tag:blogger.com,1999:blog-38054035504456547682024-03-02T10:17:18.846-08:00Large Scale & Interactive Scientific VisualizationA blog about ray-tracing and high performance computing where quantum physics meet scientific visualizationCyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comBlogger129125tag:blogger.com,1999:blog-3805403550445654768.post-74507157859077090432024-03-02T10:15:00.000-08:002024-03-02T10:16:17.310-08:00When Epilepsy Leads to Mystical Ecstasy<p></p><p><span class="break-words"><span><span dir="ltr"></span></span></span></p><p><span class="break-words"><span><span dir="ltr">I'm absolutely thrilled to share that I've had the privilege of producing an image for <a data-attribute-index="0" data-entity-type="MINI_PROFILE" href="https://www.linkedin.com/in/ACoAACmiQ_0BIK23m5GG3arHUsZC0hGwbIBCqPA">PICARD Fabienne</a> from <a data-attribute-index="2" data-entity-type="MINI_COMPANY" href="https://www.linkedin.com/company/hopitaux-universitaires-de-geneve/">HUG - Hopitaux Universitaires de Genève</a> that highlights her fascinating research on ecstatic epilepsy.</span></span></span></p><p><span class="break-words"><span><span dir="ltr"></span></span></span></p><p><span class="break-words"><span></span></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmwKUbpNA9aRbagt_fsp1gfpl-euxVQykNt2_pFVPEk3CkSnA7YIwWScY2RYiVdhYomiV186hL6rnM2QlWimTgcfDIdx0AWTllq8jn0ukN42hGdt0UhJeUgfzdkL1VC1ccJCzdm4YH-DLcIxcShMOoUiIdGxM_mMkS9c02PfGtn29hboQG68F_AJAFKdbh/s1630/linkedin_banner_round_corners_v2.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="480" data-original-width="1630" height="118" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmwKUbpNA9aRbagt_fsp1gfpl-euxVQykNt2_pFVPEk3CkSnA7YIwWScY2RYiVdhYomiV186hL6rnM2QlWimTgcfDIdx0AWTllq8jn0ukN42hGdt0UhJeUgfzdkL1VC1ccJCzdm4YH-DLcIxcShMOoUiIdGxM_mMkS9c02PfGtn29hboQG68F_AJAFKdbh/w400-h118/linkedin_banner_round_corners_v2.png" width="400" /></a></div><br /><span dir="ltr">The
presentation titled "Quand l’épilepsie amène à l’extase mystique" (When
Epilepsy Leads to Mystical Ecstasy) offers a captivating journey that
delves into the intricate workings of the brain, specifically within the
framework of the predictive coding theory. This theory suggests that
the brain generates predictions about incoming sensory information and
constantly updates these predictions based on new data. Through the lens
of this theory, the presentation explores how epilepsy can lead to
mystical experiences, altering the brain's predictive processes.<br /><br /><br /></span><div class="separator" style="clear: both; text-align: center;"><iframe allowfullscreen="" class="BLOG_video_class" height="266" src="https://www.youtube.com/embed/6BPN8Z5vlVY" width="320" youtube-src-id="6BPN8Z5vlVY"></iframe></div><br /><p></p><p></p><p><span dir="ltr">I encourage you to take a moment to watch the accompanying video and delve into the mesmerizing discoveries awaiting within.</span><span dir="ltr"> </span></p><p><span dir="ltr">Neuron morphologies: <a data-attribute-index="8" href="https://neuromorpho.org" target="_self">https://neuromorpho.org</a></span></p>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-14571900572498857032024-01-08T02:16:00.000-08:002024-01-08T02:28:00.086-08:00Wishing you an extraordinary 2024!<p><span class="break-words"><span dir="ltr">Throughout the last decade, I embarked on
impactful collaborations, ranging from Harvard Brain Magazine to the
realms of molecules and subatomic worlds, computational neuroscience,
and virology, with a specific focus on unraveling the complexities of
COVID-19. This marked the initiation of a distinctive scientific visual
exploration in these intricate domains, involving collaboration with
exceptional minds, intensive coding for CPU and GPU architectures, and
the application of cutting-edge ray tracing techniques for sophisticated
visualizations. Our findings were concurrently disseminated through
scientific publications, contributing significantly to the field and
making the journey of conveying our scientific discoveries through
advanced visuals truly exhilarating.</span></span></p><p><span class="break-words"><span dir="ltr"></span></span></p><p><span class="break-words"><span dir="ltr"></span></span></p><p><span class="break-words"></span></p><span dir="ltr"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmNsm4ev7jbqXVdqPYzDH-H7XO45-iRlVvLU5AgPyLN3r9jKAZfoO9P1y-6esgHC6JvRVnwF5EeQLcOdTYVhxtlG4zesJNtfphKibPYHj4qTXEYmOKlMJ4ZFmNXFy8BINHLTVkt_AqtOVjLZfnksqRUSF8yXBeccN_5hsoZNn4uhEUBxp_5yVWve82YS2w/s1896/2024.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1896" data-original-width="1758" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmNsm4ev7jbqXVdqPYzDH-H7XO45-iRlVvLU5AgPyLN3r9jKAZfoO9P1y-6esgHC6JvRVnwF5EeQLcOdTYVhxtlG4zesJNtfphKibPYHj4qTXEYmOKlMJ4ZFmNXFy8BINHLTVkt_AqtOVjLZfnksqRUSF8yXBeccN_5hsoZNn4uhEUBxp_5yVWve82YS2w/w371-h400/2024.png" width="371" /></a></div><br />This body of work not only
made substantial contributions to scientific publications but also
afforded opportunities to showcase our achievements at prestigious
venues such as the Centre Pompidou in Paris, as well as the CCCB in
Barcelona and Madrid. These exhibitions underscored the global relevance
and significance of our research.<br /><br />As the Blue Brain Project
approaches its conclusion in 2024, I eagerly anticipate new ventures.
Beyond my daily 4km swim, my commitment to accuracy and visual
excellence remains pivotal in the development of software for
distributed and high-performance computation, data visualization,
exploration, and communication.<br /><br /></span><p></p><br />Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-59688523252493127322023-12-08T07:14:00.000-08:002023-12-08T07:14:45.844-08:00Unveiling the Potential of the GPU-accelerated Signed Distance Field Technique in computational neuroscience.<p>The intricacies of the brain, a marvel of complexity, encompass billions of neurons, astrocytes, and a network of elaborate blood vessels. Unraveling the structure and interactions within this intricate organ is paramount in the realm of neuroscience.</p><div class="separator" style="clear: both; text-align: center;"><iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dyHRMMf_ttuEtwbXRxe--iz70Isw-BIAyQPaasRWaiE6xgQnXGh-Jv3mTzgYG-sZ4CfVPT6FbJ2U976mwAEMA' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div><p></p><p>A powerful technique that has emerged in recent years is the application of signed distance fields (SDFs) to construct realistic shapes directly from raw data, eliminating the need for meshes. These shapes are dynamically generated at rendering time from simple primitives such as spheres, cylinders, cones, etc.</p><p><br /></p><p>The signed distance field technique excels in generating high-fidelity graphics that faithfully represent the complexities of biological structures. By encoding distance information for each point in space, this technique facilitates the creation of intricate and realistic 3D reconstructions directly from raw data (.h5 or .swc). </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_K7f8G4OE2u3P7aohy0ao4qZfH7Vv1L-x5XmL4QRscoUdX0ln-DvV610baFdNZt8CyUcb6-ExaMn-oesDY6fxsR1IWat6DzjUkRsnbv7YalI0gPScY0d8FQYByn467DQn_vLKVVaBEwNu6WQ2476-dO_ctm1OM2Yr-SAmPH5TTjOOX-tWQut1y5ZfNkJF/s1920/Screenshot%20from%202023-12-08%2015-04-26.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1080" data-original-width="1920" height="180" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_K7f8G4OE2u3P7aohy0ao4qZfH7Vv1L-x5XmL4QRscoUdX0ln-DvV610baFdNZt8CyUcb6-ExaMn-oesDY6fxsR1IWat6DzjUkRsnbv7YalI0gPScY0d8FQYByn467DQn_vLKVVaBEwNu6WQ2476-dO_ctm1OM2Yr-SAmPH5TTjOOX-tWQut1y5ZfNkJF/s320/Screenshot%20from%202023-12-08%2015-04-26.png" width="320" /></a></div><br /><p><br /></p><p>A notable advantage of employing signed distance fields is their capacity to enable interactive exploration. Researchers can seamlessly navigate through reconstructed 3D models of neurons, astrocytes, and blood vessels, gaining a dynamic and immersive understanding of their spatial relationships. This interactive feature enhances the exploration process, fostering a more intuitive and insightful analysis of the data.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfx4YyrXhCV2U3qxyAdvcwumJ83DKcGLvD2z7fy_z5T5VJsqCBwQIjda2q26q-3Q7NO7zmWV_fJBay4souf0WgxNXYK27Re7PU-4w77fgWBjfq5EK5RP4PB7r1_g0hjkm86s1I1E-rafiun30270HOnbIr9BLAbC01_i-GnO_1kGlbeG6V-r9ZKf0qtS-1/s1920/Screenshot%20from%202023-12-08%2015-10-00.