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23 results on '"Katja Heuer"'

1. New results on implementation of neuroscience methods in the study of bear brain

Author: Mónica Villalba de Alvarado, Elena Santos, Katja Heuer, Roberto Toro, Marc Herbin, Éric Bardinet, Mélanie Didier, Mathieu Santin, Andréa Filippo, and Antoine Balzeau
Subjects: History of Civilization, CB3-482
Published: 2025
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2. Phylogenetic comparative analysis of the cerebello-cerebral system in 34 species highlights primate-general expansion of cerebellar crura I-II

Author: Neville Magielse, Roberto Toro, Vanessa Steigauf, Mahta Abbaspour, Simon B. Eickhoff, Katja Heuer, and Sofie L. Valk
Subjects: Biology (General), QH301-705.5
Abstract: Abstract The reciprocal connections between the cerebellum and the cerebrum have been suggested to simultaneously play a role in brain size increase and to support a broad array of brain functions in primates. The cerebello-cerebral system has undergone marked functionally relevant reorganization. In particular, the lateral cerebellar lobules crura I-II (the ansiform) have been suggested to be expanded in hominoids. Here, we manually segmented 63 cerebella (34 primate species; 9 infraorders) and 30 ansiforms (13 species; 8 infraorders) to understand how their volumes have evolved over the primate lineage. Together, our analyses support proportional cerebellar-cerebral scaling, whereas ansiforms have expanded faster than the cerebellum and cerebrum. We did not find different scaling between strepsirrhines and haplorhines, nor between apes and non-apes. In sum, our study shows primate-general structural reorganization of the ansiform, relative to the cerebello-cerebral system, which is relevant for specialized brain functions in an evolutionary context.
Published: 2023
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3. From fossils to mind

Author: Alexandra A. de Sousa, Amélie Beaudet, Tanya Calvey, Ameline Bardo, Julien Benoit, Christine J. Charvet, Colette Dehay, Aida Gómez-Robles, Philipp Gunz, Katja Heuer, Martijn P. van den Heuvel, Shawn Hurst, Pascaline Lauters, Denné Reed, Mathilde Salagnon, Chet C. Sherwood, Felix Ströckens, Mirriam Tawane, Orlin S. Todorov, Roberto Toro, and Yongbin Wei
Subjects: Biology (General), QH301-705.5
Abstract: Abstract Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology’s approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.
Published: 2023
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4. Evolution of cortical geometry and its link to function, behaviour and ecology

Author: Ernst Schwartz, Karl-Heinz Nenning, Katja Heuer, Nathan Jeffery, Ornella C. Bertrand, Roberto Toro, Gregor Kasprian, Daniela Prayer, and Georg Langs
Subjects: Science
Abstract: Abstract Studies in comparative neuroanatomy and of the fossil record demonstrate the influence of socio-ecological niches on the morphology of the cerebral cortex, but have led to oftentimes conflicting theories about its evolution. Here, we study the relationship between the shape of the cerebral cortex and the topography of its function. We establish a joint geometric representation of the cerebral cortices of ninety species of extant Euarchontoglires, including commonly used experimental model organisms. We show that variability in surface geometry relates to species’ ecology and behaviour, independent of overall brain size. Notably, ancestral shape reconstruction of the cortical surface and its change during evolution enables us to trace the evolutionary history of localised cortical expansions, modal segregation of brain function, and their association to behaviour and cognition. We find that individual cortical regions follow different sequences of area increase during evolutionary adaptations to dynamic socio-ecological niches. Anatomical correlates of this sequence of events are still observable in extant species, and relate to their current behaviour and ecology. We decompose the deep evolutionary history of the shape of the human cortical surface into spatially and temporally conscribed components with highly interpretable functional associations, highlighting the importance of considering the evolutionary history of cortical regions when studying their anatomy and function.
Published: 2023
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5. TOWARDS MAPPING AND MODELLING DEVELOPMENT OF BRAIN CONNECTIVITY

Author: Vaibhav Sahu, Katja Heuer, Laura Mouton, Mathieu Santin, Stepahne Lehericy, and Roberto Toro
Subjects: Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Published: 2023
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6. Diversity and evolution of cerebellar folding in mammals

Author: Katja Heuer, Nicolas Traut, Alexandra Allison de Sousa, Sofie Louise Valk, Julien Clavel, and Roberto Toro
Subjects: folding, cerebellum, evolution, histology, mammals, phylogenetic comparative methods, Medicine, Science, Biology (General), QH301-705.5
Abstract: The process of brain folding is thought to play an important role in the development and organisation of the cerebrum and the cerebellum. The study of cerebellar folding is challenging due to the small size and abundance of its folia. In consequence, little is known about its anatomical diversity and evolution. We constituted an open collection of histological data from 56 mammalian species and manually segmented the cerebrum and the cerebellum. We developed methods to measure the geometry of cerebellar folia and to estimate the thickness of the molecular layer. We used phylogenetic comparative methods to study the diversity and evolution of cerebellar folding and its relationship with the anatomy of the cerebrum. Our results show that the evolution of cerebellar and cerebral anatomy follows a stabilising selection process. We observed two groups of phenotypes changing concertedly through evolution: a group of ‘diverse’ phenotypes – varying over several orders of magnitude together with body size, and a group of ‘stable’ phenotypes varying over less than 1 order of magnitude across species. Our analyses confirmed the strong correlation between cerebral and cerebellar volumes across species, and showed in addition that large cerebella are disproportionately more folded than smaller ones. Compared with the extreme variations in cerebellar surface area, folial anatomy and molecular layer thickness varied only slightly, showing a much smaller increase in the larger cerebella. We discuss how these findings could provide new insights into the diversity and evolution of cerebellar folding, the mechanisms of cerebellar and cerebral folding, and their potential influence on the organisation of the brain across species.
Published: 2023
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7. Insights from an autism imaging biomarker challenge: Promises and threats to biomarker discovery

Author: Nicolas Traut, Katja Heuer, Guillaume Lemaître, Anita Beggiato, David Germanaud, Monique Elmaleh, Alban Bethegnies, Laurent Bonnasse-Gahot, Weidong Cai, Stanislas Chambon, Freddy Cliquet, Ayoub Ghriss, Nicolas Guigui, Amicie de Pierrefeu, Meng Wang, Valentina Zantedeschi, Alexandre Boucaud, Joris van den Bossche, Balázs Kegl, Richard Delorme, Thomas Bourgeron, Roberto Toro, and Gaël Varoquaux
Subjects: Autism, diagnostic, machine learning, benchmark, overfit, prediction, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: MRI has been extensively used to identify anatomical and functional differences in Autism Spectrum Disorder (ASD). Yet, many of these findings have proven difficult to replicate because studies rely on small cohorts and are built on many complex, undisclosed, analytic choices. We conducted an international challenge to predict ASD diagnosis from MRI data, where we provided preprocessed anatomical and functional MRI data from > 2,000 individuals. Evaluation of the predictions was rigorously blinded. 146 challengers submitted prediction algorithms, which were evaluated at the end of the challenge using unseen data and an additional acquisition site. On the best algorithms, we studied the importance of MRI modalities, brain regions, and sample size. We found evidence that MRI could predict ASD diagnosis: the 10 best algorithms reliably predicted diagnosis with AUC∼0.80 – far superior to what can be currently obtained using genotyping data in cohorts 20-times larger. We observed that functional MRI was more important for prediction than anatomical MRI, and that increasing sample size steadily increased prediction accuracy, providing an efficient strategy to improve biomarkers. We also observed that despite a strong incentive to generalise to unseen data, model development on a given dataset faces the risk of overfitting: performing well in cross-validation on the data at hand, but not generalising. Finally, we were able to predict ASD diagnosis on an external sample added after the end of the challenge (EU-AIMS), although with a lower prediction accuracy (AUC=0.72). This indicates that despite being based on a large multisite cohort, our challenge still produced biomarkers fragile in the face of dataset shifts.
Published: 2022
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8. Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?

Author: Kurt G. Schilling, François Rheault, Laurent Petit, Colin B. Hansen, Vishwesh Nath, Fang-Cheng Yeh, Gabriel Girard, Muhamed Barakovic, Jonathan Rafael-Patino, Thomas Yu, Elda Fischi-Gomez, Marco Pizzolato, Mario Ocampo-Pineda, Simona Schiavi, Erick J. Canales-Rodríguez, Alessandro Daducci, Cristina Granziera, Giorgio Innocenti, Jean-Philippe Thiran, Laura Mancini, Stephen Wastling, Sirio Cocozza, Maria Petracca, Giuseppe Pontillo, Matteo Mancini, Sjoerd B. Vos, Vejay N. Vakharia, John S. Duncan, Helena Melero, Lidia Manzanedo, Emilio Sanz-Morales, Ángel Peña-Melián, Fernando Calamante, Arnaud Attyé, Ryan P. Cabeen, Laura Korobova, Arthur W. Toga, Anupa Ambili Vijayakumari, Drew Parker, Ragini Verma, Ahmed Radwan, Stefan Sunaert, Louise Emsell, Alberto De Luca, Alexander Leemans, Claude J. Bajada, Hamied Haroon, Hojjatollah Azadbakht, Maxime Chamberland, Sila Genc, Chantal M.W. Tax, Ping-Hong Yeh, Rujirutana Srikanchana, Colin D. Mcknight, Joseph Yuan-Mou Yang, Jian Chen, Claire E. Kelly, Chun-Hung Yeh, Jerome Cochereau, Jerome J. Maller, Thomas Welton, Fabien Almairac, Kiran K Seunarine, Chris A. Clark, Fan Zhang, Nikos Makris, Alexandra Golby, Yogesh Rathi, Lauren J. O'Donnell, Yihao Xia, Dogu Baran Aydogan, Yonggang Shi, Francisco Guerreiro Fernandes, Mathijs Raemaekers, Shaun Warrington, Stijn Michielse, Alonso Ramírez-Manzanares, Luis Concha, Ramón Aranda, Mariano Rivera Meraz, Garikoitz Lerma-Usabiaga, Lucas Roitman, Lucius S. Fekonja, Navona Calarco, Michael Joseph, Hajer Nakua, Aristotle N. Voineskos, Philippe Karan, Gabrielle Grenier, Jon Haitz Legarreta, Nagesh Adluru, Veena A. Nair, Vivek Prabhakaran, Andrew L. Alexander, Koji Kamagata, Yuya Saito, Wataru Uchida, Christina Andica, Masahiro Abe, Roza G. Bayrak, Claudia A.M. Gandini Wheeler-Kingshott, Egidio D'Angelo, Fulvia Palesi, Giovanni Savini, Nicolò Rolandi, Pamela Guevara, Josselin Houenou, Narciso López-López, Jean-François Mangin, Cyril Poupon, Claudio Román, Andrea Vázquez, Chiara Maffei, Mavilde Arantes, José Paulo Andrade, Susana Maria Silva, Vince D. Calhoun, Eduardo Caverzasi, Simone Sacco, Michael Lauricella, Franco Pestilli, Daniel Bullock, Yang Zhan, Edith Brignoni-Perez, Catherine Lebel, Jess E Reynolds, Igor Nestrasil, René Labounek, Christophe Lenglet, Amy Paulson, Stefania Aulicka, Sarah R. Heilbronner, Katja Heuer, Bramsh Qamar Chandio, Javier Guaje, Wei Tang, Eleftherios Garyfallidis, Rajikha Raja, Adam W. Anderson, Bennett A. Landman, and Maxime Descoteaux
Subjects: Tractography, Bundle segmentation, White matter, Fiber pathways, Dissection, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same intended white matter pathways, which directly affects tractography results, quantification, and interpretation. In this study, we aim to evaluate and quantify the variability that arises from different protocols for bundle segmentation. Through an open call to users of fiber tractography, including anatomists, clinicians, and algorithm developers, 42 independent teams were given processed sets of human whole-brain streamlines and asked to segment 14 white matter fascicles on six subjects. In total, we received 57 different bundle segmentation protocols, which enabled detailed volume-based and streamline-based analyses of agreement and disagreement among protocols for each fiber pathway. Results show that even when given the exact same sets of underlying streamlines, the variability across protocols for bundle segmentation is greater than all other sources of variability in the virtual dissection process, including variability within protocols and variability across subjects. In order to foster the use of tractography bundle dissection in routine clinical settings, and as a fundamental analytical tool, future endeavors must aim to resolve and reduce this heterogeneity. Although external validation is needed to verify the anatomical accuracy of bundle dissections, reducing heterogeneity is a step towards reproducible research and may be achieved through the use of standard nomenclature and definitions of white matter bundles and well-chosen constraints and decisions in the dissection process.
Published: 2021
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9. Comparison between diffusion MRI tractography and histological tract-tracing of cortico-cortical structural connectivity in the ferret brain

