Nature Methods

Community-developed checklists for publishing images and image analyses

Feb 01, 2024

Christopher Schmied, Michael S. Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T. Carvalho, Catalin Chiritescu, Jana Christopher, Beth A. Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Marie Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G. Martins, Aastha Mathur, Kota Miura, Paula Montero Llopis, Roland Nitschke, Alison North, Adam C. Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T. Scott, Arne Seitz, Olaf Selchow, Ved P. Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Douglas Taatjes, Christian Tischer, Helena Klara Jambor

Biophysical Journal

Building the next generation of virtual cells to understand cellular biology

Sep 19, 2023

Graham T. Johnson, Eran Agmon, Matthew Akamatsu, Emma Lundberg, Blair Lyons, Wei Ouyang, Omar A. Quintero-Carmona, Megan Riel-Mehan, Susanne Rafelski, Rick Horwitz

Histochemistry and Cell Biology

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

Sep 01, 2023

Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John Bogovic, Jordão Bragantini, Eva M. Brown, Jean-Marie Burel, Xavier Casas Moreno, Gustavo de Medeiros, Erin E. Diel, David Gault, Satrajit S. Ghosh, Ilan Gold, Yaroslav O. Halchenko, Matthew Hartley, Dave Horsfall, Mark S. Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü Yoldaş, Koji Kyoda, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Dominik Lindner, Melissa Linkert, Joel Lüthi, Jeremy Maitin-Shepard, Trevor Manz, Luca Marconato, Matthew McCormick, Merlin Lange, Khaled Mohamed, William Moore, Nils Norlin, Wei Ouyang, Bugra Özdemir, Giovanni Palla, Constantin Pape, Lucas Pelkmans, Tobias Pietzsch, Stephan Preibisch, Martin Prete, Norman Rzepka, Sameeul Samee, Nicholas Schaub, Hythem Sidky, Ahmet Can Solak, David R. Stirling, Jonathan Striebel, Christian Tischer, Daniel Toloudis, Isaac Virshup, Petr Walczysko, Alan M. Watson, Erin Weisbart, Frances Wong, Kevin A. Yamauchi, Omer Bayraktar, Beth A. Cimini, Nils Gehlenborg, Muzlifah Haniffa, Nathan Hotaling, Shuichi Onami, Loic A. Royer, Stephan Saalfeld, Oliver Stegle, Fabian J. Theis, Jason R. Swedlow

Nature Methods

When seeing is not believing: application-appropriate validation matters for quantitative bioimage analysis

Jul 01, 2023

Jianxu Chen, Matheus P. Viana, Susanne M. Rafelski

STAR Protocols

Reporting reproducible imaging protocols

Mar 01, 2023

DeLaine D. Larsen, Nathalie Gaudreault, Holly C. Gibbs

Nature

Integrated intracellular organization and its variations in human iPS cells

Jan 01, 2023

Matheus P. Viana, Jianxu Chen, Theo A. Knijnenburg, Ritvik Vasan, Calysta Yan, Joy E. Arakaki, Matte Bailey, Ben Berry, Antoine Borensztejn, Eva M. Brown, Sara Carlson, Julie A. Cass, Basudev Chaudhuri, Kimberly R. Cordes Metzler, Mackenzie E. Coston, Zach J. Crabtree, Steve Davidson, Colette M. DeLizo, Shailja Dhaka, Stephanie Q. Dinh, Thao P. Do, Justin Domingus, Rory M. Donovan-Maiye, Alexandra J. Ferrante, Tyler J. Foster, Christopher L. Frick, Griffin Fujioka, Margaret A. Fuqua, Jamie L. Gehring, Kaytlyn A. Gerbin, Tanya Grancharova, Benjamin W. Gregor, Lisa J. Harrylock, Amanda Haupt, Melissa C. Hendershott, Caroline Hookway, Alan R. Horwitz, H. Christopher Hughes, Eric J. Isaac, Gregory R. Johnson, Brian Kim, Andrew N. Leonard, Winnie W. Leung, Jordan J. Lucas, Susan A. Ludmann, Blair M. Lyons, Haseeb Malik, Ryan McGregor, Gabe E. Medrash, Sean L. Meharry, Kevin Mitcham, Irina A. Mueller, Timothy L. Murphy-Stevens, Aditya Nath, Angelique M. Nelson, Sandra A. Oluoch, Luana Paleologu, T. Alexander Popiel, Megan M. Riel-Mehan, Brock Roberts, Lisa M. Schaefbauer, Magdalena Schwarzl, Jamie Sherman, Sylvain Slaton, M. Filip Sluzewski, Jacqueline E. Smith, Youngmee Sul, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Daniel M. Toloudis, Andrew P. Tucker, Veronica Valencia, Winfried Wiegraebe, Thushara Wijeratna, Ruian Yang, Rebecca J. Zaunbrecher, Ramon Lorenzo D. Labitigan, Adrian L. Sanborn, Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot, Susanne M. Rafelski

