MITI Minimum Information guidelines for highly multiplexed tissue images

Authors: Schapiro, Denis, Yapp, Clarence, Sokolov, Artem, Reynolds, Sheila M., Chen, Yu-An, Sudar, Damir, Xie, Yubin, Muhlich, Jeremy L., Arias-Camison, Raquel, Arena, Sarah, Taylor, Adam J., Nikolov, Milen, Tyler, Madison, Lin, Jia-Ren, Burlingame, Erik A., Network, Human Tumor Atlas, Chang, Young H., Farhi, Samouil L, Thorsson, Vésteinn, Venkatamohan, Nithya, Drewes, Julia L., Pe'er, Dana, Gutman, David A., Herrmann, Markus D., Gehlenborg, Nils, Bankhead, Peter, Roland, Joseph T., Herndon, John M., Snyder, Michael P., Angelo, Michael, Nolan, Garry, Swedlow, Jason R., Schultz, Nikolaus, Merrick, Daniel T., Mazzilli, Sarah A., Cerami, Ethan, Rodig, Scott J., Santagata, Sandro, Sorger, Peter K.

Subject Terms: Quantitative Biology - Other Quantitative Biology, Electrical Engineering and Systems Science - Image and Video Processing

Access URL: http://arxiv.org/abs/2108.09499

Essential Metadata for 3D BRAIN Microscopy

Authors: Ropelewski, Alexander J., Rizzo, Megan A., Swedlow, Jason R., Huisken, Jan, Osten, Pavel, Khanjani, Neda, Weiss, Kurt, Bakalov, Vesselina, Engle, Michelle, Gridley, Lauren, Krzyzanowski, Michelle, Madden, Tom, Maiese, Deborah, Waterfield, Justin, Williams, David, Hamilton, Carol, Huggins, Wayne

Subject Terms: Quantitative Biology - Other Quantitative Biology

Access URL: http://arxiv.org/abs/2105.09158

QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

Authors: Nelson, Glyn, Boehm, Ulrike, Bagley, Steve, Bajcsy, Peter, Bischof, Johanna, Brown, Claire M, Dauphin, Aurelien, Dobbie, Ian M, Eriksson, John E, Faklaris, Orestis, Fernandez-Rodriguez, Julia, Ferrand, Alexia, Gelman, Laurent, Gheisari, Ali, Hartmann, Hella, Kukat, Christian, Laude, Alex, Mitkovski, Miso, Munck, Sebastian, North, Alison J, Rasse, Tobias M, Resch-Genger, Ute, Schuetz, Lucas C, Seitz, Arne, Strambio-De-Castillia, Caterina, Swedlow, Jason R, Alexopoulos, Ioannis, Aumayr, Karin, Avilov, Sergiy, Bakker, Gert-Jan, Bammann, Rodrigo R, Bassi, Andrea, Beckert, Hannes, Beer, Sebastian, Belyaev, Yury, Bierwagen, Jakob, Birngruber, Konstantin A, Bosch, Manel, Breitlow, Juergen, Cameron, Lisa A, Chalfoun, Joe, Chambers, James J, Chen, Chieh-Li, Conde-Sousa, Eduardo, Corbett, Alexander D, Cordelieres, Fabrice P, Del Nery, Elaine, Dietzel, Ralf, Eismann, Frank, Fazeli, Elnaz, Felscher, Andreas, Fried, Hans, Gaudreault, Nathalie, Goh, Wah Ing, Guilbert, Thomas, Hadleigh, Roland, Hemmerich, Peter, Holst, Gerhard A, Itano, Michelle S, Jaffe, Claudia B, Jambor, Helena K, Jarvis, Stuart C, Keppler, Antje, Kirchenbuechler, David, Kirchner, Marcel, Kobayashi, Norio, Krens, Gabriel, Kunis, Susanne, Lacoste, Judith, Marcello, Marco, Martins, Gabriel G, Metcalf, Daniel J, Mitchell, Claire A, Moore, Joshua, Mueller, Tobias, Nelson, Michael S, Ogg, Stephen, Onami, Shuichi, Palmer, Alexandra L, Paul-Gilloteaux, Perrine, Pimentel, Jaime A, Plantard, Laure, Podder, Santosh, Rexhepaj, Elton, Royon, Arnaud, Saari, Markku A, Schapman, Damien, Schoonderwoert, Vincent, Schroth-Diez, Britta, Schwartz, Stanley, Shaw, Michael, Spitaler, Martin, Stoeckl, Martin T, Sudar, Damir, Teillon, Jeremie, Terjung, Stefan, Thuenauer, Roland, Wilms, Christian D, Wright, Graham D, Nitschke, Roland

Source: J. Microsc. 2021;1-18

Subject Terms: Quantitative Biology - Other Quantitative Biology, Physics - Instrumentation and Detectors

Access URL: http://arxiv.org/abs/2101.09153

A Global View of Standards for Open Image Data Formats and Repositories

Authors: Swedlow, Jason R., Kankaanpää, Pasi, Sarkans, Ugis, Goscinski, Wojtek, Galloway, Graham, Sullivan, Ryan P., Brown, Claire M., Wood, Chris, Keppler, Antje, Loos, Ben, Zullino, Sara, Longo, Dario Livio, Aime, Silvio, Onami, Shuichi

Subject Terms: Quantitative Biology - Other Quantitative Biology

Access URL: http://arxiv.org/abs/2010.10107

Male contraceptive development: A medicinal chemistry perspective

Authors: Norcross, Neil R., Georgiou, Irene, Johnston, Zoe C., Gruber, Franz S., Swedlow, Jason R., Read, Kevin D., Barratt, Christopher LR., Gilbert, Ian H.