Author: Céline Delettre, Arnaud Messé, Leigh-Anne Dell, Ophélie Foubet, Katja Heuer, Benoit Larrat, Sebastien Meriaux, Jean-Francois Mangin, Isabel Reillo, Camino de Juan Romero, Victor Borrell, Roberto Toro, and Claus C. Hilgetag
Subjects: Electronic computers. Computer science, QA75.5-76.95
Published: 2021
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10. Imaging evolution of the primate brain: the next frontier?

Author: Patrick Friedrich, Stephanie J. Forkel, Céline Amiez, Joshua H. Balsters, Olivier Coulon, Lingzhong Fan, Alexandros Goulas, Fadila Hadj-Bouziane, Erin E. Hecht, Katja Heuer, Tianzi Jiang, Robert D. Latzman, Xiaojin Liu, Kep Kee Loh, Kaustubh R. Patil, Alizée Lopez-Persem, Emmanuel Procyk, Jerome Sallet, Roberto Toro, Sam Vickery, Susanne Weis, Charles R. E. Wilson, Ting Xu, Valerio Zerbi, Simon B. Eickoff, Daniel S. Margulies, Rogier B. Mars, and Michel Thiebaut de Schotten
Subjects: Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Evolution, as we currently understand it, strikes a delicate balance between animals' ancestral history and adaptations to their current niche. Similarities between species are generally considered inherited from a common ancestor whereas observed differences are considered as more recent evolution. Hence comparing species can provide insights into the evolutionary history. Comparative neuroimaging has recently emerged as a novel subdiscipline, which uses magnetic resonance imaging (MRI) to identify similarities and differences in brain structure and function across species. Whereas invasive histological and molecular techniques are superior in spatial resolution, they are laborious, post-mortem, and oftentimes limited to specific species. Neuroimaging, by comparison, has the advantages of being applicable across species and allows for fast, whole-brain, repeatable, and multi-modal measurements of the structure and function in living brains and post-mortem tissue. In this review, we summarise the current state of the art in comparative anatomy and function of the brain and gather together the main scientific questions to be explored in the future of the fascinating new field of brain evolution derived from comparative neuroimaging.
Published: 2021
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11. A collaborative resource platform for non-human primate neuroimaging

Author: Adam Messinger, Nikoloz Sirmpilatze, Katja Heuer, Kep Kee Loh, Rogier B. Mars, Julien Sein, Ting Xu, Daniel Glen, Benjamin Jung, Jakob Seidlitz, Paul Taylor, Roberto Toro, Eduardo A. Garza-Villarreal, Caleb Sponheim, Xindi Wang, R. Austin Benn, Bastien Cagna, Rakshit Dadarwal, Henry C. Evrard, Pamela Garcia-Saldivar, Steven Giavasis, Renée Hartig, Claude Lepage, Cirong Liu, Piotr Majka, Hugo Merchant, Michael P. Milham, Marcello G.P. Rosa, Jordy Tasserie, Lynn Uhrig, Daniel S. Margulies, and P. Christiaan Klink
Subjects: Open science, Resource sharing, Toolbox, Pipeline, Structural, Functional, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience. Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions. In recent years, the global NHP neuroimaging community has made significant efforts to transform the field towards more open and collaborative practices. Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging. PRIME-RE caters to both researchers and developers who are either new to the field, looking to stay abreast of the latest developments, or seeking to collaboratively advance the field .
Published: 2021
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12. 26th Annual Computational Neuroscience Meeting (CNS*2017): Part 2