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1080" data-original-width="1920" height="180" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfx4YyrXhCV2U3qxyAdvcwumJ83DKcGLvD2z7fy_z5T5VJsqCBwQIjda2q26q-3Q7NO7zmWV_fJBay4souf0WgxNXYK27Re7PU-4w77fgWBjfq5EK5RP4PB7r1_g0hjkm86s1I1E-rafiun30270HOnbIr9BLAbC01_i-GnO_1kGlbeG6V-r9ZKf0qtS-1/s320/Screenshot%20from%202023-12-08%2015-10-00.png" width="320" /></a></div><br /><p></p><p>The utilization of the signed distance field technique to visualize and explore neurons, astrocytes, and blood vessels signifies a substantial advancement in the field of neuroscience. This potent approach, originally developed with insights from <a class="ql-mention" data-entity-urn="urn:li:fsd_profile:ACoAAAEYdZIBowQygF9y2nhRCITM7Y6EA6Ww5nU" data-guid="1" data-object-urn="urn:li:fsd_profile:ACoAAAEYdZIBowQygF9y2nhRCITM7Y6EA6Ww5nU" data-original-text="Inigo Quilez" data-test-ql-mention="true" href="https://www.linkedin.com/feed/#" spellcheck="false">Inigo Quilez</a>'s blog, provides high-quality graphics that empower researchers to study the intricacies of the brain's architecture.</p><p></p><p>The implementation of the signed distance field technique, initially available in the <a href="https://github.com/BlueBrain/BioExplorer" target="_blank">Blue Brain BioExplorer</a> CPU back-end, underwent a transformative upgrade. Over the last two days, I successfully ported the technique to GPU using the CUDA programming language and the <a href="https://developer.nvidia.com/rtx/ray-tracing/optix" target="_blank">NVIDIA OptiX ray-tracing framework</a>. This enhancement not only accelerates the visualization process but also opens new horizons for real-time, high-performance exploration of intricate neural structures. This collaborative fusion of cutting-edge technologies ensures that the exploration of neural intricacies remains at the forefront of scientific discovery, propelling our understanding of the brain into new dimensions.</p><ul style="text-align: left;"><li class="article-editor-content__paragraph">Blue Brain BioExplorer: <a class="article-editor-content__link article-editor-content__link article-editor-content__link" href="https://github.com/BlueBrain/BioExplorer" rel="noopener noreferrer">https://github.com/BlueBrain/BioExplorer</a></li></ul><ul class="article-editor-content__bullet-list" data-pm-slice="3 3 []"><li class="article-editor-content__list-item"><p class="article-editor-content__paragraph">Inigo Quilez - articles- distance functions: <a class="article-editor-content__link article-editor-content__link" href="https://iquilezles.org/articles/distfunctions/" rel="noopener noreferrer">https://iquilezles.org/articles/distfunctions/</a></p></li><li class="article-editor-content__list-item"><p class="article-editor-content__paragraph">SDF Tracing visualization: <a class="article-editor-content__link article-editor-content__link article-editor-content__link" href="https://www.shadertoy.com/view/lslXD8" rel="noopener noreferrer">https://www.shadertoy.com/view/lslXD8</a></p></li></ul><p> </p>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-71845557935616829642023-10-26T05:23:00.006-07:002023-10-26T05:23:48.356-07:00Interactive visualization of the Fusion Reactor Tokamak plasma<p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMEyjF-VNnjxOryxLAwGN-DkCwSqbx2OwPl1FuUk3ccvlsmDEOMDKFGmYSHFvdnT9_wPUs7TZoqCBeJn31HdBTrwqxanP1_A5plqz1MJzJKNAQFGIzT23sKLyXys4IWiPNSdOMBUvRSS_9UMoXJYP4jSXURpzEQ8zbnwlC3FyQ5zWXM-ZQeE8zh8yZ0NG8/s1551/FusionReactorTokamak.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="950" data-original-width="1551" height="245" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMEyjF-VNnjxOryxLAwGN-DkCwSqbx2OwPl1FuUk3ccvlsmDEOMDKFGmYSHFvdnT9_wPUs7TZoqCBeJn31HdBTrwqxanP1_A5plqz1MJzJKNAQFGIzT23sKLyXys4IWiPNSdOMBUvRSS_9UMoXJYP4jSXURpzEQ8zbnwlC3FyQ5zWXM-ZQeE8zh8yZ0NG8/w400-h245/FusionReactorTokamak.png" width="400" /></a></div><div><br /></div>In my dedicated efforts to advance nuclear fusion, I embarked on a journey to translate conceptual ideas into tangible actions. This mission commenced with the creation of a test dataset, meticulously crafted with insights derived from engaging discussions within our team. To expedite the visualization and exploration of this data, I turned to the remarkable open-source application known as <a href="https://github.com/BlueBrain/BioExplorer" target="_blank">BioExplorer</a>.<br /><br /><a href="https://github.com/BlueBrain/BioExplorer" target="_blank">BioExplorer</a>, originally developed for biological datasets, proved to be an invaluable asset in our venture. While its roots lay in the realm of biology, its adaptability and versatility allowed it to seamlessly integrate with our nuclear fusion research. This application, once primarily designed for biological data, had evolved to accommodate and process a wide range of scientific datasets, transcending its initial domain.<br /><br />In the context of nuclear fusion, the core challenge lies in modeling the behavior of superheated plasma, the fuel for this revolutionary energy source. To visually represent this complex phenomenon, I envisioned the plasma as an array of particles, with each particle intricately characterized by its position and direction. The direction vector of each particle not only represented its position but also served as a direct indicator of the particle's charge, a crucial factor in the fusion reaction.<br /><br />Efficiency was paramount in this ambitious undertaking, and BioExplorer played a pivotal role. This open-source application, known for its adaptability, provided a user-friendly platform to visually explore and analyze the scientific datasets, irrespective of their origin. It allowed us to gain valuable insights and a deeper understanding of the plasma's behavior, further propelling our research forward.<br /><br />To ensure real-time visualization of the plasma's behavior, I harnessed the formidable processing power of Graphics Processing Units (GPUs). These GPUs were thoughtfully optimized with a tree-based acceleration structure, making them an ideal choice for handling the intricate calculations required for real-time visual representation of the plasma's behavior.<br /><br />Perhaps the most astonishing aspect of this project was its efficiency. What might seem like a Herculean task was accomplished in no more than two days of relentless work. This achievement not only underscores the power of modern computational tools but also highlights the immense potential of nuclear fusion as a clean and virtually limitless energy source, hinting at a future where our energy needs may be met sustainably and efficiently, with the invaluable assistance of open-source applications like the versatile and adaptable <a href="https://github.com/BlueBrain/BioExplorer" target="_blank">BioExplorer</a>.<p></p>Check out the <a href="https://github.com/BlueBrain/BioExplorer" target="_blank">BioExplorer source code</a> and the <a href="https://github.com/BlueBrain/BioExplorer/blob/master/extensions/physics/nuclearfusion/notebooks/NuclearFusion.ipynb" target="_blank">Python Jupyter Notebook</a> used to create the image above.<div><br /></div>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-24983063549621549232023-05-27T01:20:00.009-07:002023-05-27T01:25:51.446-07:00Particles Composition and Interactions Using the Nuon Model<div style="text-align: justify;"><span style="font-family: Arial;">Drawing
inspiration from <a href="https://www.linkedin.com/in/rene-brun-b9128871/" target="_blank">René Brun</a>'s remarkable publication titled "<a href="https://www.scirp.org/journal/paperinformation.aspx?paperid=124395" target="_blank">Particles Composition and Interactions Using the Nuon Model</a>" I embarked on a
venture to visualize the magnetic fields engendered by sub-particles