Current Opinion in Biotechnology

The dawn of interoperating spatial models in cell biology

Dec 01, 2022

Janet H Iwasa, Blair Lyons, Graham T Johnson

Nature Methods

The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models

May 01, 2022

Blair Lyons, Eric Isaac, Na Hyung Choi, Thao P. Do, Justin Domingus, Janet Iwasa, Andrew Leonard, Megan Riel-Mehan, Emily Rodgers, Lisa Schaefbauer, Daniel Toloudis, Olivia Waltner, Lyndsay Wilhelm, Graham T. Johnson

Does Organelle Shape Matter?: Exploring Patterns in Cell Shape and Structure with High-Throughput (HT) Imaging

Jan 27, 2022

Carlos C. Goller*, Graham T. Johnson, Kaitlyn Casimo

Molecular Cell

The new era of quantitative cell imaging-challenges and opportunities

Jan 20, 2022

Neda Bagheri, Anne E. Carpenter, Emma Lundberg, Anne L. Plant, Rick Horwitz

PLOS Computational Biology

A deep generative model of 3D single-cell organization

Jan 18, 2022

Rory M. Donovan-Maiye, Jackson M. Brown, Caleb K. Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A. Theriot, Mary M. Maleckar, Theo A. Knijnenburg, Gregory R. Johnson

Scientific Reports

A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes

Aug 04, 2021

Tanya Grancharova, Kaytlyn A. Gerbin, Alexander B. Rosenberg, Charles M. Roco, Joy E. Arakaki, Colette M. DeLizo, Stephanie Q. Dinh, Rory M. Donovan-Maiye, Matthew Hirano, Angelique M. Nelson, Joyce Tang, Julie A. Theriot, Calysta Yan, Vilas Menon, Sean P. Palecek, Georg Seelig, Ruwanthi N. Gunawardane

Nature Cell Biology

It’s time to incorporate diversity into our basic science and disease models

Dec 01, 2021

Rick Horwitz, Ekemini A. U. Riley, Maria T. Millan, Ruwanthi N. Gunawardane

Nature Methods

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

Dec 01, 2021

Mathias Hammer, Maximiliaan Huisman, Alessandro Rigano, Ulrike Boehm, James J. Chambers, Nathalie Gaudreault, Alison J. North, Jaime A. Pimentel, Damir Sudar, Peter Bajcsy, Claire M. Brown, Alexander D. Corbett, Orestis Faklaris, Judith Lacoste, Alex Laude, Glyn Nelson, Roland Nitschke, Farzin Farzam, Carlas S. Smith, David Grunwald, Caterina Strambio-De-Castillia

Journal of Microscopy

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

Oct 01, 2021

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

Biophysical Journal

A mechanism for sarcomere breathing: volume change and advective flow within the myofilament lattice

Sep 21, 2021

Julie A. Cass, C. David Williams, Thomas C. Irving, Eric Lauga, Sage Malingen, Thomas L. Daniel, Simon N. Sponberg

Cell Systems

Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Jun 16, 2021

Kaytlyn A. Gerbin, Tanya Grancharova, Rory M. Donovan-Maiye, Melissa C. Hendershott, Helen G. Anderson, Jackson M. Brown, Jianxu Chen, Stephanie Q. Dinh, Jamie L. Gehring, Gregory R. Johnson, HyeonWoo Lee, Aditya Nath, Angelique M. Nelson, M. Filip Sluzewski, Matheus P. Viana, Calysta Yan, Rebecca J. Zaunbrecher, Kimberly R. Cordes Metzler, Nathalie Gaudreault, Theo A. Knijnenburg, Susanne M. Rafelski, Julie A. Theriot, Ruwanthi N. Gunawardane

PLOS ONE

A Bayesian framework for the detection of diffusive heterogeneity

May 07, 2020

Julie A. Cass, C. David Williams, Julie Theriot