Author: Leonid L. Rubchinsky, Sungwoo Ahn, Wouter Klijn, Ben Cumming, Stuart Yates, Vasileios Karakasis, Alexander Peyser, Marmaduke Woodman, Sandra Diaz-Pier, James Deraeve, Eliana Vassena, William Alexander, David Beeman, Pawel Kudela, Dana Boatman-Reich, William S. Anderson, Niceto R. Luque, Francisco Naveros, Richard R. Carrillo, Eduardo Ros, Angelo Arleo, Jacob Huth, Koki Ichinose, Jihoon Park, Yuji Kawai, Junichi Suzuki, Hiroki Mori, Minoru Asada, Sorinel A. Oprisan, Austin I. Dave, Tahereh Babaie, Peter Robinson, Alejandro Tabas, Martin Andermann, André Rupp, Emili Balaguer-Ballester, Henrik Lindén, Rasmus K. Christensen, Mari Nakamura, Tania R. Barkat, Zach Tosi, John Beggs, Davide Lonardoni, Fabio Boi, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Joanna Jędrzejewska-Szmek, Daniel B. Dorman, Kim T. Blackwell, Christoph Bauermeister, Hanna Keren, Jochen Braun, João V. Dornas, Eirini Mavritsaki, Silvio Aldrovandi, Emma Bridger, Sukbin Lim, Nicolas Brunel, Anatoly Buchin, Clifford Charles Kerr, Anton Chizhov, Gilles Huberfeld, Richard Miles, Boris Gutkin, Martin J. Spencer, Hamish Meffin, David B. Grayden, Anthony N. Burkitt, Catherine E. Davey, Liangyu Tao, Vineet Tiruvadi, Rehman Ali, Helen Mayberg, Robert Butera, Cengiz Gunay, Damon Lamb, Ronald L. Calabrese, Anca Doloc-Mihu, Víctor J. López-Madrona, Fernanda S. Matias, Ernesto Pereda, Claudio R. Mirasso, Santiago Canals, Alice Geminiani, Alessandra Pedrocchi, Egidio D’Angelo, Claudia Casellato, Ankur Chauhan, Karthik Soman, V. Srinivasa Chakravarthy, Vignayanandam R. Muddapu, Chao-Chun Chuang, Nan-yow Chen, Mehdi Bayati, Jan Melchior, Laurenz Wiskott, Amir Hossein Azizi, Kamran Diba, Sen Cheng, Elena Y. Smirnova, Elena G. Yakimova, Anton V. Chizhov, Nan-Yow Chen, Chi-Tin Shih, Dorian Florescu, Daniel Coca, Julie Courtiol, Viktor K. Jirsa, Roberto J. M. Covolan, Bartosz Teleńczuk, Richard Kempter, Gabriel Curio, Alain Destexhe, Jessica Parker, Alexander N. Klishko, Boris I. Prilutsky, Gennady Cymbalyuk, Felix Franke, Andreas Hierlemann, Rava Azeredo da Silveira, Stefano Casali, Stefano Masoli, Martina Rizza, Martina Francesca Rizza, Yinming Sun, Willy Wong, Faranak Farzan, Daniel M. Blumberger, Zafiris J. Daskalakis, Svitlana Popovych, Shivakumar Viswanathan, Nils Rosjat, Christian Grefkes, Silvia Daun, Damiano Gentiletti, Piotr Suffczynski, Vadym Gnatkovski, Marco De Curtis, Hyeonsu Lee, Se-Bum Paik, Woochul Choi, Jaeson Jang, Youngjin Park, Jun Ho Song, Min Song, Vicente Pallarés, Matthieu Gilson, Simone Kühn, Andrea Insabato, Gustavo Deco, Katharina Glomb, Adrián Ponce-Alvarez, Petra Ritter, Adria Tauste Campo, Alexander Thiele, Farah Deeba, P. A. Robinson, Sacha J. van Albada, Andrew Rowley, Michael Hopkins, Maximilian Schmidt, Alan B. Stokes, David R. Lester, Steve Furber, Markus Diesmann, Alessandro Barri, Martin T. Wiechert, David A. DiGregorio, Alexander G. Dimitrov, Catalina Vich, Rune W. Berg, Antoni Guillamon, Susanne Ditlevsen, Romain D. Cazé, Benoît Girard, Stéphane Doncieux, Nicolas Doyon, Frank Boahen, Patrick Desrosiers, Edward Laurence, Louis J. Dubé, Russo Eleonora, Daniel Durstewitz, Dominik Schmidt, Tuomo Mäki-Marttunen, Florian Krull, Francesco Bettella, Christoph Metzner, Anna Devor, Srdjan Djurovic, Anders M. Dale, Ole A. Andreassen, Gaute T. Einevoll, Solveig Næss, Torbjørn V. Ness, Geir Halnes, Eric Halgren, Klas H. Pettersen, Marte J. Sætra, Espen Hagen, Alina Schiffer, Axel Grzymisch, Malte Persike, Udo Ernst, Daniel Harnack, Udo A. Ernst, Nergis Tomen, Stefano Zucca, Valentina Pasquale, Giuseppe Pica, Manuel Molano-Mazón, Michela Chiappalone, Stefano Panzeri, Tommaso Fellin, Kelvin S. Oie, David L. Boothe, Joshua C. Crone, Alfred B. Yu, Melvin A. Felton, Isma Zulfiqar, Michelle Moerel, Peter De Weerd, Elia Formisano, Kelvin Oie, Piotr Franaszczuk, Roland Diggelmann, Michele Fiscella, Domenico Guarino, Jan Antolík, Andrew P. Davison, Yves Frègnac, Benjamin Xavier Etienne, Flavio Frohlich, Jérémie Lefebvre, Encarni Marcos, Maurizio Mattia, Aldo Genovesio, Leonid A. Fedorov, Tjeerd M.H. Dijkstra, Louisa Sting, Howard Hock, Martin A. Giese, Laure Buhry, Clément Langlet, Francesco Giovannini, Christophe Verbist, Stefano Salvadé, Michele Giugliano, James A. Henderson, Hendrik Wernecke, Bulcsú Sándor, Claudius Gros, Nicole Voges, Paulina Dabrovska, Alexa Riehle, Thomas Brochier, Sonja Grün, Yifan Gu, Pulin Gong, Grégory Dumont, Nikita A. Novikov, Boris S. Gutkin, Parul Tewatia, Olivia Eriksson, Andrei Kramer, Joao Santos, Alexandra Jauhiainen, Jeanette H. Kotaleski, Jovana J. Belić, Arvind Kumar, Jeanette Hellgren Kotaleski, Masanori Shimono, Naomichi Hatano, Subutai Ahmad, Yuwei Cui, Jeff Hawkins, Johanna Senk, Karolína Korvasová, Tom Tetzlaff, Moritz Helias, Tobias Kühn, Michael Denker, PierGianLuca Mana, David Dahmen, Jannis Schuecker, Sven Goedeke, Christian Keup, Katja Heuer, Rembrandt Bakker, Paul Tiesinga, Roberto Toro, Wei Qin, Alex Hadjinicolaou, Michael R. Ibbotson, Tatiana Kameneva, William W. Lytton, Lealem Mulugeta, Andrew Drach, Jerry G. Myers, Marc Horner, Rajanikanth Vadigepalli, Tina Morrison, Marlei Walton, Martin Steele, C. Anthony Hunt, Nicoladie Tam, Rodrigo Amaducci, Carlos Muñiz, Manuel Reyes-Sánchez, Francisco B. Rodríguez, Pablo Varona, Joseph T. Cronin, Matthias H. Hennig, Elisabetta Iavarone, Jane Yi, Ying Shi, Bas-Jan Zandt, Werner Van Geit, Christian Rössert, Henry Markram, Sean Hill, Christian O’Reilly, Rodrigo Perin, Huanxiang Lu, Alexander Bryson, Michal Hadrava, Jaroslav Hlinka, Ryosuke Hosaka, Mark Olenik, Conor Houghton, Nicolangelo Iannella, Thomas Launey, Rebecca Kotsakidis, Jaymar Soriano, Takatomi Kubo, Takao Inoue, Hiroyuki Kida, Toshitaka Yamakawa, Michiyasu Suzuki, Kazushi Ikeda, Samira Abbasi, Amber E. Hudson, Detlef H. Heck, Dieter Jaeger, Joel Lee, Skirmantas Janušonis, Maria Luisa Saggio, Andreas Spiegler, William C. Stacey, Christophe Bernard, Davide Lillo, Spase Petkoski, Mark Drakesmith, Derek K. Jones, Ali Sadegh Zadeh, Chandra Kambhampati, Jan Karbowski, Zeynep Gokcen Kaya, Yair Lakretz, Alessandro Treves, Lily W. Li, Joseph Lizier, Cliff C. Kerr, Timothée Masquelier, Saeed Reza Kheradpisheh, Hojeong Kim, Chang Sub Kim, Julia A. Marakshina, Alexander V. Vartanov, Anastasia A. Neklyudova, Stanislav A. Kozlovskiy, Andrey A. Kiselnikov, Kanako Taniguchi, Katsunori Kitano, Oliver Schmitt, Felix Lessmann, Sebastian Schwanke, Peter Eipert, Jennifer Meinhardt, Julia Beier, Kanar Kadir, Adrian Karnitzki, Linda Sellner, Ann-Christin Klünker, Lena Kuch, Frauke Ruß, Jörg Jenssen, Andreas Wree, Paula Sanz-Leon, Stuart A. Knock, Shih-Cheng Chien, Burkhard Maess, Thomas R. Knösche, Charles C. Cohen, Marko A. Popovic, Jan Klooster, Maarten H.P. Kole, Erik A. Roberts, Nancy J. Kopell, Daniel Kepple, Hamza Giaffar, Dima Rinberg, Alex Koulakov, Caroline Garcia Forlim, Leonie Klock, Johanna Bächle, Laura Stoll, Patrick Giemsa, Marie Fuchs, Nikola Schoofs, Christiane Montag, Jürgen Gallinat, Ray X. Lee, Greg J. Stephens, Bernd Kuhn, Luiz Tauffer, Philippe Isope, Katsuma Inoue, Yoshiyuki Ohmura, Shogo Yonekura, Yasuo Kuniyoshi, Hyun Jae Jang, Jeehyun Kwag, Marc de Kamps, Yi Ming Lai, Filipa dos Santos, K. P. Lam, Peter Andras, Julia Imperatore, Jessica Helms, Tamas Tompa, Antonieta Lavin, Felicity H. Inkpen, Michael C. Ashby, Nathan F. Lepora, Aaron R. Shifman, John E. Lewis, Zhong Zhang, Yeqian Feng, Christian Tetzlaff, Tomas Kulvicius, Yinyun Li, Rodrigo F. O. Pena, Davide Bernardi, Antonio C. Roque, Benjamin Lindner, Sebastian Vellmer, Ausra Saudargiene, Tiina Maninen, Riikka Havela, Marja-Leena Linne, Arthur Powanwe, Andre Longtin, Jesús A. Garrido, Joe W. Graham, Salvador Dura-Bernal, Sergio L. Angulo, Samuel A. Neymotin, and Srdjan D. Antic
Subjects: Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurophysiology and neuropsychology, QP351-495
Published: 2017
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13. Open Neuroimaging Laboratory

Author: Katja Heuer, Satrajit Ghosh, Amy Robinson Sterling, and Roberto Toro
Subjects: Neuroimaging, Collaboration, Open Science, Co-e, Science
Published: 2016
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14. Insights from an autism imaging biomarker challenge: Promises and threats to biomarker discovery

Author: Monique Elmaleh, Freddy Cliquet, Nicolas Guigui, David Germanaud, Ayoub Ghriss, Balázs Kégl, Anita Beggiato, Roberto Toro, Richard Delorme, Amicie de Pierrefeu, Valentina Zantedeschi, Joris Van den Bossche, Nicolas Traut, Laurent Bonasse-Gahot, Alexandre Boucaud, Alban Bethegies, Guillaume Lemaitre, Thomas Bourgeron, Katja Heuer, Meng Wang, Gael Varauquaux, Weidong Cai, Stanislas Chambon, Institut Pasteur [Paris], Centre de Recherche Interdisciplinaire / Center for Research and Interdisciplinarity [Paris, France] (CRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), Max Planck Institute for Human Cognitive and Brain Sciences [Leipzig] (IMPNSC), Max-Planck-Gesellschaft, Méthodes computationnelles et mathématiques pour comprendre la société et la santé à partir de données (SODA), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université Paris-Saclay, AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service NEUROSPIN (NEUROSPIN), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, hosa.io, Centre d'Analyse et de Mathématique sociales (CAMS), École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, rythm.co, University of Colorado [Boulder], University of Chinese Academy of Sciences [Beijing] (UCAS), Institute of Automation - Chinese Academy of Sciences, Laboratoire Hubert Curien [Saint Etienne] (LHC), Institut d'Optique Graduate School (IOGS)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), HUAWEI Technologies France (HUAWEI), Montreal Neurological Institute and Hospital, McGill University = Université McGill [Montréal, Canada], Département de Neuroscience - Department of Neuroscience, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Paris sciences et lettres (PSL), Institut d'Optique Graduate School (IOGS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Huawei Technologies France, Huawei Technologies France [Boulogne-Billancourt], Lassailly-Bondaz, Anne, and Laboratoire Hubert Curien (LHC)
Subjects: Imaging biomarker, Computer science, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Autism Spectrum Disorder, Autism, [SDV.MHEP.PSM] Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health, [INFO.INFO-IM] Computer Science [cs]/Medical Imaging, diagnostic, Overfitting, computer.software_genre, MESH: Magnetic Resonance Imaging, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], benchmark, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], Biomarker discovery, MESH: Autism Spectrum Disorder, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Brain, Replicate, Magnetic Resonance Imaging, machine learning, Neurology, Autism spectrum disorder, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Cognitive Neuroscience, MESH: Autistic Disorder, Machine learning, MESH: Brain, overfit, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], medicine, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Humans, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Autistic Disorder, Modalities, MESH: Humans, business.industry, prediction, [INFO.INFO-LG] Computer Science [cs]/Machine Learning [cs.LG], medicine.disease, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, Sample size determination, [SDV.MHEP.PSM]Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health, MESH: Biomarkers, Artificial intelligence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, Biomarkers
Abstract: MRI has been extensively used to identify anatomical and functional differences in Autism Spectrum Disorder (ASD). Yet, many of these findings have proven difficult to replicate because studies rely on small cohorts and are built on many complex, undisclosed, analytic choices. We conducted an international challenge to predict ASD diagnosis from MRI data, where we provided preprocessed anatomical and functional MRI data from > 2,000 individuals. Evaluation of the predictions was rigorously blinded. 146 challengers submitted prediction algorithms, which were evaluated at the end of the challenge using unseen data and an additional acquisition site. On the best algorithms, we studied the importance of MRI modalities, brain regions, and sample size. We found evidence that MRI could predict ASD diagnosis: the 10 best algorithms reliably predicted diagnosis with AUC∼0.80 – far superior to what can be currently obtained using genotyping data in cohorts 20-times larger. We observed that functional MRI was more important for prediction than anatomical MRI, and that increasing sample size steadily increased prediction accuracy, providing an efficient strategy to improve biomarkers. We also observed that despite a strong incentive to generalise to unseen data, model development on a given dataset faces the risk of overfitting: performing well in cross-validation on the data at hand, but not generalising. Finally, we were able to predict ASD diagnosis on an external sample added after the end of the challenge (EU-AIMS), although with a lower prediction accuracy (AUC=0.72). This indicates that despite being based on a large multisite cohort, our challenge still produced biomarkers fragile in the face of dataset shifts.
Published: 2022
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15. Toward next-generation primate neuroscience: A collaboration-based strategic plan for integrative neuroimaging

