh, Roger, Linkert, Melissa, Allan, Chris, Burel, Jean-Marie, Carroll, Mark, Gault, David, Gozim, Riad, Li, Simon, Lindner, Dominik

Source: Lecture notes in computer science. 11435:3-10

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCCN605338225&indx=1&recIds=ETOCCN605338225

Towards a project community approach to academic scientific software development

Authors: Loynton, Scott, Sloan, David, Burel, Jean-Marie, Macaulay, Catriona

Source: 2009 5th IEEE International Conference on E-Science Workshops E-Science Workshops, 2009 5th IEEE International Conference on. :120-124 Dec, 2009

Relation: 2009 5th IEEE International Conference On E-Science Workshops

Metadata management for high content screening in OMERO

Authors: Li, Simon, Besson, Sébastien, Blackburn, Colin, Carroll, Mark, Ferguson, Richard K., Flynn, Helen, Gillen, Kenneth, Leigh, Roger, Lindner, Dominik, Linkert, Melissa, Moore, William J., Ramalingam, Balaji, Rozbicki, Emil, Rustici, Gabriella, Tarkowska, Aleksandra, Walczysko, Petr, Williams, Eleanor, Allan, Chris, Burel, Jean-Marie, Moore, Josh, Swedlow, Jason R.

Source: In Methods 1 March 2016 96:27-32

"Be sustainable": EOSC‐Life recommendations for implementation of FAIR principles in life science data handling.

Authors: David, Romain, Rybina, Arina, Burel, Jean‐Marie, Heriche, Jean‐Karim, Audergon, Pauline, Boiten, Jan‐Willem, Coppens, Frederik, Crockett, Sara, Exter, Katrina, Fahrner, Sven, Fratelli, Maddalena, Goble, Carole, Gormanns, Philipp, Grantner, Tobias, Grüning, Björn, Gurwitz, Kim Tamara, Hancock, John M, Harmse, Henriette, Holub, Petr, Juty, Nick

Source: EMBO Journal; Dec2023, Vol. 42 Issue 23, p1-23, 23p

Subject Terms: LIFE sciences, OPEN scholarship, DIGITAL technology, SOFTWARE development tools, DATA management

OME-Zarr: a cloud-optimized bioimaging file format with international community support.

Authors: Moore, Josh, Basurto-Lozada, Daniela, Besson, Sébastien, Bogovic, John, Bragantini, Jordão, Brown, Eva M., Burel, Jean-Marie, Casas Moreno, Xavier, de Medeiros, Gustavo, Diel, Erin E., Gault, David, Ghosh, Satrajit S., Gold, Ilan, Halchenko, Yaroslav O., Hartley, Matthew, Horsfall, Dave, Keller, Mark S., Kittisopikul, Mark, Kovacs, Gabor, Küpcü Yoldaş, Aybüke

Source: Histochemistry & Cell Biology; Sep2023, Vol. 160 Issue 3, p223-251, 29p

Subject Terms: COMMUNITY support, TASK analysis, DATA management, DATA analysis, SCALABILITY, PUBLIC spaces

Metadata matters: access to image data in the real world

Authors: Linkert, Melissa, Rueden, Curtis T., Allan, Chris, Burel, Jean-Marie, Moore, Will, Patterson, Andrew, Loranger, Brian, Moore, Josh, Neves, Carlos, MacDonald, Donald, Tarkowska, Aleksandra, Sticco, Caitlin, Hill, Emma, Rossner, Mike, Eliceiri, Kevin W., Swedlow, Jason R.

Source: The Journal of Cell Biology, 2010 May . 189(5), 777-782.

Access URL: https://www.jstor.org/stable/27811023

CONFORMAL SUBFOLIATIONS OF PRESCRIBED GEODESIC CURVATURE

Authors: BAIRD, PAUL, BUREL, JEAN-MARIE

Source: Mathematica Scandinavica, 2003 Jan 01. 93(2), 221-239.