within the realm of collisions.</span></div><h2 style="text-align: center;"> <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimTgDuIwoWAdCURMsniWgY0hEAbSh6t4BXFCmk01qEJ3xrxR2EXKZnLTX2Me1pZnsMyhxJynqNVKzxoYqOv3ZAqP3bnbGQe3JyBDkE4a07p18ld9sSndr_jZhf5izLe_8j0uzPEVXNnENlZQA42Cu907ppXaFXVmQAEHrkLdF_59c9hutBHYR0866HBg/s1358/banner.png" style="color: black; margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="243" data-original-width="1358" height="71" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimTgDuIwoWAdCURMsniWgY0hEAbSh6t4BXFCmk01qEJ3xrxR2EXKZnLTX2Me1pZnsMyhxJynqNVKzxoYqOv3ZAqP3bnbGQe3JyBDkE4a07p18ld9sSndr_jZhf5izLe_8j0uzPEVXNnENlZQA42Cu907ppXaFXVmQAEHrkLdF_59c9hutBHYR0866HBg/w400-h71/banner.png" width="400" /></a></h2><h2 style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: left;"><span style="font-family: Arial;"></span></h2><div class="separator" style="clear: both; text-align: center;"><h2></h2><h2></h2><div style="text-align: justify;"><span style="font-family: Arial;">Although the data I employed differs from
that presented in the paper, I found the concept of moving away from the
conventional depiction of particles as simple spheres and instead
illustrating their genuine magnetic fields to be captivating.</span></div><div style="text-align: justify;"><span style="font-family: Arial;"> </span></div><div><span style="font-family: Arial;"> </span><iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dw-yLZ6ofHuhNMty9VZ0SXxCGR-ocQW8bp2HXY06Gj0pnW0t7iHOZtyAZbVZH7S8EaRbdFc685xQi5E5TQ9Qw' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div></div><br /><div><span style="font-family: Arial;">With the computational capabilities readily accessible on ordinary consumer PCs today, it is now possible to calculate these fields in real-time, opening up novel avenues for visualizing and exploring the intricacies of the sub-atomic world.</span></div><br />Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-53883957525211026882023-05-17T14:57:00.003-07:002023-05-17T14:57:35.148-07:00The Harvard Brain<p><span class="break-words"><span><span dir="ltr">So proud to appear in the Harvard Brain Spring 2023 issue.</span></span></span></p><p><span class="break-words"><span><span dir="ltr"></span></span></span></p><p><span class="break-words"><span></span></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhym7rO8EgLquZI9rDX8VGzc8BZrSTFyh7VtDoCBMxBQI_JGwJ2hgWlykRY7NcJJMVN_6CmwQYnOGXHLjU2Rw7Qj9VsC9czJbMaAXd-bdziTHa9d_v1MSu8naDNl1zutGZy1ailyY6ZfRJox9OEpmhxnzpXim4-iWRqjidJGNVOIM5yTvimDcVn_veWIQ/s5120/Banner1.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="853" data-original-width="5120" height="66" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhym7rO8EgLquZI9rDX8VGzc8BZrSTFyh7VtDoCBMxBQI_JGwJ2hgWlykRY7NcJJMVN_6CmwQYnOGXHLjU2Rw7Qj9VsC9czJbMaAXd-bdziTHa9d_v1MSu8naDNl1zutGZy1ailyY6ZfRJox9OEpmhxnzpXim4-iWRqjidJGNVOIM5yTvimDcVn_veWIQ/w400-h66/Banner1.jpg" width="400" /></a></div><span dir="ltr"><br />Studies In Silico: An Interview With Cyrille Favreau On EPFL’s Blue Brain Project, by Lara Ota, Buse Toksöz, and Kei Hayashi</span><p></p><p><span class="break-words"><span><span dir="ltr">http://www.theharvardbrain.com/spring-2023-8203lara-ota-buse-toksoumlz-and-kei-hayashi.html <br /></span></span></span></p>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-41128957770795238122023-04-26T08:15:00.003-07:002023-04-26T08:15:15.701-07:00Blue Brain BioExplorer goes RTX!<p><span class="css-901oao css-16my406 r-poiln3 r-bcqeeo r-qvutc0">Exciting news! I just released the version 1.6.0 of the Blue Brain BioExplorer. It now goes </span><span class="r-18u37iz"><a class="css-4rbku5 css-18t94o4 css-901oao css-16my406 r-1cvl2hr r-1loqt21 r-poiln3 r-bcqeeo r-qvutc0" dir="ltr" href="https://twitter.com/hashtag/NVDIARTX?src=hashtag_click" role="link">#NVDIARTX</a></span><span class="css-901oao css-16my406 r-poiln3 r-bcqeeo r-qvutc0"> with OptiX backend compatibility, </span><span class="r-18u37iz"><a class="css-4rbku5 css-18t94o4 css-901oao css-16my406 r-1cvl2hr r-1loqt21 r-poiln3 r-bcqeeo r-qvutc0" dir="ltr" href="https://twitter.com/hashtag/AI?src=hashtag_click" role="link">#AI</a></span><span class="css-901oao css-16my406 r-poiln3 r-bcqeeo r-qvutc0"> denoiser, and new stereo camera! High-quality rendering of scientific datasets and </span><span class="r-18u37iz"><a class="css-4rbku5 css-18t94o4 css-901oao css-16my406 r-1cvl2hr r-1loqt21 r-poiln3 r-bcqeeo r-qvutc0" dir="ltr" href="https://twitter.com/hashtag/VR?src=hashtag_click" role="link">#VR</a></span><span class="css-901oao css-16my406 r-poiln3 r-bcqeeo r-qvutc0"> use-cases with pure ray-tracing.</span></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh06PRGOmvuvSu13TZ-xAdvHsAg7v5sVWNbUtIwxLGTBaAo-os4vN-uk-5O35bPjw7jf5XDIQd-I_T1iXlhhaxr2BMH70dbSzX38-dUg-Pa81xiWRq8AcZYWVCqDcr3snR8WrDugRmecwPGQOgkdse1C6acRgXUhaamGz97o5rGFjApvgVb5zYTx-l5SQ/s375/BioExplorer_1.6.0.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="210" data-original-width="375" height="224" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh06PRGOmvuvSu13TZ-xAdvHsAg7v5sVWNbUtIwxLGTBaAo-os4vN-uk-5O35bPjw7jf5XDIQd-I_T1iXlhhaxr2BMH70dbSzX38-dUg-Pa81xiWRq8AcZYWVCqDcr3snR8WrDugRmecwPGQOgkdse1C6acRgXUhaamGz97o5rGFjApvgVb5zYTx-l5SQ/w400-h224/BioExplorer_1.6.0.gif" width="400" /></a></div><br /><span class="css-901oao css-16my406 r-poiln3 r-bcqeeo r-qvutc0"></span><p></p><p>Open source code: <a href="https://github.com/BlueBrain/BioExplorer">https://github.com/BlueBrain/BioExplorer</a><br /></p>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-78978764354164433052023-03-25T03:08:00.005-07:002023-03-25T03:08:53.087-07:00Machine Learning and understanding the role of blood glucose levels in the severity of COVID-19<p><span class="break-words"><span><span dir="ltr">On the third anniversary
of the first lock-down, we look back at how Machine Learning helped
reveal the role of blood glucose levels in the severity of COVID-19.<br /><br />With access to enough open data, imagine what other problems could be tackled.</span></span></span></p><p><span class="break-words"><span><span dir="ltr"></span></span></span></p><p><span class="break-words"><span><span dir="ltr"></span></span></span><span class="break-words"><span><span dir="ltr">So proud we made it! 😀 <br /><br />For the 3D visualization part of the movie, I developed the open-source Blue Brain Explorer, in collaboration with <a data-attribute-index="0" data-entity-type="MINI_PROFILE" href="https://www.linkedin.com/in/ACoAABBR7cgBWaum01iKtea_fFAfN96VznZMObM">Emmanuelle Logette</a> for the scientific part. Check it out:<br /><br /><a href="https://github.com/BlueBrain/BioExplorer">https://github.com/BlueBrain/BioExplorer</a><br /><br />Watch the documentary:</span></span></span></p><p><span class="break-words"><span><span dir="ltr"> </span></span></span></p><div class="separator" style="clear: both; text-align: center;"><iframe allowfullscreen="" class="BLOG_video_class" height="266" src="https://www.youtube.com/embed/iIJuG4K8nTk" width="320" youtube-src-id="iIJuG4K8nTk"></iframe></div><p><br /><br />Read more: <a data-attribute-index="4" href="https://lnkd.in/dW7m6Ea">https://lnkd.in/dW7m6Ea</a></p><p><span class="break-words"><span><span dir="ltr"><a data-attribute-index="2" href="https://www.linkedin.com/feed/hashtag/?keywords=scivis&highlightedUpdateUrns=urn%3Ali%3Aactivity%3A7044966384006483968">#scivis</a> <a data-attribute-index="3" href="https://www.linkedin.com/feed/hashtag/?keywords=scientificvisualization&highlightedUpdateUrns=urn%3Ali%3Aactivity%3A7044966384006483968">#ScientificVisualization</a> <a data-attribute-index="4" href="https://www.linkedin.com/feed/hashtag/?keywords=scientificexploration&highlightedUpdateUrns=urn%3Ali%3Aactivity%3A7044966384006483968">#ScientificExploration</a> <a data-attribute-index="5" href="https://www.linkedin.com/feed/hashtag/?keywords=raytracing&highlightedUpdateUrns=urn%3Ali%3Aactivity%3A7044966384006483968">#RayTracing</a> <a data-attribute-index="6" href="https://www.linkedin.com/feed/hashtag/?keywords=covid19&highlightedUpdateUrns=urn%3Ali%3Aactivity%3A7044966384006483968">#covid19</a> <a data-attribute-index="7" href="https://www.linkedin.com/feed/hashtag/?keywords=sarscov2&highlightedUpdateUrns=urn%3Ali%3Aactivity%3A7044966384006483968">#sarscov2</a> <a data-attribute-index="8" href="https://www.linkedin.com/feed/hashtag/?keywords=covid19pandemic&highlightedUpdateUrns=urn%3Ali%3Aactivity%3A7044966384006483968">#covid19pandemic</a></span></span></span></p><p><span class="break-words"><span><span dir="ltr"><br /></span></span></span></p><p> </p><p></p>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-83110195159590161182023-02-20T06:17:00.001-08:002023-03-12T01:00:35.827-08:00Visual scientific exploration at Blue Brain, and beyond<div style="text-align: left;">
by