Author: David C. Van Essen, Caspar M. Schwiedrzik, Takuro Ikeda, Shaomin Zhang, Marcello G. P. Rosa, Ning Liu, Aidan Murphy, Li Min Chen, Pinglei Bao, Julia Lehman, Yuki Hori, Pengcheng Li, Julien Vezoli, Peter H. Rudebeck, Yao Meng, Julian 'Bene' Ramirez, Pierre Pouget, Guillermo Gallardo, Rogier B. Mars, Charles E. Schroeder, Minqing Jiang, Steve Frey, Michael P. Milham, Mohammad Hadi Aarabi, Pascal Belin, Patrick Friedrich, Bichan Wu, Hector Figueroa, Ye He, Charles L. Wilson, Melanie Wilke, Eunha Baeg, Fadila Hadj-Bouziane, Danny Garside, Marco Pagani, Ting-Yat Wong, Igor Kagan, Abdelhadi Essamlali, Bharat B. Biswal, Wasana Ediri Arachchi, Julio Villalon, Zheng Wang, Kacie Dougherty, Neo Sunhang Shi, Luciano Simone, Roberto Toro, Benjamin Jung, Masaki Fukunaga, Zhanguang Zuo, Loïc Magrou, Xiaowei Song, Kadharbatcha S. Saleem, Michele A. Basso, Eduardo A. Garza-Villarreal, Chihiro Yokoyama, Aaron Tanenbaum, Brian E. Russ, Alexandre Rosa Franco, Alison R. Weiss, Isabel Restrepo, Alan C. Evans, Lixia Gao, Nobuyuki Kimura, Augix Guohua Xu, Piotr Majka, Colline Poirier, Justine Cléry, Bassem Hiba, Alessandro Gozzi, Xiaojie Wang, Nick Upright, Stan Colcombe, Yang Gao, Won Mok Shim, Eduardo Rojas Hortelano, Takuya Hayashi, Anna S. Mitchell, Andrew F. Rossi, Itamar Kahn, Jorge Jaramillo, Henry C. Evrard, Xin Yumeng, Gregory Kiar, Sean Froudist-Walsh, Elise Roger, Roberto A. Gulli, Yufan Wang, Damien A. Fair, Yuguang Zhao, Stephen J. Sawiak, Boris C. Bernhardt, Ulysse Klatzmann, Ashkan Alvand, Kep Kee Loh, David Schaeffer, Virginie Sivan, Daniel S. Margulies, Carly M. Drzewiecki, Tomoko Sakai, Ting Xu, Cirong Liu, Essa Yacoub, Theresa M. Desrochers, Seok-Jun Hong, Sethu Boopathy, Reza Azadi, Lu Yuheng, Aarit Ahuja, Zhifeng Liang, Elena Borra, Fernanda Ponce, Robert Dahnke, Julien Sein, Li Deying, Jitendra Sharma, A.J. Mitchell, Roger Little, Luqi Cheng, Du Xiao, Choong-Wan Woo, Xinhui Li, Chris Petkov, Ruiliang Bai, D Zaldivar, Sheyla Mejia, Haidong D. Lu, Nikoloz Sirmpilatze, Diego Emanuel Ortuzar Martinez, Suzanne N. Haber, Catherine Elorette, Yue Cui, Michael Hawrylycz, Jerome Sallet, Wim Vanduffel, Daniel R. Glen, Ralph Adolphs, Dongrong Xu, Simon Clavagnier, Rakshit Dadarwal, Marzio Gerbella, Hannah Doyle, Ningrong Ye, Xiaojin Liu, Xinyu Liu, Quansheng He, Christopher R. Madan, Vikas Pareek, James Cavanaugh, Sze Chai Kwok, Zhang Ying, Sam Vickery, Xiaoguang Tian, Zhou Xufeng, Bevil R. Conway, Mark Postans, Wei-an Sheng, Gianfranco Chavez, Rober Boshra, Yuki Kikuchi, Michael Ortiz-Rios, Céline Amiez, Felix Hoffstaedter, Elizabeth A. Buffalo, Amy Howard, Hsin-Yi Lai, Marianne Duyck, Samy Rima, Froesel Mathilda, Towela Mvula, Guilherme Freches, Alfonso Fajardo, Maria de la Iglesia-Vaya, Ana Rita Ribeiro Gomes, Xiongjie Yu, Afonso C. Silva, Andrew S. Fox, Long Cao, Anna W. Roe, Meizhen Qian, David Meunier, Erika Raven, Nicola Palomero-Gallagher, Jordy Tasserie, Joonas A. Autio, Francois Chouinard-Decorte, Hank P. Jedema, Shasha Yue, Xinjian Li, Xiaodong Chen, Kathleen Rockland, Satoka Hashimoto Fujimoto, Amiez Celine, Melina Cordeau, Olivier Coulon, Ravi S. Menon, Sandra Gonzalez Torrecilla, Bjørg Elisabeth Kilavik, Adam Messinger, Hecheng Jin, Steven Giavasis, Pierce Perkins, Conor Liston, Yujie Hou, Jakob Seidlitz, Kelly Shen, Yvonne Bennett, Franck Lamberton, Maxime Gaudet-Trafit, Suliann Ben Hamed, Chris Klink, Sabine Kastner, Lucas R. Trambaiolli, Lucija Jankovic-Rapan, Atsushi Fujimoto, Nadira Yusif Rodriguez, Maeva Gacoin, Amir Shmuel, Katja Heuer, Austin K. Behel, Susann Boretius, Paul A. Taylor, Child Mind Institute, Institute of Neurosciences and Psychology [Glasgow], University of Glasgow, Institut des sciences cognitives Marc Jeannerod - Centre de neuroscience cognitive - UMR5229 (ISC-MJ), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), University of Tübingen, Oregon Health and Science University [Portland] (OHSU), New York University [New York] (NYU), NYU System (NYU), Princeton Neuroscience Institute [Princeton], Consortium, PRIMatE Data and Resource Exchange (PRIME-DRE) Global Collaboration Workshop and, Institut des sciences cognitives Marc Jeannerod - Centre de neuroscience cognitive - UMR5229 (CNC), Nathan S. Kline Institute for Psychiatric Research (NKI), New York State Office of Mental Health, Institut de Neurosciences de la Timone (INT), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Nencki Institute of Experimental Biology, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Monash University [Clayton], Wellcome Trust Centre for Integrative Neuroimaging (WIN - FMRIB), University of Oxford, Donders Institute for Brain, Cognition and Behaviour, Radboud University [Nijmegen], National Institute of Mental Health (NIMH), Newcastle University [Newcastle], McConnell Brain Imaging Centre (MNI), Montreal Neurological Institute and Hospital, McGill University = Université McGill [Montréal, Canada]-McGill University = Université McGill [Montréal, Canada], Laboratorium voor Neuro- en Psychofysiologie, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), and Washington University in Saint Louis (WUSTL)
Subjects: Strategic planning, 0303 health sciences, Open science, biology, Action, intention, and motor control, Resource exchange, [SCCO.NEUR]Cognitive science/Neuroscience, Neuroscience(all), General Neuroscience, Nonhuman primate, 03 medical and health sciences, 0302 clinical medicine, Neuroimaging, biology.animal, Primate, Beacon - Precision Imaging, ddc:610, Psychology, Neuroscience, ComputingMilieux_MISCELLANEOUS, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Contains fulltext : 239574.pdf (Publisher’s version ) (Closed access) Open science initiatives are creating opportunities to increase research coordination and impact in nonhuman primate (NHP) imaging. The PRIMatE Data and Resource Exchange community recently developed a collaboration-based strategic plan to advance NHP imaging as an integrative approach for multiscale neuroscience. 5 p.
Published: 2022
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16. Centering inclusivity in the design of online conferences - An OHBM - Open Science perspective