Access URL: https://www.jstor.org/stable/24493506

Open Tools for Storage and Management of Quantitative Image Data

Authors: Moore, Joshua, Allan, Chris, Burel, Jean‐Marie, Loranger, Brian, MacDonald, Donald, Monk, Jonathan, Swedlow, Jason R.

Source: In Methods in Cell Biology 2008 85:555-570

Quantitative Image Analysis and the Open Microscopy Environment

Authors: Swedlow, Jason R, Allan, Chris, Falconi, Andrea, Burel, Jean-Marie

Source: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 2005, v. 5, p2187-2194.

Subject Terms: Information storage and retrieval, Microscopy, Molecules, Information management software, Image processing software

Publishing and sharing multi-dimensional image data with OMERO.

Authors: Burel, Jean-Marie¹, Besson, Sébastien¹, Blackburn, Colin¹, Carroll, Mark¹, Ferguson, Richard¹, Flynn, Helen¹, Gillen, Kenneth¹, Leigh, Roger¹, Li, Simon¹, Lindner, Dominik¹, Linkert, Melissa², Moore, William¹, Ramalingam, Balaji¹, Rozbicki, Emil², Tarkowska, Aleksandra¹, Walczysko, Petr¹, Allan, Chris², Moore, Josh, Swedlow, Jason jrswedlow@dundee.ac.uk

Source: Mammalian Genome. Oct2015, Vol. 26 Issue 9/10, p441-447. 7p.

Subject Terms: *MEDICAL sciences, *CYTOLOGICAL research, *DATA acquisition systems, *MULTIDIMENSIONAL databases, *DATA analysis

Applications et morphismes harmoniques à valeurs dans une surface

Authors: Burel, Jean-Marie

Source: In Comptes Rendus de l'Academie des Sciences Series I Mathematics 2001 332(5):441-446

OMERO: flexible, model-driven data management for experimental biology.

Authors: Allan, Chris¹, Burel, Jean-Marie¹, Moore, Josh², Blackburn, Colin³, Linkert, Melissa², Loynton, Scott³, MacDonald, Donald³, Moore, William J³, Neves, Carlos², Patterson, Andrew³, Porter, Michael³, Tarkowska, Aleksandra³, Loranger, Brian³, Avondo, Jerome⁴, Lagerstedt, Ingvar⁵, Lianas, Luca⁶, Leo, Simone⁶, Hands, Katherine³, Hay, Ron T³, Patwardhan, Ardan⁵

Source: Nature Methods. Mar2012, Vol. 9 Issue 3, p245-253. 9p. 3 Color Photographs, 1 Diagram, 1 Graph.

Subject Terms: *COMPUTER software, *MIDDLEWARE, *ELECTRON microscopy, *OPEN source software, *MOLECULAR dynamics, *EXPERIMENTAL biology

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OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies

Authors: Moore, Josh, Allan, Chris, Besson, Sébastien, Burel, Jean-Marie, Diel, Erin, Gault, David, Kozlowski, Kevin, Lindner, Dominik, Linkert, Melissa, Manz, Trevor, Moore, Will, Pape, Constantin, Tischer, Christian, Swedlow, Jason R.

Source: Nature Methods; December 2021, Vol. 18 Issue: 12 p1496-1498, 3p

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The Open Microscopy Environment: open image informatics for the biological sciences

Authors: Chiozzi, Gianluca, Guzman, Juan C., Blackburn, Colin, Allan, Chris, Besson, Sébastien, Burel, Jean-Marie, Carroll, Mark, Ferguson, Richard K., Flynn, Helen, Gault, David, Gillen, Kenneth, Leigh, Roger, Leo, Simone, Li, Simon, Lindner, Dominik, Linkert, Melissa, Moore, Josh, Moore, William J., Ramalingam, Balaji, Rozbicki, Emil, Rustici, Gabriella, Tarkowska, Aleksandra, Walczysko, Petr, Williams, Eleanor, Swedlow, Jason R.

Source: Proceedings of SPIE; July 2016, Vol. 9913 Issue: 1 p991324-991324-8