<span class="author">
<span><a href="https://www.linkedin.com/in/cyrillefavreau/" target="_blank">Cyrille Favreau</a></span>
<span class="affiliation">
<span class="text">(<span>EPFL</span>)</span></span></span>, <span class="author">
<a href="https://www.linkedin.com/in/evelyneschmidosborne/" target="_blank"> <span>Evelyne Schmid Osborne</span></a>
<span class="affiliation">
<span class="text">(<span>EPFL</span>)</span></span></span>
</div>
<div class="event-date">
<i class="icon-calendar header-data" data-qtip-oldtitle="Start/end date/time of the event"></i>
<span class="event-time-data">
<time datetime="2023-02-17T10:00:00+00:00" itemprop="startDate"> </time></span></div><div class="event-date"><span class="event-time-data"><time datetime="2023-02-17T10:00:00+00:00" itemprop="startDate">Friday
Feb 17, 2023, 11:00 AM
</time>
→
<time datetime="2023-02-17T11:00:00+00:00" itemprop="endDate">
12:00 PM
</time>
<span class="timezone">Europe/Zurich</span>
</span>
</div>
<span class="location-info header-data" data-qtip-html=".qtip-hidden-content" data-qtip-oldtitle="" data-qtip-opts="{"hide": {"fixed": true, "delay": 500}}">
<i class="icon-location"></i>
<span class="text">503/1-001 - Council Chamber (CERN)</span>
</span><p></p><p>Scientific exploration relies on building software that combines data
integration, analysis and interactive visualization to build, modify
and navigate through large scientific datasets. For this, Blue Brain
built and open-sourced the Blue Brain BioExplorer. The <a href="https://github.com/BlueBrain/BioExplorer" target="_blank">Blue Brain BioExplorer</a> was originally developed to answer key scientific questions
related to the Coronavirus as a use case and to deliver a visualization
tool. Today, the BioExplorer allows reconstructing, visualizing,
exploring and describing in detail the structure and function of
highly-detailed biological structures such as molecular systems,
neurons, astrocytes, blood vessels, and more.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLntayX1dM6ugDjxdBfU7-VTFkgQArXNquuHFJgaDMf7eMvY9VnkAhMg9GJCGPQb8CwMt9kz5uRP26An5fFPGe3wLEL8fGKf4kwGyNA-SuFQQ6NnegCdll3-IWyeSgpk-xvulz6CmBQG4CRQE3_4Fze1x9HS7bHZU2nKaTQSPNjXhXV27EKGHxNyahRw/s2048/1676717471663.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1536" data-original-width="2048" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLntayX1dM6ugDjxdBfU7-VTFkgQArXNquuHFJgaDMf7eMvY9VnkAhMg9GJCGPQb8CwMt9kz5uRP26An5fFPGe3wLEL8fGKf4kwGyNA-SuFQQ6NnegCdll3-IWyeSgpk-xvulz6CmBQG4CRQE3_4Fze1x9HS7bHZU2nKaTQSPNjXhXV27EKGHxNyahRw/s320/1676717471663.jpeg" width="320" /></a></div> <p></p><p>The BioExplorer is
built as an extension of Brayns, the official underlying and generic
rendering platform that was designed to easily adapt to all fields of
science.</p><div class="separator" style="clear: both; text-align: center;"></div><p></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjY9apM-w4nNx6StgvkG65GYKOzK8Hc4w1T3OM-dIZ1Ju5Gpp1UxyLdn0HFlYIUa4t2f-A64PT6Qzmfa8Dh0F3UWPeEGYdNhcG6umvte1T9rmgASy67UBCJ8WFCQGEGepMWRwiMQ5QFVqmh83IlNGHJBfovFiaAxgKarAIHQqitCI344zXwG2x_vv2kVQ/s2048/1676717474254.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1536" data-original-width="2048" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjY9apM-w4nNx6StgvkG65GYKOzK8Hc4w1T3OM-dIZ1Ju5Gpp1UxyLdn0HFlYIUa4t2f-A64PT6Qzmfa8Dh0F3UWPeEGYdNhcG6umvte1T9rmgASy67UBCJ8WFCQGEGepMWRwiMQ5QFVqmh83IlNGHJBfovFiaAxgKarAIHQqitCI344zXwG2x_vv2kVQ/s320/1676717474254.jpeg" width="320" /></a></div> <p></p><p>In this very visual talk, we will present EPFL's Blue
Brain Project, and explain how we could architecture and build the
application that is now being used to produce high quality and high
fidelity media, as well as interactive and immersive experiences of the
digital reconstruction of the mouse brain.</p><p>We will finally discuss the impact of using real raw data for science communication and dissemination.</p><p></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhzJzQrpR63xYZNjoe5lHNeoHJ_70ps3n6K5Eaini6jBUR8zUkq-qbzd4O_RNNbeOZHbqwPqyuawwL12qDR-tcy6YFilOgI5ghsWv99FUPAJPE3BX7VmhGxfJNlpfAuukK4knfbODX6aD1KRqlPCarm9o0VFD0Jp7xSXHOHEUbRy36zJ6ceo_YFn9YjQA/s2048/1676717472201.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1536" data-original-width="2048" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhzJzQrpR63xYZNjoe5lHNeoHJ_70ps3n6K5Eaini6jBUR8zUkq-qbzd4O_RNNbeOZHbqwPqyuawwL12qDR-tcy6YFilOgI5ghsWv99FUPAJPE3BX7VmhGxfJNlpfAuukK4knfbODX6aD1KRqlPCarm9o0VFD0Jp7xSXHOHEUbRy36zJ6ceo_YFn9YjQA/s320/1676717472201.jpeg" width="320" /></a></div><p></p><br /><p>CERN reference: <a href="https://indico.cern.ch/event/1253917/">https://indico.cern.ch/event/1253917/</a></p>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-71979896931276324072022-12-31T05:17:00.004-08:002022-12-31T05:17:47.636-08:00Happy New Year 2023<p><span class="break-words"><span><span dir="ltr">Dear followers,<br /><br />Another
year has passed, and I was once again lucky enough to work on some
outstanding projects and share amazing times with very precious people.
Kind, smart and sensitive people who touched my heart, and brought me
back to life. I was simply given the chance to be in good company, and
that counts more than anything else.<br /><br />The project I am most proud
of if the one that was used to generate the wishing card: <a href="https://github.com/favreau/Sol-R">Quantum of Sol-R</a>. A good old (but still fast!) ray-tracer that makes use of real
photons to improve the quality of the rendering. By using a random
generator device based on quantum properties of real photons, the
ray-tracer is now capable of using pure randomness to process light
transport. God does play dice, and that’s good news to me.</span></span></span></p><p><span class="break-words"><span><span dir="ltr"></span></span></span></p><p><span class="break-words"><span></span></span></p><div class="separator" style="clear: both; text-align: center;"><span class="break-words"><span><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6l5nT2cICcGy2eiJ0toXDIMoC8SPW7PgrrPriga8EGooRTgzGSrvma7FjgePvinYD_Es6qsEPLmqTXmMtPyMX-zqwYIvfpRIrOxJBakiqULkOVWUxub6ZUmagMCZgiKyx39u3BfVklOq-4Wfwq_zwLUDCpIGmqkNx8L-_d0iJ-dvSMqv8r-jOTgScMg/s1920/QuantumOfSolR_dragon.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1280" data-original-width="1920" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6l5nT2cICcGy2eiJ0toXDIMoC8SPW7PgrrPriga8EGooRTgzGSrvma7FjgePvinYD_Es6qsEPLmqTXmMtPyMX-zqwYIvfpRIrOxJBakiqULkOVWUxub6ZUmagMCZgiKyx39u3BfVklOq-4Wfwq_zwLUDCpIGmqkNx8L-_d0iJ-dvSMqv8r-jOTgScMg/w400-h266/QuantumOfSolR_dragon.jpg" width="400" /></a></span></span></div><span class="break-words"><span><span dir="ltr"><br />I am wishing you all a wonderful 2023. Take care of yourselves, and be kind to each other. We’re only humans after all.</span></span></span><p></p>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-3946735149103704652022-10-14T07:41:00.008-07:002022-10-15T04:19:59.906-07:00Quantum of Sol-R: A singular graphics engine making use of quantum physics<p>Ten years ago I wrote a graphics engine as a personal project, perhaps one of the first to want to access the Holy Grail of computer-generated imagery: real-time ray tracing.<br /><br />To learn this extraordinary news that is the awarding of the Nobel Prize in Physics to Mr Alain Aspect sounded like a reminder. It's been a while that I wanted to integrate in one way or another a little quantum in my work, the opportunity to get started was too good.</p><p></p><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjBQ5v7udzNJ55n-gdNJn8Xq_OiOW0D9jolcv3kbfxMeDLEuuS6WckvRdA2yDmNPQuLnWJnXH5zisZjFjVp9YI6S3gZbRLdRX6gaXb8nEvzRTbLeWjWw99afVWxwX61i8TiCfzgTT94Op8H9JfAE5jNkAD3aRBM8_XtGPulc4SJzxw9VCqAKouwjx5FAA/s990/QuantumOfSolR_001.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="990" data-original-width="990" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjBQ5v7udzNJ55n-gdNJn8Xq_OiOW0D9jolcv3kbfxMeDLEuuS6WckvRdA2yDmNPQuLnWJnXH5zisZjFjVp9YI6S3gZbRLdRX6gaXb8nEvzRTbLeWjWw99afVWxwX61i8TiCfzgTT94Op8H9JfAE5jNkAD3aRBM8_XtGPulc4SJzxw9VCqAKouwjx5FAA/s320/QuantumOfSolR_001.png" width="320" /></a></div></div></div><p>Quantum coincidence or not, I work in Geneva and the company <a href="https://www.idquantique.com/" target="_blank">ID Quantique</a> happens to have its premises in Carouge, a 30-minute walk from my home. This company designs, produces and markets a <a href="https://www.idquantique.com/random-number-generation/products/" target="_blank">random number generator</a> based on the quantum properties of photons, and my graphics engine is in dire need of random numbers.