Author: Elizabeth Levitis, Cassandra Doris Gould van Praag, Remi Gau, Stephan Heunis, Elizabeth DuPre, Greg Kiar, Katherine L Bottenhorn, Tristan Glatard, Aki Nikolaidis, Kirstie Jane Whitaker, Matteo Mancini, Guiomar Niso, Soroosh Afyouni, Eva Alonso Ortiz, Stefan Appelhoff, Aurina Arnatkeviciute, Melvin Selim ATAY, Tibor Auer, Giulia Baracchini, Johanna Margarete Marianne Bayer, Michael J. S. Beauvais, Janine Diane Bijsterbosch, Isil Poyraz Bilgin, Saskia Bollmann, Steffen Bollmann, Rotem Botvinik-Nezer, Molly G Bright, Vince D Calhoun, Xiao Chen, Sidhant Chopra, Hu Chuan-Peng, Thomas Close, Savannah Cookson, Cameron Craddock, Alejandro De La Vega, Benjamin De Leener, Damion Demeter, Paola Di Maio, Erin W Dickie, Simon B Eickhoff, Oscar Esteban, Karolina Finc, Matteo Frigo, Saampras Ganesan, Melanie Ganz, Kelly Garner, Eduardo A. Garza-Villarreal, Gabriel Gonzalez-Escamilla, Rohit Goswami, John David Griffiths, Tijl Grootswagers, Samuel Guay, Olivia Guest, Daniel A. Handwerker, Peer Herholz, Katja Heuer, Dorien Huijser, Vittorio Iacovella, Michael Joseph, Agah Karakuzu, David Keator, Xenia Kobeleva, Manoj Kumar, Angie Laird, Linda J. Larson-Prior, Alexandra Lautarescu, Alberto Lazari, Jon Haitz Legarreta Gorroño, Jeff jeffers, Jinglei Lv, Sina Mansour L., David Meunier, Dustin Moraczewski, Tulika Nandi, Samuel A. Nastase, Matthias Nau, Stephanie Noble, Martin Norgaard, Johnes Obungoloch, Robert Oostenveld, Edwina R Orchard, Ana Luísa Pinho, Russell Poldrack, Anqi Qiu, Pradeep Reddy Raamana, Ariel Rokem, Saige Rutherford, Malvika Sharan, Thomas Shaw, Warda T Syeda, Meghan M. Testerman, Roberto Toro, Sofie L. Valk, Sofie Van Den Bossche, Gael P. Varoquaux, Frantisek Vasa, Michele Veldsman, Jakub Vohryzek, Adina Svenja Wagner, Reubs J Walsh, Tonya White, null zuxfoucault, Xihe Xie, Chao-Gan Yan, Yu-Fang Yang, Yohan Yee, Gaston E Zanitti, Ana Van Gulick, Eugene Duff, Camille MAUMET, National Institute of Mental Health (NIMH), University College of London [London] (UCL), University of Oxford, Université Catholique de Louvain = Catholic University of Louvain (UCL), Eindhoven University of Technology [Eindhoven] (TU/e), McGill University = Université McGill [Montréal, Canada], Florida International University [Miami] (FIU), Concordia University [Montreal], Child Mind Institute, The Alan Turing Institute, University of Sussex, Cardiff University, École Polytechnique de Montréal (EPM), Indiana University [Bloomington], Indiana University System, Universidad Politécnica de Madrid (UPM), Max Planck Institute for Human Development, Max-Planck-Gesellschaft, Monash University [Melbourne], Middle East Technical University [Ankara] (METU), University of Surrey (UNIS), Montreal Neurological Institute and Hospital, University of Melbourne, Orygen Youth Health Research Centre [Melbourne], Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), University of Reading (UOR), University of Queensland [Brisbane], Dartmouth College [Hanover], Northwestern University [Evanston], Georgia State University, University System of Georgia (USG), Institute of Psychology [Beijing], Chinese Academy of Sciences [Changchun Branch] (CAS), University of Chinese Academy of Sciences [Beijing] (UCAS), Nanjing Normal University (NNU), The University of Sydney, University of California (UC), University of Texas at Austin [Austin], CHU Sainte Justine [Montréal], Institute for Globally Distributed Open Research and Education (IGDORE ), Centre for Addiction and Mental Health [Toronto] (CAMH), University of Toronto, Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Jülich Research Centre, Université de Lausanne = University of Lausanne (UNIL), Nicolaus Copernicus University [Toruń], Université Côte d'Azur (UCA), Computational Imaging of the Central Nervous System (ATHENA), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Rigshospitalet [Copenhagen], Copenhagen University Hospital, University of Copenhagen = Københavns Universitet (UCPH), University of Birmingham [Birmingham], Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), University of Iceland [Reykjavik], Indian Institute of Technology Kanpur (IIT Kanpur), Western Sydney University, Université de Montréal (UdeM), Radboud University [Nijmegen], Centre de Recherche Interdisciplinaire / Center for Research and Interdisciplinarity [Paris, France] (CRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Max Planck Institute for Human Cognitive and Brain Sciences [Leipzig] (IMPNSC), Erasmus University Rotterdam, Universiteit Leiden, University of Trento [Trento], Université du Québec à Montréal = University of Québec in Montréal (UQAM), University Hospital Bonn, German Research Center for Neurodegenerative Diseases - Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Princeton University, University of Arkansas for Medical Sciences (UAMS), Arkansas Children's Research Institute, King‘s College London, Université de Sherbrooke (UdeS), Aarhus University [Aarhus], Institut de Neurosciences de la Timone (INT), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Yale University [New Haven], Stanford University, Mbarara University of Science and Technology [Mbarara] (MUST), Karolinska Institutet [Stockholm], Université Paris-Saclay, National University of Singapore (NUS), Johns Hopkins University (JHU), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), University of Washington [Seattle], Radboud University Medical Center [Nijmegen], University of Michigan [Ann Arbor], University of Michigan System, Institut Pasteur [Paris] (IP), Universiteit Gent = Ghent University (UGENT), Vrije Universiteit Amsterdam [Amsterdam] (VU), Department of Public Health, Erasmus University Medical Centre, Rotterdam, Erasmus University Medical Centre, Rotterdam, Academia Sinica, Weill Medical College of Cornell University [New York], Chinese Academy of Sciences [Beijing] (CAS), University of Würzburg, The Hospital for sick children [Toronto] (SickKids), Carnegie Mellon University [Pittsburgh] (CMU), Neuroimagerie: méthodes et applications (Empenn), Institut National de la Santé et de la Recherche Médicale (INSERM)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SIGNAUX ET IMAGES NUMÉRIQUES, ROBOTIQUE (IRISA-D5), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), R25-DA051675, National Institutes of Health, 1631325, National Science Foundation, 5R21MH118556-02, National Institute of Mental Health, BB/S008314/1, Biotechnology and Biological Sciences Research Council, G036716N, Fonds Wetenschappelijk Onderzoek, University of Oxford [Oxford], University of California, University of Lausanne (UNIL), University of Copenhagen = Københavns Universitet (KU), Universidad Nacional Autónoma de México (UNAM), Johannes Gutenberg - Universität Mainz (JGU), Radboud university [Nijmegen], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Leiden University, Institut Pasteur [Paris], Universiteit Gent = Ghent University [Belgium] (UGENT), Empenn, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Maumet, Camille
Subjects: SDG 16 - Peace, collaborative events, [SCCO.NEUR]Cognitive science/Neuroscience, [SCCO.NEUR] Cognitive science/Neuroscience, SDG 16 - Peace, Justice and Strong Institutions, Review, Justice and Strong Institutions, online conferences, diversity, World Wide Web, inclusivity, open science, ddc:610, Sociology
Abstract: As the global health crisis unfolded throughout the world, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical and legal barriers and effectively enabled many individuals who have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g. caregiving responsibilities. Yet, the mere existence of online conferences is unfortunately no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the setup of the conference can provide more visibility to well-established researchers and reduce opportunities for early career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design.Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to: attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.
Published: 2021
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17. Reorient: A Web tool for reorienting and cropping MRI data

Author: Roberto Toro, Katja Heuer, Centre de Recherche Interdisciplinaire / Center for Research and Interdisciplinarity [Paris, France] (CRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Max Planck Institute for Human Cognitive and Brain Sciences [Leipzig] (IMPNSC), Max-Planck-Gesellschaft, Neuroanatomie Appliquée et Théorique / Applied and Theoretical Neuroanatomy (NAAT), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), and Toro, Roberto
Subjects: World Wide Web, Computer science, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Web tool, Cropping
Abstract: International audience; Reorient (https://neuroanatomy.github.io/reorient) is an open source Web application for the manual alignment and cropping of MRI nifti volumes in an intuitive way. The MRI data is dragged onto the Web interface and visualised in an interactive stereotaxic viewer. Users can then translate and rotate the brain by simply dragging inside the 3 view planes, and an adjustable selection box allows to define the crop of the image. Users can save the resulting affine matrix, selection box as well as the reoriented and cropped volume. The affine matrix and selection box can be used later within a scripted workflow, able to reproduce the reoriented volume from the original data. Existing rotation matrices can be loaded or appended.
Published: 2020
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18. Brainhack: Developing a culture of open, inclusive, community-driven neuroscience