Source: In European Journal of Medicinal Chemistry 5 December 2022 243

Public archives for biological image data

Authors: Ellenberg, Jan, Swedlow, Jason R, Barlow, Mary, Cook, Charles E, Patwardhan, Ardan, Brazma, Alvis, Birney, Ewan

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1801.10189

Compounds enhancing human sperm motility identified using a high-throughput phenotypic screening platform

Authors: Gruber, Franz S, Johnston, Zoe C, Norcross, Neil R, Georgiou, Irene, Wilson, Caroline, Read, Kevin D, Gilbert, Ian H, Swedlow, Jason R, Martins da Silva, Sarah, Barratt, Christopher L R

Source: Human reproduction. 37(3):466-475

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100148801034.0x000001&indx=1&recIds=ETOCvdc_100148801034.0x000001

The BioImage Archive – Building a Home for Life-Sciences Microscopy Data

Authors: Hartley, Matthew, Kleywegt, Gerard J., Patwardhan, Ardan, Sarkans, Ugis, Swedlow, Jason R., Brazma, Alvis

Source: In Journal of Molecular Biology 15 June 2022 434(11)

Proteomic and functional comparison between human induced and embryonic stem cells.

Authors: Brenes, Alejandro J., Griesser, Eva, Sinclair, Linda V., Davidson, Lindsay, Prescott, Alan R., Singh, Francois, Hogg, Elizabeth K. J., Espejo-Serrano, Carmen, Hao Jiang, Harunori Yoshikawa, Platani, Melpomeni, Swedlow, Jason R., Findlay, Greg M., Cantrell, Doreen A., Lamond, Angus I.

Source: eLife; 11/14/2024, p1-25, 25p

Numerically Enhanced Stimulated Emission Depletion Microscopy with Adaptive Optics for Deep-Tissue Super-Resolved Imaging

Authors: Zdańkowski, Piotr, Trusiak, Maciej, McGloin, David, Swedlow, Jason R.

Source: ACS nano. 14(1):394-405

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN623138791&indx=1&recIds=ETOCRN623138791

Usability and User-Centered Design in Scientific Software Development

Authors: Macaulay, Catriona, Sloan, David, Jiang, Xinyi, Forbes, Paula, Loynton, Scott, Swedlow, Jason R., Gregor, Peter

Source: IEEE Software IEEE Softw. Software, IEEE. 26(1):96-102 Jan, 2009

Measuring Tubulin Content in Toxoplasma gondii: A Comparison of Laser-Scanning Confocal and Wide-Field Fluorescence Microscopy

Authors: Swedlow, Jason R., Hu, Ke, Andrews, Paul D., Roos, David S., Murray, John M.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2002 Feb . 99(4), 2014-2019.

Access URL: https://www.jstor.org/stable/3057910

In Vivo Analysis of Cajal Body Movement, Separation, and Joining in Live Human Cells

Authors: Platani, Melpomeni, Goldberg, Ilya, Swedlow, Jason R., Lamond, Angus I.

Source: The Journal of Cell Biology, 2000 Dec . 151(7), 1561-1574.

Access URL: https://www.jstor.org/stable/1620145

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

Sperm Toolbox—A selection of small molecules to study human spermatozoa.

Authors: Gruber, Franz S., Richardson, Anthony, Johnston, Zoe C., Myles, Rachel, Norcross, Neil R., Day, David P., Georgiou, Irene, Sesma-Sanz, Laura, Wilson, Caroline, Read, Kevin D., Martins da Silva, Sarah, Barratt, Christopher L. R., Gilbert, Ian H., Swedlow, Jason R.

Source: PLoS ONE; 2/20/2024, Vol. 19 Issue 2, p1-16, 16p

Subject Terms: SMALL molecules, REPRODUCTIVE technology, ACROSOME reaction, MALE contraceptives, HUMAN experimentation, SPERMATOZOA, FROZEN semen

Informatics and Quantitative Analysis in Biological Imaging

Authors: Swedlow, Jason R., Goldberg, Ilya, Brauner, Erik, Sorger, Peter K.

Source: Science, 2003 Apr 01. 300(5616), 100-102.

Access URL: https://www.jstor.org/stable/3834307

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB

Authors: Lagerstedt, Ingvar, Moore, William J., Patwardhan, Ardan, Sanz-García, Eduardo, Best, Christoph, Swedlow, Jason R., Kleywegt, Gerard J.

Source: In Journal of Structural Biology November 2013 184(2):173-181

At the (Kineto)chore, Yeast Really Are Like People

Authors: Swedlow, Jason R.

Source: In Cell 29 August 2013 154(5):959-961

PHD1 Links Cell-Cycle Progression to Oxygen Sensing through Hydroxylation of the Centrosomal Protein Cep192

Authors: Moser, Sandra C., Bensaddek, Dalila, Ortmann, Brian, Maure, Jean-Francois, Mudie, Sharon, Blow, J. Julian, Lamond, Angus I., Swedlow, Jason R., Rocha, Sonia

Source: In Developmental Cell 26 August 2013 26(4):381-392

Sds22 regulates aurora B activity and microtubule—kinetochore interactions at mitosis

Authors: Posch, Markus, Khoudoli, Guennadi A., Swift, Sam, King, Emma M., DeLuca, Jennifer G., Swedlow, Jason R.

Source: The Journal of Cell Biology, 2010 Oct 01. 191(1), 61-74.

Access URL: https://www.jstor.org/stable/20789849