<br /><br />Better, it is the quality of the randomness which determines the beauty of the final image. What could be better than asking the best experts, the photons themselves, to help me transport light correctly in this virtual world?</p><p></p><div class="separator" style="clear: both; text-align: center;"><iframe allowfullscreen="" class="BLOG_video_class" height="266" src="https://www.youtube.com/embed/s4_4sYNJv8A" width="320" youtube-src-id="s4_4sYNJv8A"></iframe></div><p>The complete source code of the graphics engine is online, and available to everyone but I am still waiting for the Quantum device provider to allow me to make the code public. In the meantime, run it, modify it and improve it. The beauty of science is endless, it's up to you to bring it to light! (As if light could play a role in this world 😉 )</p><p><a href="https://github.com/favreau/Sol-R">https://github.com/favreau/Sol-R</a><br /><br />If it is still impossible for me to visualize the quantum world, perhaps it is given me now to be able to contemplate the random it creates.</p><p style="text-align: center;"></p><p></p><p></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHN_bqxfTx3y2gQipeCOG8O8PwVjBQRVtIWMbj-q5mnMUhuRVWFbG8yz7VPeI7gmF7eSaS9k0hSCtiEe7BVb5IN3ryCErOZV8-0wqOJoZO6cgeKBOZGku6YSzDUcgeogafvKScV1tloNs7qe5N1ek8hmotdNbyQeDnIbJmE-tuqj6TNX6SL-eMgk0acw/s990/QuantumOfSolR_002.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="990" data-original-width="990" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHN_bqxfTx3y2gQipeCOG8O8PwVjBQRVtIWMbj-q5mnMUhuRVWFbG8yz7VPeI7gmF7eSaS9k0hSCtiEe7BVb5IN3ryCErOZV8-0wqOJoZO6cgeKBOZGku6YSzDUcgeogafvKScV1tloNs7qe5N1ek8hmotdNbyQeDnIbJmE-tuqj6TNX6SL-eMgk0acw/s320/QuantumOfSolR_002.png" width="320" /></a></div><br />Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-92150598501008207322022-10-01T03:03:00.009-07:002022-10-01T03:55:53.866-07:00Scientific Exploration<p> </p><div class="separator" style="clear: both; text-align: center;"></div><div class="separator" style="clear: both; text-align: center;"><a href="https://github.com/BlueBrain/BioExplorer/raw/master/bioexplorer/pythonsdk/notebooks/bioexplorer_banner.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="217" data-original-width="800" height="109" src="https://github.com/BlueBrain/BioExplorer/raw/master/bioexplorer/pythonsdk/notebooks/bioexplorer_banner.png" width="400" /></a></div><p></p><p>My work at the <a href="https://www.epfl.ch/research/domains/bluebrain/" target="_blank">Blue Brain Project</a> is all about scientific exploration.</p><p></p><div class="separator" style="clear: both; text-align: center;"><iframe allowfullscreen="" class="BLOG_video_class" height="266" src="https://www.youtube.com/embed/Xu5T9KQxcg8" width="320" youtube-src-id="Xu5T9KQxcg8"></iframe></div><p></p><p>Exploration relies on building software that combines data integration, analysis and interactive visualization to build, modify and navigate through large scientific datasets. For this, Blue Brain built and open-sourced the Blue Brain BioExplorer.</p><p></p><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://github.com/BlueBrain/BioExplorer/raw/master/bioexplorer/pythonsdk/notebooks/bioexplorer_coronavirus_banner.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="217" data-original-width="800" height="109" src="https://github.com/BlueBrain/BioExplorer/raw/master/bioexplorer/pythonsdk/notebooks/bioexplorer_coronavirus_banner.png" width="400" /></a></div></div><p>The <a href="https://github.com/BlueBrain/BioExplorer" target="_blank">Blue Brain BioExplorer</a> (BBBE), which started as an internal project, is now open source. It was originally developed to answer key scientific questions related to the Coronavirus as a use case and to deliver a visualization tool.</p><p style="text-align: center;"> <a href="https://github.com/BlueBrain/BioExplorer/raw/master/bioexplorer/pythonsdk/doc/source/images/microcircuit.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="217" data-original-width="800" height="109" src="https://github.com/BlueBrain/BioExplorer/raw/master/bioexplorer/pythonsdk/doc/source/images/microcircuit.png" width="400" /></a></p><p>Today, the BioExplorer allows to reconstruct, visualize, explore and describe in detail the structure and function of highly-detailed biological structures such as molecular systems, neurons, astrocytes, blood vessels, and more. You can see the first application of the BioExplorer in ‘<a href="https://www.frontiersin.org/articles/10.3389/fpubh.2021.695139/full?utm_source=fweb&utm_medium=nblog&utm_campaign=ba-sci-fpubh-covid-19-elevated-blood-glucose-blue-brain" target="_blank">A Machine-Generated View of the Role of Blood Glucose Levels in the Severity of COVID-19</a>’ study.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://github.com/BlueBrain/BioExplorer/raw/master/bioexplorer/pythonsdk/notebooks/bioexplorer_neuromodulation_banner.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="217" data-original-width="800" height="109" src="https://github.com/BlueBrain/BioExplorer/raw/master/bioexplorer/pythonsdk/notebooks/bioexplorer_neuromodulation_banner.png" width="400" /></a></div><p></p><p>More information <a href="https://portal.bluebrain.epfl.ch/resources/software/exploration " target="_blank">here</a>.</p><p><br /></p>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-75880573148020799892022-07-12T01:34:00.003-07:002022-07-28T10:40:04.357-07:00Brain(s) - CCCB - Barcelona (27 July — 11 December 2022)<p>The human brain is the most complex object we know of and the one that raises most questions in the fields of both science and philosophy. <i>Brain(s)</i> looks at how, throughout history, art, science, and philosophy have studied and represented this fascinating organ <br /></p><p style="text-align: center;"> <img alt="" class="img-fluid" height="179" src="https://www.cccb.org/rcs_gene/cervells_1001x560.jpg" width="320" /></p><p style="text-align: center;"><a href="https://www.cccb.org/en/exhibitions/file/brains/237851">https://www.cccb.org/en/exhibitions/file/brains/237851</a></p><p>I am proud to contribute to that project by creating an open-source software (<a href="https://github.com/favreau/BioExplorer">Blue Brain BioExplorer</a>) that could generate the images that stand aside of Cajal's originals.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhJqCJ4fc6VQHMQxidWZKGTj-qSVf9ViXqYFoOXI_K7KbZc-Aqs7ORpV9zoUV37iTawqGT6ERBrlqzsig_5H6abl-NWZA_sfs5Ay6JqXmgLUn_A97mMRRx_NIfK-vDqjW7br8X2splkMjQx3fStmaWs06CDnGcL1gkoAMcHIBL48HGdsPbMQrxxp7U31A/s4032/PXL_20220726_164140622.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="2268" data-original-width="4032" height="222" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhJqCJ4fc6VQHMQxidWZKGTj-qSVf9ViXqYFoOXI_K7KbZc-Aqs7ORpV9zoUV37iTawqGT6ERBrlqzsig_5H6abl-NWZA_sfs5Ay6JqXmgLUn_A97mMRRx_NIfK-vDqjW7br8X2splkMjQx3fStmaWs06CDnGcL1gkoAMcHIBL48HGdsPbMQrxxp7U31A/w395-h222/PXL_20220726_164140622.jpg" width="395" /></a></div><br /> <p></p>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-75519265634143950452021-05-03T09:04:00.009-07:002021-07-28T01:24:54.161-07:00A Machine-Generated View of the Role of Blood Glucose Levels in the Severity of COVID-19<p></p><div class="section abstract" id="abstract-1"><h2>Abstract</h2><div style="text-align: left;">SARS-CoV-2 started spreading toward the end of 2019 causing COVID-19, a
disease that reached pandemic proportions among the human population
within months. The reasons for the spectrum of differences in the
severity of the disease across the population, and in particular why the
disease affects more severely the aging population and those with
specific preconditions are unclear. We developed machine learning models
to mine 240,000 scientific articles openly accessible in the CORD-19
database, and constructed knowledge graphs to synthesize the extracted
information and navigate the collective knowledge in an attempt to
search for a potential common underlying reason for disease severity.
The machine-driven framework we developed repeatedly pointed to elevated
blood glucose as a key facilitator in the progression of COVID-19.