Author: Selim Melvin Atay, Iska Moxon-Emre, Anders Eklund, Paula P. Brooks, Nandita Vijayakumar, Anibal Sólon Heinsfeld, Jean-Baptiste Poline, Yaroslav O. Halchenko, David Meunier, Daniela M. Hohmann, Martin Szinte, Arshitha Basavaraj, Andrija Štajduhar, Link Tejavibulya, Michael Dayan, Anisha Keshavan, Chao Jiang, Felix Hoffstaedter, Michael P. Milham, Davide Momi, Hua Xie, Ai Wern Chung, Georg Langs, Hao-Ting Wang, Xenia Kobeleva, Robert Oostenveld, Thomas G. Close, Lena Dorfschmidt, Jesse A. Brown, Serge Koudoro, J.P. Manzano-Patron, Isil P. Bilgin, Shreyas Fadnavis, Sylvain Takerkart, R. Cameron Craddock, Stephan Heunis, Scott Peltier, Kathryn Berluti, Hayli Spence, Pablo F. Damasceno, David H. O’Connor, Eleftherios Garyfallidis, Eugene P. Duff, Rudolph Pienaar, Nicolas Traut, AmanPreet Badhwar, Ali R. Khan, Marissa Laws, Abigail S. Greene, Richard A. I. Bethlehem, Angela R. Laird, Krista DeStasio, Ina Thome, Camille Maumet, Alexandru D. Iordan, P. Christiaan Klink, Damion V. Demeter, John A. Onofrey, Cassandra D. Gould van Praag, Jakub Vohryzek, Suzanne T. Witt, Aysha Motala, Valerie Hayot-Sasson, Geetika Gupta, Alexandre Rosa Franco, John W. VanMeter, Michel Thiebaut de Schotten, James M. Shine, Lucina Q. Uddin, Thomas S. Hartmann, Guillaume Flandin, Clara Moreau, Tomislav Lipic, Claire Bradley, Fernando A. Barrios, Daniel S. Margulies, R. Austin Benn, Sofie Van Den Bossche, Lydia Riedl, Xihe Xie, Christopher R. Madan, Roberto Toro, Viviana Siless, Fabrizio De Vico Fallani, Nikoloz Sirmpilatze, Emily Olafson, Anqi Qiu, Theresa W. Cheng, Valentina Borghesani, Sidhant Chopra, Claire Cury, Giorgio Marinato, Horea-Ioan Ioanas, Giorgia Cona, Michael Joseph, Angela Tam, Mathias Scharinger, Daniel A. Handwerker, Katherine L. Bottenhorn, Sina Mansour L, Kathryn L. Mills, Christopher J. Markiewicz, Elizabeth Levitis, Cyril Pernet, Stephanie J. Forkel, Agah Karakuzu, Edwina R Orchard, Sarah L. Dziura, Saige Rutherford, Kamalaker Dadi, Enrico Glerean, Desiree Lussier, Davide Poggiali, Molly Simmonite, Jason Kai, Jessica Flannery, Ting Xu, Jon Haitz Legarreta, Nasim Anousheh, Marco Bedini, Tristan Glatard, Thomas E. Nichols, Joscelin Rocha-Hidalgo, Erin W. Dickie, Dipankar Bachar, Malin Sandström, Xi-Nian Zuo, Pedro Pinheiro-Chagas, Laura C. Rice, Jakša Vukojević, Javier Gonzalez-Castillo, José C. García Alanis, Lorenzo Pasquini, Yu-Fang Yang, Matteo Mancini, Deena Shariq, Chao-Gan Yan, Laura Tomaz da Silva, César Caballero-Gaudes, Yasmine Bassil, Aurina Arnatkeviciute, Dustin Scheinost, Satrajit S. Ghosh, Gaël Varoquaux, Etienne Combrisson, Bramsh Qamar Chandio, Kelly Garner, Tiago Quendera, Patrick Friedrich, Shawn A. Rhoads, Roxane Licandro, Elizabeth DuPre, Aki Nikolaidis, Simon Schwab, Stephanie Noble, Guillaume Auzias, Daniel J. Lurie, Mahboobeh Parsapoor, Eneko Uruñuela, Andrew Doyle, Peer Herholz, Saampras Ganesan, Vincent Koppelmans, Corey Horien, Samir Das, Junaid S. Merchant, Siyuan Gao, Matheus Marcon, Nathalia Bianchini Esper, B.T. Thomas Yeo, Katja Heuer, Caroline O’Brien, Micaela Y. Chan, Sook-Lei Liew, Lindsay D. Oliver, Kirstie Whitaker, Christoph Vogelbacher, Dylan M. Nielson, Krisanne Litinas, Dorien C. Huijser, Pierre Bellec, R. Todd Constable, David N. Kennedy, Julia Sprenger, Lea-Theresa Mais, Oscar Esteban, Patrick J. Park, Patrick Callahan, Christopher R. Nolan, Johanna Bayer, Guillaume Dumas, Elise Bannier, Elizabeth A. McDevitt, Ariel Rokem, Samuel A. Nastase, Olivia W. Stanley, Ruggero Basanisi, Daniele Marinazzo, Gregory Kiar, Lisa Novello, Samuel Guay, John C. Flournoy, Stefano Moia, Kendra Oudyk, Fang-Cheng Yeh, Gustav Nilsonne, Thomas B. Shaw, Steve Wideman, Saskia Bollmann, Steffen Bollmann, Julia M. Huntenburg, Augusto Buchweitz, Matteo Visconti di Oleggio Castello, Dimitra Maoutsa, Lucy B. Whitmore, Catherine Alice Hahn, Antonino Vallesi, Remi Gau, Felipe Meneguzzi, Université Catholique de Louvain = Catholic University of Louvain (UCL), Yale University [New Haven], Max Planck Institute for Human Cognitive and Brain Sciences [Leipzig] (IMPNSC), Max-Planck-Gesellschaft, Florida International University [Miami] (FIU), University of Reading (UOR), University of Würzburg, Champalimaud Centre for the Unknown [Lisbon], University of Melbourne, University of Cambridge [UK] (CAM), Georgetown University [Washington] (GU), Philipps Universität Marburg = Philipps University of Marburg, Université de Montréal (UdeM), University College of London [London] (UCL), University of Sussex, Universiteit Gent = Ghent University (UGENT), German Research Center for Neurodegenerative Diseases - Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Université de Sherbrooke (UdeS), Middle East Technical University [Ankara] (METU), McGill University = Université McGill [Montréal, Canada], Modelling brain structure, function and variability based on high-field MRI data (PARIETAL), Service NEUROSPIN (NEUROSPIN), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Universiteit Leiden, Karolinska Institutet [Stockholm], Princeton University, Universität Zürich [Zürich] = University of Zurich (UZH), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), University medical center and campus biotech Geneva, Emory University [Atlanta, GA], Cardiff University's Brain Research Imaging Centre [Cardiff] (CUBRIC), School of Psychology [Cardiff University], Cardiff University-Cardiff University, The University of Sydney, Weill Cornell Medicine [Cornell University], Cornell University [New York], Università degli Studi di Padova = University of Padua (Unipd), Jülich Research Centre, University of Texas at Austin [Austin], Institut Pasteur [Paris] (IP), Centre de Recherche Interdisciplinaire / Center for Research and Interdisciplinarity [Paris, France] (CRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Basque Center on Cognition Brain and Language [Gipuzkoa, Espagne] (BCBL), Linköping University (LIU), University of Queensland [Brisbane], University of New South Wales [Sydney] (UNSW), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), University of Maryland [College Park], University of Maryland System, University of Washington [Seattle], Harvard Medical School [Boston] (HMS), Child Mind Institute, University of Western Ontario (UWO), Indiana University [Bloomington], Indiana University System, Monash university, Institut de Neurosciences de la Timone (INT), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Neuroimagerie: méthodes et applications (Empenn), Institut National de la Santé et de la Recherche Médicale (INSERM)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SIGNAUX ET IMAGES NUMÉRIQUES, ROBOTIQUE (IRISA-D5), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), National Institute of Mental Health (NIMH), Università degli Studi di Trento (UNITN), Centro Nacional de Investigaciones Cardiovasculares Carlos III [Madrid, Spain] (CNIC), Instituto de Salud Carlos III [Madrid] (ISC), Queensland University of Technology [Brisbane] (QUT), University of California [San Francisco] (UC San Francisco), University of California (UC), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), University of Texas at Dallas [Richardson] (UT Dallas), University of Oregon [Eugene], Monash University [Melbourne], Boston Children's Hospital, Algorithms, models and methods for images and signals of the human brain (ARAMIS), Sorbonne Université (SU)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Neuroimagerie: méthodes et applications (EMPENN), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SIGNAL, IMAGE ET LANGAGE (IRISA-D6), Chinese Academy of Sciences [Beijing] (CAS), Beijing Normal University (BNU), This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 867458 awarded to Julia M. Huntenburg, from ANR-19-DATA-0025 NeuroWebLab for Katja Heuer, Roberto Toro, and Nicholas Traut, and from NIH K00MH122372 for Stephanie Noble., Brainhack Community: Nasim Anousheh, Aurina Arnatkeviciute, Guillaume Auzias, Dipankar Bachar, Elise Bannier, Ruggero Basanisi, Arshitha Basavaraj, Marco Bedini, Pierre Bellec, R Austin Benn, Kathryn Berluti, Steffen Bollmann, Saskia Bollmann, Claire Bradley, Jesse Brown, Augusto Buchweitz, Patrick Callahan, Micaela Y Chan, Bramsh Q Chandio, Theresa Cheng, Sidhant Chopra, Ai Wern Chung, Thomas G Close, Etienne Combrisson, Giorgia Cona, R Todd Constable, Claire Cury, Kamalaker Dadi, Pablo F Damasceno, Samir Das, Fabrizio De Vico Fallani, Krista DeStasio, Erin W Dickie, Lena Dorfschmidt, Eugene P Duff, Elizabeth DuPre, Sarah Dziura, Nathalia B Esper, Oscar Esteban, Shreyas Fadnavis, Guillaume Flandin, Jessica E Flannery, John Flournoy, Stephanie J Forkel, Alexandre R Franco, Saampras Ganesan, Siyuan Gao, José C García Alanis, Eleftherios Garyfallidis, Tristan Glatard, Enrico Glerean, Javier Gonzalez-Castillo, Cassandra D Gould van Praag, Abigail S Greene, Geetika Gupta, Catherine Alice Hahn, Yaroslav O Halchenko, Daniel Handwerker, Thomas S Hartmann, Valérie Hayot-Sasson, Stephan Heunis, Felix Hoffstaedter, Daniela M Hohmann, Corey Horien, Horea-Ioan Ioanas, Alexandru Iordan, Chao Jiang, Michael Joseph, Jason Kai, Agah Karakuzu, David N Kennedy, Anisha Keshavan, Ali R Khan, Gregory Kiar, P Christiaan Klink, Vincent Koppelmans, Serge Koudoro, Angela R Laird, Georg Langs, Marissa Laws, Roxane Licandro, Sook-Lei Liew, Tomislav Lipic, Krisanne Litinas, Daniel J Lurie, Désirée Lussier, Christopher R Madan, Lea-Theresa Mais, Sina Mansour L, J P Manzano-Patron, Dimitra Maoutsa, Matheus Marcon, Daniel S Margulies, Giorgio Marinato, Daniele Marinazzo, Christopher J Markiewicz, Camille Maumet, Felipe Meneguzzi, David Meunier, Michael P Milham, Kathryn L Mills, Davide Momi, Clara A Moreau, Aysha Motala, Iska Moxon-Emre, Thomas E Nichols, Dylan M Nielson, Gustav Nilsonne, Lisa Novello, Caroline O'Brien, Emily Olafson, Lindsay D Oliver, John A Onofrey, Edwina R Orchard, Kendra Oudyk, Patrick J Park, Mahboobeh Parsapoor, Lorenzo Pasquini, Scott Peltier, Cyril R Pernet, Rudolph Pienaar, Pedro Pinheiro-Chagas, Jean-Baptiste Poline, Anqi Qiu, Tiago Quendera, Laura C Rice, Joscelin Rocha-Hidalgo, Saige Rutherford, Mathias Scharinger, Dustin Scheinost, Deena Shariq, Thomas B Shaw, Viviana Siless, Molly Simmonite, Nikoloz Sirmpilatze, Hayli Spence, Julia Sprenger, Andrija Stajduhar, Martin Szinte, Sylvain Takerkart, Angela Tam, Link Tejavibulya, Michel Thiebaut de Schotten, Ina Thome, Laura Tomaz da Silva, Nicolas Traut, Lucina Q Uddin, Antonino Vallesi, John W VanMeter, Nandita Vijayakumar, Matteo Visconti di Oleggio Castello, Jakub Vohryzek, Jakša Vukojević, Kirstie Jane Whitaker, Lucy Whitmore, Steve Wideman, Suzanne T Witt, Hua Xie, Ting Xu, Chao-Gan Yan, Fang-Cheng Yeh, B T Thomas Yeo, Xi-Nian Zuo, ANR-19-DATA-0025,NeuroWebLab,Un laboratoire de neuroscience collectif: Au delà de FAIR(2019), European Project: 867458,LC-FMR, Maumet, Camille, Un laboratoire de neuroscience collectif: Au delà de FAIR - - NeuroWebLab2019 - ANR-19-DATA-0025 - DONNEES - VALID, Brainhack: Developing a culture of open, inclusive, community-driven neuroscience - LC-FMR - 867458 - INCOMING, Leiden University, Weill Cornell Medicine [New York], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), Universiteit Gent = Ghent University [Belgium] (UGENT), University Hospital Bonn, Sherbrooke Connectivity Imaging Lab [Sherbrooke] (SCIL), Département d'informatique [Sherbrooke] (UdeS), Faculté des sciences [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS)-Faculté des sciences [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS), Videos and Images Theory and Analytics Laboratory (VITAL), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Service NEUROSPIN (NEUROSPIN), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Erasmus University Rotterdam, Origami (Origami), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Université Lumière - Lyon 2 (UL2), Princeton Neuroscience Institute [Princeton], Human Neuroscience Platform, Brighton and Sussex Medical School (BSMS), Azienda Ospedale Università di Padova = Hospital-University of Padua (AOUP), Institute of Neuroscience and Medicine [Jülich] (INM-1), Département de Neuroscience - Department of Neuroscience, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), Queensland Brain Institute, Universidad Nacional Autónoma de México (UNAM), Radboud university [Nijmegen], McGovern Institute for Brain Research [Cambridge], Massachusetts Institute of Technology (MIT), The Brainhack Community - https://pubmed.ncbi.nlm.nih.gov/33932337, Philipps University of Marburg, University of the Basque Country [Bizkaia] (UPV/EHU), Universita degli Studi di Padova, Philipps Universität Marburg, Institut Pasteur [Paris], Empenn, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), University of California [San Francisco] (UCSF), University of California, Geochemistry, and University of Padova [Padova, Italy]
Subjects: 0301 basic medicine, Open science, Community building, Best practice, Neuroscience(all), Brainhack, Article, neuroscience, 03 medical and health sciences, 0302 clinical medicine, best practices, collaboration, community building, hackathon, inclusivity, open science, reproducibility, training, Congresses as Topic, Neurosciences, Practice Guidelines as Topic, Communication, Internet, Research community, Medical Bioscience, Psychology, ddc:610, Sociology, Brainhack Community, Training, Neurology & Neurosurgery, Scientific progress, organization & administration [Neurosciences], General Neuroscience, [SCCO.NEUR]Cognitive science/Neuroscience, [SCCO.NEUR] Cognitive science/Neuroscience, Medicinsk biovetenskap, 030104 developmental biology, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Cognitive Sciences, Engineering ethics, 030217 neurology & neurosurgery
Abstract: Available online 30 April 2021. Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress. The present manuscript is part of a growing community effort to collate Brainhack-related insights and expertise into a Jupyter Book (http://brainhack.org/brainhack_jupyter_book/) that will serve as a centralized set of resources for the community; we acknowledge all the individuals who contributed and will make ongoing contributions to these resources. A pre-print version of the present manuscript is available as part of the Jupyter Book. Moreover, we would like to acknowledge all Brainhack organizers, supporters, presenters, and participants for their contribution to growing and maintaining this community. The benefits described in this manuscript would not be possible without them. We also thank all institutions, labs, and organizations who have helped this community grow, meet in stimulating environments, and add an excellent educational resource pool and agenda. With an expanding community, Brainhack’s support network keeps growing, and we thank all labs and individual researchers for their dedication and expertise offered to this community (see http://brainhack.org/brainhack_jupyter_book/acknowledgments.html for a full list of individual acknowledgments; an updated list will be maintained in the Jupyter Book). Grants and funding bodies: This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 867458 awarded to Julia M. Huntenburg; from ANR-19-DATA-0025 NeuroWebLab for Katja Heuer, Roberto Toro, and Nicholas Traut; and from NIH K00MH122372 for Stephanie Noble. The Brainhack Community member list and contributions of the different authors are detailed at http://brainhack.org/brainhack_jupyter_book/contributors.html. Our crediting system is described here: http://brainhack.org/brainhack_jupyter_book/neuroview_authorship-agreement.html.
Published: 2021
Full Text: View/download PDF

19. Accelerating the Evolution of Nonhuman Primate Neuroimaging

Author: Olivier Coulon, Michael P. Milham, Patrik Lindenfors, Karl-Heinz Nenning, Xiaojin Liu, Ravi S. Menon, Stephanie J. Forkel, Adam Messinger, Zheng Wang, Alexander Thiele, Luciano Simone, Benjamin Jung, Chika Sato, Jamie Nagy, Sean Froudist-Walsh, Kelvin Mok, Renée Hartig, Julien Sein, Alessandro Gozzi, Julien Vezoli, Tomoko Sakai, Lynn Uhrig, Martine Meunier, Christienne G. Damatac, Bonhwang Koo, Roberto Toro, Rogier B. Mars, Henrietta Howells, Lea Roumazeilles, Ming Zhan, Ann-Marie Mallon, Román Rossi-Pool, Elinor L. Sullivan, Yannick Becker, Doris Y. Tsao, Antoine Grigis, Lei Ai, Céline Amiez, Sara Wells, Reza Rajimehr, Aki Nikolaidis, Anna S. Mitchell, Simon M. Reader, Michele A. Basso, Béchir Jarraya, Amir Raz, Wim Vanduffel, Charles R.E. Wilson, Brian E. Russ, Christopher R. Madan, Orlin S. Todorov, Wasana Madushanka, Carole Guedj, Mark A. Pinsk, Clémentine Bodin, Hugo Merchant, Jennifer Nacef, Damien A. Fair, Anna W. Roe, Sze Chai Kwok, Stephen J. Sawiak, Essa Yacoub, Bastien Cagna, Kevin N. Laland, Wilbert Zarco, Charles E. Schroeder, Ting Xu, P. Christiaan Klink, Stanislas Dehaene, Takuya Hayashi, Matthew F. S. Rushworth, Amir Shmuel, Fadila Hadj-Bouziane, Katja Heuer, Ioana-Sabina Rautu, Andrew S. Fox, Austin Benn, Sabine Kastner, Thomas Brochier, Emmanuel Procyk, Marco Pagani, David C. Van Essen, Frank Q. Ye, Dirk Jan Ardesch, Régis Trapeau, Jakob Seidlitz, Marike Schiffer, Bassem Hiba, John H. Morrison, David A. Rudko, Paula L. Croxson, Patrick Friedrich, Augix Guohua Xu, Lazar Fleysher, Piotr Majka, Jonathan Smallwood, Aihua Chen, Timothy D. Griffiths, Fabien Balezeau, Stefan Everling, Michael C. Schmid, Robert Leech, Leslie G. Ungerleider, Mark G. Baxter, Afonso C. Silva, Clare Kelly, Zhi-ming Shen, Daniel S. Margulies, Mark J. Prescott, Pascal Belin, Erwin L. A. Blezer, Igor Kagan, Suliann Ben Hamed, David A. Leopold, Adrien Meguerditchian, Wendy Jarrett, Michel Thiebaut de Schotten, Nikoloz Sirmpilatze, Julia Sliwa, Henry Kennedy, Vikas Pareek, Yong-di Zhou, Michael Ortiz-Rios, Sherif Hamdy El-Gohary, Susann Boretius, Christopher I. Petkov, Pamela Garcia-Saldivar, Bella Williams, Jordy Tasserie, Hank P. Jedema, Jerome Sallet, Pieter R. Roelfsema, Winrich A. Freiwald, Eduardo A. Garza-Villarreal, Noam Harel, Caspar M. Schwiedrzik, Kevin Marche, Colline Poirier, Yang Gao, Henry C. Evrard, Ashkan Alvand, ANS - Cellular & Molecular Mechanisms, Laboratoire des Sciences de l'Information et des Systèmes (LSIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Centre National de la Recherche Scientifique (CNRS), Institut cellule souche et cerveau (SBRI), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Collège de France - Chaire Psychologie cognitive expérimentale, Collège de France (CdF (institution)), Institut des sciences cognitives Marc Jeannerod - Centre de neuroscience cognitive - UMR5229 (ISC-MJ), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Consortium, PRIMatE Data Exchange Global Collaboration Workshop and, Nathan S. Kline Institute for Psychiatric Research (NKI), New York State Office of Mental Health, Newcastle University [Newcastle], Max Planck Institute for Human Cognitive and Brain Sciences [Leipzig] (IMPNSC), Max-Planck-Gesellschaft, Medical Oncology, Department of Internal Medicine, Università Cattolica del Sacro Cuore [Roma] (Unicatt), Voice Neurocognition Laboratory, University of Glasgow, Oregon Health and Science University [Portland] (OHSU), Manchester Royal Infirmary, University of Manchester [Manchester], Princeton Neuroscience Institute [Princeton], University of Pennsylvania [Philadelphia], National Institute of Mental Health (NIMH), Harvard Medical School [Boston] (HMS), Washington University in St Louis, Laboratoire de psychologie cognitive (LPC), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut des sciences cognitives Marc Jeannerod - Centre de neuroscience cognitive - UMR5229 (CNC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Institut de Neurosciences de la Timone (INT), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institute of Psychiatry, Psychology & Neuroscience, King's College London, King‘s College London, New York University [New York] (NYU), NYU System (NYU), State Key Laboratory of Novel Software Technology, University of Nanjing, Center for Nanotechnology Innovation, @NEST (CNI), National Enterprise for nanoScience and nanoTechnology (NEST), Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA)-Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA), Unité Analyse et Traitement de l'Information (UNATI), Service NEUROSPIN (NEUROSPIN), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Neuroimagerie cognitive - Psychologie cognitive expérimentale (UNICOG-U992), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Saclay (COmUE), Institut cellule souche et cerveau (U846 Inserm - UCBL1), Royal Netherlands Academy of Arts and Sciences (KNAW), East China Normal University [Shangaï] (ECNU), The Computational, Cognitive and Clinical Neuroimaging Lab, Imperial College London, Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Medical Research Counc, Station de primatologie (SP), Centre National de la Recherche Scientifique (CNRS), Institute of Language, Communication and the Brain (ILCB), The University of Western Ontario, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Institute of integrative biology (Liverpool), University of Liverpool, McGovern Institute for Brain Research [Cambridge], Massachusetts Institute of Technology (MIT), University of Cambridge [UK] (CAM), Rockefeller University [New York], McConnell Brain Imaging Centre (MNI), Montreal Neurological Institute and Hospital, McGill University = Université McGill [Montréal, Canada]-McGill University = Université McGill [Montréal, Canada], Laboratory for Neuro- and Psychofysiology, katho, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of York [York, UK], Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière (CRICM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Génétique Humaine et Fonctions Cognitives, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Tianjin University of Science and Technology (TUST), Child Mind Institute, Center for Magnetic Resonance Research [Minneapolis] (CMRR), University of Minnesota Medical School, University of Minnesota System-University of Minnesota System, Institut cellule souche et cerveau / Stem Cell and Brain Research Institute (U1208 Inserm - UCBL1 / SBRI), Icahn School of Medicine at Mount Sinai [New York] (MSSM), University Medical Center [Utrecht], Radboud university [Nijmegen], Chaire Psychologie cognitive expérimentale, Centre de recherche en neurosciences de Lyon (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of St Andrews [Scotland], Stockholm University, Hôpital du Bocage, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Princeton University, Utrecht University [Utrecht], Netherlands Institute for Neuroscience, Wellcome Trust Centre for Integrative Neuroimaging (WIN - FMRIB), University of Oxford [Oxford], National Institute of Environmental Health Sciences [Durham] (NIEHS-NIH), National Institutes of Health [Bethesda] (NIH), Oregon National Primate Research Center (ONPRC), California Institute of Technology (CALTECH), Johns Hopkins University (JHU), The PRIMatE Data Exchange (PRIME-DE) Global Collaboration Workshop and Consortium, ANR-16-CONV-0002,ILCB,ILCB: Institute of Language Communication and the Brain(2016), Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Complex Trait Genetics, Centre National de la Recherche Scientifique (CNRS)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Université de Toulon (UTLN)-Aix Marseille Université (AMU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA), and Vanduffel, Wim
Subjects: Primates, 0301 basic medicine, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, education, Neuroimaging, Article, [SPI]Engineering Sciences [physics], 03 medical and health sciences, 0302 clinical medicine, London, Psychology, Animals, Humans, Sociology, ComputingMilieux_MISCELLANEOUS, Cognitive science, Science & Technology, Human Connectome Project, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Action, intention, and motor control, Information Dissemination, General Neuroscience, Neurosciences, Brain, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, Congresses as Topic, Nonhuman primate, 030104 developmental biology, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Neurosciences & Neurology, Life Sciences & Biomedicine, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, 030217 neurology & neurosurgery
Abstract: Contains fulltext : 217200.pdf (Publisher’s version ) (Closed access) Nonhuman primate neuroimaging is on the cusp of a transformation, much in the same way its human counterpart was in 2010, when the Human Connectome Project was launched to accelerate progress. Inspired by an open data-sharing initiative, the global community recently met and, in this article, breaks through obstacles to define its ambitions. 4 p.
Published: 2020
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20. A method to describe folding patterns across species