Indeed, when we systematically retraced the steps of the SARS-CoV-2
infection, we found evidence linking elevated glucose to each major step
of the life-cycle of the virus, progression of the disease, and
presentation of symptoms. Specifically, elevations of glucose provide
ideal conditions for the virus to evade and weaken the first level of
the immune defense system in the lungs, gain access to deep alveolar
cells, bind to the ACE2 receptor and enter the pulmonary cells,
accelerate replication of the virus within cells increasing cell death
and inducing an pulmonary inflammatory response, which overwhelms an
already weakened innate immune system to trigger an avalanche of
systemic infections, inflammation and cell damage, a cytokine storm and
thrombotic events. We tested the feasibility of the hypothesis by
manually reviewing the literature referenced by the machine-generated
synthesis, reconstructing atomistically the virus at the surface of the
pulmonary airways, and performing quantitative computational modeling of
the effects of glucose levels on the infection process. We conclude
that elevation in glucose levels can facilitate the progression of the
disease through multiple mechanisms and can explain much of the
differences in disease severity seen across the population. The study
provides diagnostic considerations, new areas of research and potential
treatments, and cautions on treatment strategies and critical care
conditions that induce elevations in blood glucose levels.</div><div style="text-align: left;"> </div><div style="text-align: left;">Full paper: <a href="https://www.frontiersin.org/articles/10.3389/fpubh.2021.695139/full?utm_source=fweb&utm_medium=nblog&utm_campaign=ba-sci-fpubh-covid-19-elevated-blood-glucose-blue-brain">https://www.frontiersin.org/articles/10.3389/fpubh.2021.695139/full?utm_source=fweb&utm_medium=nblog&utm_campaign=ba-sci-fpubh-covid-19-elevated-blood-glucose-blue-brain</a><br /></div><div style="text-align: left;"> </div><div style="text-align: left;"><br /></div><div style="text-align: left;"><div class="separator" style="clear: both; text-align: center;"><iframe allowfullscreen="" class="BLOG_video_class" height="266" src="https://www.youtube.com/embed/Czn-YGLGfiA" width="320" youtube-src-id="Czn-YGLGfiA"></iframe></div></div><div style="text-align: left;"><br /><div style="text-align: left;">Checkout the Blue Brain Portal for details on how the movie was made:</div><div style="text-align: left;"><br /></div><div style="text-align: left;"><a href="https://portal.bluebrain.epfl.ch/resources/software/exploration/">https://portal.bluebrain.epfl.ch/resources/software/exploration/</a></div><div style="text-align: left;"> </div><div style="text-align: left;"> </div><div style="text-align: left;"><br /></div></div></div>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-43289562224167985022021-04-22T10:36:00.005-07:002021-05-03T09:06:37.674-07:00Blue Brain BioExplorer<p>I have just released the <a href="https://github.com/BlueBrain/BioExplorer" target="_blank">Blue Brain BioExplorer</a>, a tool for
scientists to extract and analyse scientific data from visualization.
BBBE is built on top of <a href="https://github.com/BlueBrain/Brayns">Blue Brain Brayns</a>, the Blue Brain rendering platform.</p><p> </p><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsDY-v1FoTa-hu_1wWFFwqdHUZ6Br-Q-_6wXI3SAI6GtMReeui2NFP0Lgz5gWwm7GKb0up7Ew0Dvc_ZecEULQOjlykx_MhKysEypxCN2hqsVubwhrB9FsssY8_pKL6hOh2-RPwI9LBHzfo/s1024/BBBE_banner.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="256" data-original-width="1024" height="143" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsDY-v1FoTa-hu_1wWFFwqdHUZ6Br-Q-_6wXI3SAI6GtMReeui2NFP0Lgz5gWwm7GKb0up7Ew0Dvc_ZecEULQOjlykx_MhKysEypxCN2hqsVubwhrB9FsssY8_pKL6hOh2-RPwI9LBHzfo/w570-h143/BBBE_banner.png" width="570" /></a></div></div></div><div class="separator" style="clear: both; text-align: center;"> </div><div class="separator" style="clear: both; text-align: center;">Source code -> <a href="https://github.com/BlueBrain/BioExplorer">https://github.com/BlueBrain/BioExplorer</a><br /></div>
<h2>Architecture</h2>
<p>The <i>BBBE</i> application is built on top of Brayns, the Blue
Brain rendering platform. The role of the application is to use the
underlying technical capabilities of the rendering platform to create
large scale and accurate 3D scenes from Jupyter notebooks.</p>
<h2>General components</h2>
<h3>Assemblies</h3>
<p>Assemblies are groups of biological elements, such as proteins,
membranes, glycans, etc.
As an example, a virion is made of a lipid membrane, spikes proteins, an
RNA sequence, etc, and all those elements belong to the same object.
That’s why they need to belong to the same container, the assembly.
Assemblies can have different shapes: Sphere, Cube, etc, that are
automatically generated according to the parameters of individual
components.</p>
<h3>Proteins</h3>
<p>Proteins are loaded from PDB files. Atoms, non-polymer chemicals and
bonds can be loaded and displayed in various colour schemes: chain id,
atom, residue, etc.
Proteins also contain the amino acid sequences of the individual chains.
Sequences that can be used to query glycosylation sites, or functional
regions of the protein.</p>
<h3>Glycans</h3>
<p>Glycans are small proteins that are attached to an existing protein
of the assembly. Individual glycan trees are loaded from PDB files and
attached to the glycosylation sites of the specified protein. By
default, glycans are attached to all available glycosylation sites, but a
set of specific sites can be specified.</p>
<h3>RNA sequence</h3>
<p>An RNA sequence can be loaded from a text sequence of codons.
Various shapes can be selected to represent the RNA sequence: Trefoil
knot, torus, star, etc. This allows the sequence to be efficiently
packed into a given volume. A different color is assigned per type of
codon.</p>
<h3>Mesh-based membranes</h3>
<p>Mesh-based membranes create membranes based on 3D meshes. This allows
the construction of complex membranes where mesh faces are filled with
proteins.</p>
<h2>Python SDK</h2>
<p>A simple API if exposed via the <i>BBBE</i> python library. The API allows scientists to easily create and modify assemblies, according the biological parameters. The <i>BBBE</i>
programming language is not necessarily reflecting the underlying
implementation, but is meant to be as simple as close as possible to the
language used by the scientists to describe biological assemblies.</p>
<h2>Documentation</h2>
<p>See <a href="https://bluebrain.github.io/BioExplorer/" rel="nofollow">here</a> for detailed documentation of the source code.</p>
<h2>Deployment</h2>
<p>BBBE binaries are publicaly available as docker images. BBE is
designed to run in distributed mode, and is composed of 3 modules: A <a href="https://hub.docker.com/r/bluebrain/bioexplorer" rel="nofollow">server</a>, a <a href="https://hub.docker.com/r/bluebrain/bioexplorer-python-sdk" rel="nofollow">python SDK</a>, and a <a href="https://hub.docker.com/r/bluebrain/bioexplorer-ui" rel="nofollow">web user interface</a>. This means that there are 3 docker images to be downloaded on run. Those images can of course run on different machines.</p>
<p>In this example, we will expose the server on port 5000, the python
SDK jupyter notebooks on port 5001, and the user inferface on port 5002.