Author: Katja Heuer and Roberto Toro
Subjects: neuroanatomy, neuroimaging, data visualization, brain evolution, primate brain, graph comparison, graph edit distance
Abstract: An A0 poster which was presented at the 2019Annual Meeting of the Organization for Human Brain Mapping (OHBM) in Rome, 9–13June. Abstract: Folding patterns are very characteristic of different species. Most quantication methods focus, however, on the estimation of the degree of folding – the description of their pattern remaining mostly qualitative. We describe a method to generate folding graphs which summarise the folding pattern of an individual brain. We illustrate the application of our method by computing folding graphs for several different mammalian species.
Published: 2019
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21. Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 34 primate species

Author: Omer Faruk Gulban, Roberto Toro, Katja Heuer, Romain Valabregue, Anastasia Osoianu, Marc Herbin, Pierre-Louis Bazin, Mathieu Santin, Toro, Roberto, Génétique humaine et fonctions cognitives - Human Genetics and Cognitive Functions (GHFC (UMR_3571 / U-Pasteur_1)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Max Planck Institute for Human Cognitive and Brain Sciences [Leipzig] (IMPNSC), Max-Planck-Gesellschaft, Centre de Recherches Interdisciplinaires (CRI), Université Paris Cité (UPCité), Maastricht University [Maastricht], Spinoza Center for Neuroimaging [Amsterdam], Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière (CRICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN), Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), KH was supported by the Max Planck International Research Network on Ageing and the Max Planck Institute for Human Cognitive and Brain Sciences. OFG was supported by NWO VIDI grant 864-13-012., We thank Marion Fouquet and Nicolas Traut for their help with the quality control and selection of the human data from ABIDE. We thank Helen D'Arcueil, Alex de Crespigny, Emmanuel Gilissen and Chet Sherwood for allowing us to make accessible their MRI data in the Brain Catalogue. We thank Spencer Arbuckle and Andrew Pruszynski for sharing their macaque data with us and making it openly available. Data acquisition was funded by the MNHN programme e-Museum. The development of BrainBox was supported by the Wellcome Trust through the Open Science Prize., Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]-Université de Paris (UP), Université de Paris (UP), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Audition, RS: FPN CN 2, Brain and Cognition, and Brein en Cognitie (Psychologie, FMG)
Subjects: SELECTION, Primates, Evolution, Cognitive Neuroscience, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MODELS, SEGMENTATION, Lemur, Neocortex, Experimental and Cognitive Psychology, Context (language use), Neuroimaging, PREFRONTAL CORTEX, GYRIFICATION, 050105 experimental psychology, 03 medical and health sciences, 0302 clinical medicine, CEREBRAL-CORTEX, biology.animal, THICKNESS, medicine, Animals, 0501 psychology and cognitive sciences, Primate, GREAT APES, Gyrification, Phylogeny, 030304 developmental biology, VOLUMES, 0303 health sciences, Phylogenesis, biology, Phylogenetic tree, Cerebrum, 05 social sciences, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, HUMANS, Phylogenetic comparative methods, Phenotype, Biological Evolution, Magnetic Resonance Imaging, Folding (chemistry), Neuroanatomy, Neuropsychology and Physiological Psychology, medicine.anatomical_structure, Evolutionary biology, Psychology, 030217 neurology & neurosurgery
Abstract: We conducted a comparative analysis of primate cerebral size and neocortical folding using magnetic resonance imaging data from 65 individuals belonging to 34 different species. We measured several neocortical folding parameters and studied their evolution using phylogenetic comparative methods. Our results suggest that the most likely model for neuroanatomical evolution is one where differences appear randomly (the Brownian Motion model), however, alternative models cannot be completely ruled out. We present estimations of the ancestral primate phenotypes as well as estimations of the rates of phenotypic change. Based on the Brownian Motion model, the common ancestor of primates may have had a folded cerebrum similar to that of a small lemur such as the aye-aye. Finally, we observed a non-linear relationship between fold wavelength and fold depth with cerebral volume. In particular, gyrencephalic primate neocortices across different groups exhibited a strikingly stable fold wavelength of about 12 mm (± 20%), despite a 20-fold variation in cerebral volume. We discuss our results in the context of current theories of neocortical folding.
Published: 2019
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22. MicroDraw

Author: Toro, Roberto and Katja Heuer
Subjects: neuroscience, cytoarchitectonic atlas creation, openscience, citizen science, microscopy
Abstract: An A0 poster which is designed for fabric print and can becut and sewed into a bag. The poster was presented at the 2015 Annual Meeting of the Organization for Human Brain Mapping (OHBM) in Hawaii, 14–18 June. MicroDraw is a web application byNAATto visualise and collaboratively annotate high resolution histology data. Annotations are vectorial, and you can use boolean operations to combine, subtract and split regions. Point MicroDraw to your own DeepZoom data, or try a sample from the Web page!As a prototype of the platform, we created MicroDraw http://microdraw.pasteur.fr/. Datasets MicroDraw can use ontologies such asNeurolexto create community curated atlases, but also to annotate staining artefacts. We are currently hosting DeepZoom versions of several macaque brains from the Allen Institute for Brain Research, a 1 micron resolution section of a human brain from the BigBrain project, a 1 micron resolution section from a vervet monkey, and 0.25 micron resolution ferret data fromproject FIIND. Application MicroDraw is based on open source frameworks to ensure its maintainability and extensibility. The interactive multi-resolution visualisation is based onOpenSeadragon. The vectorial annotation is based onPaper. The concurrent versioning is based on Git. MicroDraw is written in JavaScript, using HTML5, CSS3 and jQuery.
Published: 2015
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23. The ADAP/SKAP55 Signaling Module Regulates T-Cell Receptor-Mediated Integrin Activation through Plasma Membrane Targeting of Rap1†

Author: Mauro Togni, Katja Heuer, Xiaoqian Wang, Christian Freund, Dennis Breitling, Ana Kasirer-Friede, Burkhart Schraven, Gary A. Koretzky, Rico Pusch, Stefanie Kliche, Gaël Ménasché, Groupe d'analyse et de théorie économique (GATE Lyon Saint-Étienne), École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Otto-von-Guericke University [Magdeburg] (OVGU), Ménasché, Gaël, Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Otto-von-Guericke-Universität Magdeburg = Otto-von-Guericke University [Magdeburg] (OVGU), Groupe d'Analyse et de Théorie Economique Lyon - Saint-Etienne (GATE Lyon Saint-Étienne), École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université Lumière - Lyon 2 (UL2)-École normale supérieure - Lyon (ENS Lyon)
Subjects: [SDV.IMM] Life Sciences [q-bio]/Immunology, Proline, [SDV]Life Sciences [q-bio], Receptors, Antigen, T-Cell, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Jurkat cells, Cell membrane, src Homology Domains, 03 medical and health sciences, Jurkat Cells, Mice, 0302 clinical medicine, Membrane Microdomains, medicine, Cell Adhesion, Animals, Humans, Small GTPase, Cell adhesion, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Molecular Biology, Cells, Cultured, 030304 developmental biology, Adaptor Proteins, Signal Transducing, Mice, Knockout, 0303 health sciences, Integrin beta1, Signal transducing adaptor protein, Membrane Proteins, rap1 GTP-Binding Proteins, Cell Biology, Articles, Intercellular Adhesion Molecule-1, Phosphoproteins, Cell biology, Fibronectins, [SDV] Life Sciences [q-bio], medicine.anatomical_structure, Membrane protein, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, [SDV.IMM.IA] Life Sciences [q-bio]/Immunology/Adaptive immunology, CD18 Antigens, [SDV.IMM]Life Sciences [q-bio]/Immunology, Rap1, Signal transduction, 030215 immunology, Signal Transduction
Abstract: International audience; Adhesion of T cells after stimulation of the T-cell receptor (TCR) is mediated via signaling processes that have collectively been termed inside-out signaling. The molecular basis for inside-out signaling is not yet completely understood. Here, we show that a signaling module comprising the cytosolic adapter proteins ADAP and SKAP55 is involved in TCR-mediated inside-out signaling and, moreover, that the interaction between ADAP and SKAP55 is mandatory for integrin activation. Disruption of the ADAP/SKAP55 module leads to displacement of the small GTPase Rap1 from the plasma membrane without influencing its GTPase activity. These findings suggest that the ADAP/SKAP55 complex serves to recruit activated Rap1 to the plasma membrane. In line with this hypothesis is the finding that membrane targeting of the ADAP/SKAP55 module induces T-cell adhesion in the absence of TCR-mediated stimuli. However, it appears as if the ADAP/SKAP55 module can exert its signaling function outside of the classical raft fraction of the cell membrane.
Published: 2006
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23 results on '"Katja Heuer"'

1. New results on implementation of neuroscience methods in the study of bear brain

2. Phylogenetic comparative analysis of the cerebello-cerebral system in 34 species highlights primate-general expansion of cerebellar crura I-II

3. From fossils to mind

4. Evolution of cortical geometry and its link to function, behaviour and ecology

5. TOWARDS MAPPING AND MODELLING DEVELOPMENT OF BRAIN CONNECTIVITY

6. Diversity and evolution of cerebellar folding in mammals

7. Insights from an autism imaging biomarker challenge: Promises and threats to biomarker discovery

8. Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?

9. Comparison between diffusion MRI tractography and histological tract-tracing of cortico-cortical structural connectivity in the ferret brain

10. Imaging evolution of the primate brain: the next frontier?

11. A collaborative resource platform for non-human primate neuroimaging

12. 26th Annual Computational Neuroscience Meeting (CNS*2017): Part 2

13. Open Neuroimaging Laboratory

14. Insights from an autism imaging biomarker challenge: Promises and threats to biomarker discovery

15. Toward next-generation primate neuroscience: A collaboration-based strategic plan for integrative neuroimaging

16. Centering inclusivity in the design of online conferences - An OHBM - Open Science perspective

17. Reorient: A Web tool for reorienting and cropping MRI data

18. Brainhack: Developing a culture of open, inclusive, community-driven neuroscience

19. Accelerating the Evolution of Nonhuman Primate Neuroimaging

20. A method to describe folding patterns across species

21. Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 34 primate species

22. MicroDraw

23. The ADAP/SKAP55 Signaling Module Regulates T-Cell Receptor-Mediated Integrin Activation through Plasma Membrane Targeting of Rap1†

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23 results on '"Katja Heuer"'

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