One is free to change those ports at will.</p>
<h3>Server</h3>
<div class="highlight highlight-source-shell"><pre>docker run -ti --rm -p 5000:8200 bluebrain/bioexplorer</pre></div>
<h3>Python SDK</h3>
<div class="highlight highlight-source-shell"><pre>docker run -ti --rm -p 5001:8888 bluebrain/bioexplorer-python-sdk</pre></div>
<h3>Web User Interface</h3>
<div class="highlight highlight-source-shell"><pre>docker run -ti --rm -p 5002:8080 bluebrain/bioexplorer-ui</pre></div>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-20373522195104333142020-12-25T14:02:00.004-08:002021-04-21T03:08:51.845-07:00Black Holes Suck!<p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_JzZKGs_E37ZbCJ6vc77gAl9sDkksd4UdbCqE_AdhkTokV4Se0TNotaXfiiKdYSXymkySJTOiL6Vhx094igc_b7YxEmrYXWy2c3rRFjCqh1w0vVECGSNJ864_-E-_j2Kjx8-qAR8KVcBk/s1014/blackhole_banner.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="424" data-original-width="1014" height="168" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_JzZKGs_E37ZbCJ6vc77gAl9sDkksd4UdbCqE_AdhkTokV4Se0TNotaXfiiKdYSXymkySJTOiL6Vhx094igc_b7YxEmrYXWy2c3rRFjCqh1w0vVECGSNJ864_-E-_j2Kjx8-qAR8KVcBk/w400-h168/blackhole_banner.png" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"> </div><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgc0FdxyrkzOj3YJ4xGGrCVZLNY7U8BIYBaRnLXgci9mWrtiqmEqHzbAxraAX909c2trUViMaUBtlZwAc5tf23Nol9vHB8Nar0gI5FSwcRds_vXU3BeHhiCeBoweH7u6_lOnWQnMNHoIN1_/s512/black_hole_v1.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="512" data-original-width="512" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgc0FdxyrkzOj3YJ4xGGrCVZLNY7U8BIYBaRnLXgci9mWrtiqmEqHzbAxraAX909c2trUViMaUBtlZwAc5tf23Nol9vHB8Nar0gI5FSwcRds_vXU3BeHhiCeBoweH7u6_lOnWQnMNHoIN1_/w200-h200/black_hole_v1.jpeg" width="200" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjCX3RwZzWBDMiA5Jtva3HdlJRLfWucdFy2KhRCrG9OiAzyDOccYcmR7-Jk0Qbac91Oq78RikqdgMHKZRLi_i_qniKT8-tQFNUZT_YxmLRAgv11I20YLKgS65neDA8hn7nOP1XGTVQI8HNg/s512/black_hole_v3.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="512" data-original-width="512" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjCX3RwZzWBDMiA5Jtva3HdlJRLfWucdFy2KhRCrG9OiAzyDOccYcmR7-Jk0Qbac91Oq78RikqdgMHKZRLi_i_qniKT8-tQFNUZT_YxmLRAgv11I20YLKgS65neDA8hn7nOP1XGTVQI8HNg/w200-h200/black_hole_v3.jpeg" width="200" /></a></div></div><span class="css-901oao css-16my406 r-1qd0xha r-ad9z0x r-bcqeeo r-qvutc0"> </span></div><div class="separator" style="clear: both; text-align: left;"><span class="css-901oao css-16my406 r-1qd0xha r-ad9z0x r-bcqeeo r-qvutc0">I recently needed to explain my young 10 years old nephew what a b</span>lack hole <span class="css-901oao css-16my406 r-1qd0xha r-ad9z0x r-bcqeeo r-qvutc0">was, so I ported the </span><span class="css-901oao css-16my406 r-1qd0xha r-ad9z0x r-bcqeeo r-qvutc0"><a href="https://www.shadertoy.com/view/tsBXW3" target="_blank">Black hole with accretion disk</a> shader toy to <a href="https://github.com/BlueBrain/Brayns/releases/tag/1.0.0" target="_blank">Brayns</a></span><span class="css-901oao css-16my406 r-1qd0xha r-ad9z0x r-bcqeeo r-qvutc0">.</span><br /></div><p><span class="css-901oao css-16my406 r-1qd0xha r-ad9z0x r-bcqeeo r-qvutc0"></span></p><p><span class="css-901oao css-16my406 r-1qd0xha r-ad9z0x r-bcqeeo r-qvutc0">Code is here</span> : <br /></p><p></p><p></p><p><a href="https://github.com/favreau/Brayns-UC-BlackHole">https://github.com/favreau/Brayns-UC-BlackHole</a></p><p><br />A docker image is available:</p><p>Run Black Hole plugin back-end using:</p>
<pre><code>docker run -ti --rm -p 8200:8200 favreau/blackhole:0.1.0</code></pre>
<p>Use the Blue Brain UI to visualize the Black Hole in your browser: </p><p><a href="https://hub.docker.com/r/bluebrain/brayns-ui">https://hub.docker.com/r/bluebrain/brayns-ui</a></p>
<pre><code>docker run -ti --rm -p 8080:8080 bluebrain/brayns-ui:1.0.0</code></pre><p>Open a browser on: <a href="http://localhost:8080/?host=localhost:8200">http://localhost:8080/?host=localhost:8200</a></p>Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-53037929788205577232020-04-11T02:07:00.001-07:002020-04-11T02:20:25.393-07:00Coronavirus builder - Work in progressExplore it in VR from there:<br />
<br />
<a href="https://favreau.github.io/vrview/?image=examples%2Fgallery%2Fcoronavirus-v1.jpg">https://favreau.github.io/vrview/?image=examples/gallery/coronavirus-v1.jpg</a><br />
<br />
<a href="https://favreau.github.io/vrview/?image=examples/gallery/coronavirus-v2.jpg">https://favreau.github.io/vrview/?image=examples/gallery/coronavirus-v2.jpg</a> <br />
<br />
Data is fake for now, but working on it...<br />
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PS: Use Chrome, Firefox does not seem to like my webpage. Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-12875758725913961382020-02-26T14:24:00.000-08:002020-03-20T13:13:47.410-07:00Neurones, les intelligences simulées (Centre Pompidou)<div class="separator" style="clear: both; text-align: center;">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKAAzzlFdIsRMTSF4PwsOR-HYLOfCuoWkSNQQicn_6JRnNp2PGH0E85busGIKTKre0b6IYPl2ghVPvddzR9HI5pNMwmZKDwSrooFXk6pYs_-jgalMwtBcKpj5t1PzoE-LgIMdfJXQBSPOP/s1600/IMG_20200226_114722937.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="759" data-original-width="1600" height="94" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKAAzzlFdIsRMTSF4PwsOR-HYLOfCuoWkSNQQicn_6JRnNp2PGH0E85busGIKTKre0b6IYPl2ghVPvddzR9HI5pNMwmZKDwSrooFXk6pYs_-jgalMwtBcKpj5t1PzoE-LgIMdfJXQBSPOP/s200/IMG_20200226_114722937.jpg" width="200" /></a></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgE3OX7sDY9WhVNATnFPExz54A1sCsaYwibWz9RQeki_qliK4crtBw43-MBRPddVf8-xzHeHPue0ot2hGeZJEMzMhOM69D1vq6QpOereGbSLA4HJ9DGlVzLEBbdKUBkBOzhOOhZ9qjZSsZ1/s1600/ERsq8f0XUAA6k5z.jpeg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="576" data-original-width="1024" height="112" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgE3OX7sDY9WhVNATnFPExz54A1sCsaYwibWz9RQeki_qliK4crtBw43-MBRPddVf8-xzHeHPue0ot2hGeZJEMzMhOM69D1vq6QpOereGbSLA4HJ9DGlVzLEBbdKUBkBOzhOOhZ9qjZSsZ1/s200/ERsq8f0XUAA6k5z.jpeg" width="200" /></a>Incredibly happy and proud to have created the Blue Brain Project movie that is currently being displayed at the Centre Pompidou. A world class modern art museum located in Paris.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgA3j4y78xNPreKr_Q6SQty7KfEUhh3tBy2aeNpY0zHAt8SKeKvmc0bWkosqV0Tj0eET1oAsgYWdeHIJ5stPZUvO5wQ39BmQ4sZcQCuYnXOX2Q3hO8NXDHhnDbc5aYpO8SSylxZGISrBIsz/s1600/IMG_20200225_193352893.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="759" data-original-width="1600" height="90" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgA3j4y78xNPreKr_Q6SQty7KfEUhh3tBy2aeNpY0zHAt8SKeKvmc0bWkosqV0Tj0eET1oAsgYWdeHIJ5stPZUvO5wQ39BmQ4sZcQCuYnXOX2Q3hO8NXDHhnDbc5aYpO8SSylxZGISrBIsz/s200/IMG_20200225_193352893.jpg" width="200" /></a><i><span style="color: #6fa8dc;">"Alors que l’intelligence artificielle semble avoir envahi tous les domaines industriels du monde contemporain, de la finance au domaine médical, des jeux aux objets à comportement, de l’architecture au militaire, cette situation n’a jamais été véritablement mise en relation avec l’histoire des neurosciences et de la neuro-computation. L’exposition « Neurones, les intelligences simulées » souligne la continuité des recherches d’artistes, d’architectes, de designers et de musiciens avec celle développées par les grands laboratoires scientifiques ou ceux du monde industriel. Dans le cadre de « Mutations/Créations ».</span></i><br />
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<i><span style="color: #6fa8dc;">Avec « Mutations/Créations », le Centre Pompidou se transforme en laboratoire de la création et de l’innovation à la frontière des arts, de la science, et de l’ingénierie. Chaque année, le programme réunit des artistes, des ingénieurs, des scientifiques et des entrepreneurs. En 2020, « Mutations/Créations » poursuit sa recherche prospective au travers de deux expositions, « Neurones, les intelligences simulées » et « Jeremy Shaw », après trois éditions successivement consacrées à l’impression 3D (« Imprimer le monde » et « Ross Lovegrove » en 2017), aux langages informatiques (« Coder le monde » et « Ryoji Ikeda » en 2018) et à la création mêlant artificiel et vivant (« La Fabrique du vivant » et « Erika Verzutti » en 2019)."</span></i><br />
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<span style="text-align: right;"> </span><span style="text-align: right;">More information available </span><a href="https://www.centrepompidou.fr/cpv/agenda/event.action?param.id=FR_R-f146fa16402582d562607c9d2cbeee3e&param.idSource=FR_E-f146fa16402582d562607c9d2cbeee3e" style="text-align: right;">here</a><span style="text-align: right;">.</span><br />
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Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-49302591383668866442020-01-28T12:45:00.000-08:002020-01-30T05:01:08.104-08:00Biggest and Most Detailed Map of the Fly BrainThanks to the amazing dataset provided by HHMI Janelia, I had to to see it by myself, and decided to create the few renders below<br />
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Dataset is downloadable from here: <a href="https://www.janelia.org/news/unveiling-the-biggest-and-most-detailed-map-of-the-fly-brain-yet">https://www.janelia.org/news/unveiling-the-biggest-and-most-detailed-map-of-the-fly-brain-yet</a><br />
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<br />Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-35625572739895170392020-01-08T03:55:00.000-08:002020-01-08T03:55:35.597-08:00Happy 2020!<div class="separator" style="clear: both; text-align: center;">
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<br />Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-76556404136452412082019-12-07T14:29:00.002-08:002020-01-20T13:49:32.099-08:00Hemispheres of the Mind<div class="css-901oao r-1fmj7o5 r-1qd0xha r-a023e6 r-16dba41 r-ad9z0x r-bcqeeo r-bnwqim r-qvutc0" dir="auto" id="tweet-text" lang="en">
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<span style="font-family: inherit;"><a href="http://infinityroom2.epfl.ch/#/hemispheres">Hemispheres of the Mind</a> is a collaboration between the EPFL Laboratory of Experimental Museology and the EPFL Blue Brain Project for the ArtLab Infinity Room II 2019. </span><br />
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<span style="font-family: inherit;">A collaboration between Cyrille Favreau (Blue Brain Project), <a href="https://www.linkedin.com/in/ACoAAAGjAIAB7KFgK4Afk-jNNDx7BCDV8Rnj7BE/?lipi=urn%3Ali%3Apage%3Ad_flagship3_profile_view_base_recent_activity_details_all%3BRYq2JVyRT4igWJokXf%2B9Rg%3D%3D">Sarah Kenderdine</a> (eM+ EPFL) and <a href="https://www.linkedin.com/in/ACoAAAAbNPMBQ5YH9vsQqPlufIEXuzKkIT0eXpI/?lipi=urn%3Ali%3Apage%3Ad_flagship3_profile_view_base_recent_activity_details_all%3BRYq2JVyRT4igWJokXf%2B9Rg%3D%3D">Peter Morse</a> for ArtLab Infinity Room II 2019 celebrating 50 years of Ecole polytechnique fédérale de Lausanne.</span><br />
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<span style="font-family: inherit;">Special thanks to <a href="https://www.linkedin.com/in/ACoAAAtGPFEBakpJx5WNhW5Ok0ei2C68I-mqVyM/?lipi=urn%3Ali%3Apage%3Ad_flagship3_profile_view_base_recent_activity_details_all%3BRYq2JVyRT4igWJokXf%2B9Rg%3D%3D">Grigori Chevtchenko</a> for the fisheye camera implementation, and <a href="https://www.linkedin.com/in/ACoAABFqUdoBJk5Wwh1JXe0wz_MlwFsBDsjwkww/?lipi=urn%3Ali%3Apage%3Ad_flagship3_profile_view_base_recent_activity_details_all%3BRYq2JVyRT4igWJokXf%2B9Rg%3D%3D">Paweł Podhajski</a> for allowing the deployment of <a href="https://github.com/BlueBrain/Brayns">Brayns</a> on the Blue Brain Supercomputer.</span><br />
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Audio Production by <a href="https://www.linkedin.com/in/petermorse/">Peter Morse</a> and <a href="http://www.cathietravers.com/index.html">Cathie Travers</a>.<br />
<span style="font-family: inherit;">Music by <a href="https://www.kai-engel.com/">Kai Engel</a> & <a href="http://www.cathietravers.com/index.html">Cathie Travers</a></span><br />
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<span style="font-family: inherit;">#epfl #project #laboratory #bluebrainproject #brain #sciart</span></div>
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Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-45569377824562809762019-08-07T10:48:00.000-07:002021-04-21T03:11:43.765-07:00Results of months of work at the Blue Brain Project<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFoavb8CDE98g6aSwaL_bhDXF_q_OR1q38jqpSDFkn6jWYbSLCQ6pRSgqv75d1ElmB77z0ZF0SqfE3fGlcE2ZGrwND0Wk3yZQk64Cxr8cWDu2qJTxis_7HIot34fEj3Susop3JDctgXdzh/s1600/67495764_2460981434186848_6662950845534961664_o.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="720" data-original-width="1200" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFoavb8CDE98g6aSwaL_bhDXF_q_OR1q38jqpSDFkn6jWYbSLCQ6pRSgqv75d1ElmB77z0ZF0SqfE3fGlcE2ZGrwND0Wk3yZQk64Cxr8cWDu2qJTxis_7HIot34fEj3Susop3JDctgXdzh/s400/67495764_2460981434186848_6662950845534961664_o.jpg" width="400" /></a></div>
<br />Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-90998306670757057962019-05-21T12:00:00.001-07:002019-05-21T12:04:37.707-07:00Journal for Neuroscience cover published!<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgDi3dUEr9eDsNW1NhCMPmm26AayTpIXxV-n-Kzq1_Owuy5fxCEbZ9_tW3lJPyVxEsshVopq-vaO39bp8p_zD07GvyLCcRzZVeDwWuGe-gdZqHt2BbH_sPOkFNLIWi-n3y6lH0NzcUPhb3o/s1600/60466907_2402314270053565_6667352547063234560_n.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="548" data-original-width="436" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgDi3dUEr9eDsNW1NhCMPmm26AayTpIXxV-n-Kzq1_Owuy5fxCEbZ9_tW3lJPyVxEsshVopq-vaO39bp8p_zD07GvyLCcRzZVeDwWuGe-gdZqHt2BbH_sPOkFNLIWi-n3y6lH0NzcUPhb3o/s320/60466907_2402314270053565_6667352547063234560_n.jpg" width="255" /></a>Making an image of the brain always is a challenge. The idea behind the cover image is to pay tribute to the amazing work initiated by Camillo Golgi back in the late 19th century. His discovery of a staining technique called black reaction changed the way one could visualize brain structures. Recent studies have shown that the aesthetic of images representing data visualization in neuro-science plays a significant role in the way those image are understood.
In the last years, computer technologies have improved dramatically, together with the field of computational neuro-science. Thanks to advanced computer graphics techniques, it is now possible to reconstruct realistic shapes of neurons from a set of points and radii describing the structure of the cell. Many of those data sets for single neurons can be found on the web. Combining them together and placing them in space makes it a simple way to imagine what regions of the brain could look like if they were to be seen using Golgi’s technique.
In the near future, it seems clear that realistic, physically based rendering of in-silico data will become a necessary tool to understand how the brain functions.
But if those new tools are very promising, one should not forget the work of the pioneers, and this is what this cover image is all about.Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-26431775528652531032019-01-30T02:40:00.001-08:002019-01-30T02:40:32.905-08:00Celebrating the beauty of the brain
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So... I played, and I won :) I somehow became the winner of the <a href="https://neuroart.com/winnersgallery/#gallery/b85f350df83edbef348ac5d60f2ee540/381">NeuroArt contest for December 2018</a>, which is great</div>
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I am extremely happy to be one the winners of the NeuroArt contest for December 2018.</div>
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Making an image of
the brain always is a challenge. The idea behind the cover image is
to pay tribute to the amazing work initiated by <a href="https://de.wikipedia.org/wiki/Camillo_Golgi">Camillo Golgi</a> back in
the late 19<sup>th</sup> century. His discovery of a staining
technique called black reaction changed the way one could visualize
brain structures. Recent studies have shown that the aesthetic of
images representing data visualization in neuroscience plays a
significant role in the way those image are understood.</div>
<div style="line-height: 100%; margin-bottom: 0in;">
<br /></div>
<div style="line-height: 100%; margin-bottom: 0in;">
In the last years,
computer technologies have improved dramatically, together with the
field of computational neuroscience. Thanks to advanced computer
graphics techniques, it is now possible to reconstruct realistic
shapes of neurons from a set of points and radii describing the
structure of the cell. Many of those <a href="http://neuromorpho.org/">datasets</a> for single neurons can
be found on the web. Combining them together and placing them in
space makes it a simple way to imagine what regions of the brain
could look like if they were to be seen using Golgi’s technique.</div>
<div style="line-height: 100%; margin-bottom: 0in;">
<br /></div>
<div style="line-height: 100%; margin-bottom: 0in;">
In the near future,
it seems clear that realistic, physically based rendering of
in-silico data will become a necessary tool to understand how the
brain functions.
</div>
<div style="line-height: 100%; margin-bottom: 0in;">
But if those new
tools are very promising, one should not forget the work of the
pioneers, and this is what this cover image is all about.</div>
<div style="line-height: 100%; margin-bottom: 0in;">
<br />
</div>
<br />Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.comtag:blogger.com,1999:blog-3805403550445654768.post-4482808586806630792019-01-12T02:57:00.001-08:002019-01-12T02:57:16.565-08:00Full stack/frontend software engineer wanted!<div class="box">
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<b>Your mission if you accept it</b></h2>
The EPFL Blue Brain Project
(<a href="https://portal.bluebrain.epfl.ch/">BBP</a>), situated on the <a href="https://www.campusbiotech.ch/">Campus Biotech</a> in Geneva, Switzerland, applies
advanced neuroinformatics, data analytics, high-performance computing
and simulation-based approaches to the challenge of understanding the
structure and function of the mammalian brain in health and disease. The
BBP provides the community with regular releases of data, models and
tools to accelerate neuroscience discovery and clinical translation
through open science and global collaboration.<br /> <br /> We are looking for a self motivated <strong>full stack/frontend software engineer</strong> <strong>(W/M)</strong> to join our team and help us with the development of our visualization tools.<br /> <br />
You will be working in a dynamic team with highly skilled software
engineers and our goal is to aid scientists in visualizing and
understanding their (neuroscientific) data.</div>
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<h2>
<b>Main duties and responsibilities include :</b></h2>
Your responsibility will be to develop new features for our current interactive 3D viewer <a href="https://github.com/BlueBrain/Brayns">Brayns</a>
(on the frontend) and maintain existing ones, and to drive the
development of our new hub application where the scientists can manage
their data visualizations.</div>
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More information available <a href="https://recruiting.epfl.ch/Vacancies/755/Description/2">here</a>.</div>
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Cyrille Favreauhttp://www.blogger.com/profile/08218026827070748962noreply@blogger.com