The Fascinating Brain exhibition
A reconstruction of the first large-scale digital circuit of human neurons in the temporal lobe.
A detail of the mural artwork at full size in a bright region. Spines are visible at this scale. A tiny fraction of the actual amount of synapses is represented here with 1% of spines per cell.
This mural artwork is the first digital reconstruction of human grey matter of the temporal lobe. White matter is hidden below this mountains of cells. Colors reveal structural properties of the circuit such as layers, cell morphology type and synaptic class. Full mural artwork size: 47000*27000px, 4m by 2.2m at 300dpi.
5% of neurons are visualised from a circuit of 50 million cells. The system looks so complex that we can hardly distinguish spines – at a very low density per cell here due to memory limit. Neither glia nor vasculature are in this model. Cell nuclei are visible but there are no other organelles here.
For this project, I reviewed scientific literature, I curated data and I researched and developed two new tools. The first one is a curvature-dependent neuronal circuit builder that handles non trivial placement of neurons. The second one is a new 3D reconstruction tool made for Blender 2.8 that leverages my C++ mod of Blender/Cycles for large-scale visualization of splines, which I used for both murals presented at Bundestag, Berlin.
Paul-Löbe-Haus, Bundestag, Berlin where my artworks were presented. Picture by Ansgar Koreng.
Mural artwork based on MRI data and on The Virtual Brain. Here, I wanted to give digital neuroscience a face, an ultra-realistic one not only to show the biological source of this image but also to give us – the audience – a way in this fascinating microscopic world. The dramatic lighting and the gaze of this woman make a canvas for us to question and confront modern neuroscience with what we are as individuals, with the perception of ourselves as macro organisms.
In this illustration, I reveal multimodal data of TVB with functional pathways in the human brain as well as mathematical research on the representation of brain activity that goes beyond EEG signals that people are used to see. My deliberate choice of having a woman subject here is a hope that this image will contribute in a very modest way to inspire more women to study and do neuroscience research but more than that, to lead future research.
Scientific mural artworks
Several mural artworks were commissionned by the Human Brain Project and were revealed at Bundestag German parliament, Paul-Löbe-Haus, Berlin on the 27th of November until December 19th, 2019. After that, the exhibition will move to the state parliament of Northrhine-Westfalia in Düsseldorf from January 21st to 31st.
Scientific data kindly provided by CNCR Amsterdam, Szeged University, Institut de Neurosciences de Marseilles, Charité University Berlin and Human Brain Project.
For the production of the murals, I deployed my custom modification of Blender 2.81 for large-scale graph visualization with Docker onto a Cray supercomputer at CSCS Lugano, I automatically distributed the computing of these artworks in smaller chunks and I composited the result afterwards.
Special thanks to
Human Brain Project
CNCR Amsterdam, Netherlands
Christiaan PJ de Kock
Mohan et al
University of Szeged, Hungary
CSCS supercomputing center
Charité University Berlin
Institut de Neurosciences de Marseille
Another detail of the mural artwork at full size, this time in a dark region. Cellular somata and spines are more visible in this case.
The Neuro-Glia-Vascular ensemble
The first digital circuit of neurons, astrocytes and blood vessels made at Blue Brain Project.
This illustration is the result of an on-going long term collaboration with scientist E. Zisis. What you see here is the tip of the iceberg as a lot of my visualisation and technical research went into debugging the model with images until I could design the final illustration, a usual workflow in digital illustration for science.
In the brain, neurons are supported and regulated by other types of cells known as the glia. Among the glia, astrocytes are territorial cells – shown here in blue – that, among other complex interactions with their surroundings, take nutrients from the blood vessels in red and distribute them to neurons in yellow. But astrocytes do more than that. For instance, they support a part of the synaptic activity within their domain. What you see in this illustration of neocortical grey matter is roughly 1.5mm tall and 0.5mm wide.
Custom Python library for meshing and visualization, Blender, Cycles raytracer modification
Neuronal connectivity patterns
Looking at digital simulations of neuronal activity, scientists found connectivity patterns: neurons seem to have a preference to connect with a chosen set of neurons and the resulting connectivity forms patterns like the "rich club" in the middle of this illustration or the feed-forward vertical pattern. The emergence of a communication pattern among cells reveals a functional structure within what appears to us as a chaotic forest of cells.
Nature Neuroscience TOC, July 17
Blender, Sverchok, Cycles.
Cellular variety in a 1mm^3 neocortical brain tissue
This artwork illustrates data obtained with electron microscopes of a small brain tissue.
A variety of cells are visible here, from microglia in blue/turquoise to neurons in purple, astrocytes in orange-yellow with a perivascular process and also myelinated axons in dark blue and blood vessels, here not reconstructed as endothelial cells, which shows the limits of the reconstruction.
The 3D models except red blood cells were automatically reconstructed from EM stacks by scientist Corrado Cali.
Front. Neurosci., 25 September 2018
Digital 3D reconstruction of capillaries in the neocortex
Using field-based meshing – aka "metaballs" in Blender, I developed a way to automatically reconstruct 3D surfaces for large datasets. This method builds the mesh by blocks so it can build any dataset.
The graph skeleton was calculated by E. Zisis and the raw data was provided by Bruno Weber et al. ETHZ.
2nd place award, professional illustrators category
AEIMS 18 medical illustration congress
Eleftherios Zisis et al.
Astrocytes growing perivascular processes
A major step after reconstructing vasculature is to have synthesized astrocytes filling a good part of the volume occupied by blood vessels and neurons. Here neurons are not shown. The astrocytes in blue grow special branches in white that are about to wrap nearby capillaries in red to get nutrients and distribute them to neurons, among many other roles theses cells perform.
- Scientific poster, SfN 2017
- Le grand Atlas du cerveau, 2018
This is the first illustration that could benefit from a mesh-less concept based on Cycles raytracer, enabling large-scale visualisation in Blender.
This inspired BBP visualisation team to explore similar techniques for large-scale visualization.
Meshless objects: 260 million splines
Surface meshes: 12 million polygons
Synaptome of a layer 5 pyramidal neuron
A close-up view of the 4138 local connections – input spines and output boutons – that this neuron forms with other cells (invisible here) in a neocortical circuit. Given points on the surface of the branches and end points, I developed a way to represent spines in a realistic way, based on scientific papers documenting neuron spine types and sizes.
2nd place award, professional illustrators category
AEIMS 18 medical illustration congress
Custom Python library for meshing and visualization, Blender, Cycles.
Eilif Muller et al.
Cerebral Cortex journal cover
From a collaboration with post-doc L. Kanari, I recreated a digital neuronal circuit given cellular densities for the illustration of the scientists' publication on the automatic classification of neuronal cells. When the artwork was submitted to Cerebral Cortex journal, it was chosen as the cover for its April 2019 issue. After that, it has been published in many science news websites such as medicalxpress.com, sciencedaily.com and eurekalert.org.
Cerebral Cortex journal
Lida Kanari, Srikanth Ramaswamy et al.
Topology, a mathematical tool for interpreting brain activity
Illustration concept of algebraic topology coupled with neuronal simulation. Using simulation data on the left hand, I revealed the other "multidimensional side" in an orthogonal projection. Black and white here is a visual code I chose for domains that are beyond our sight. When many neurons are connected together at a given time, they form simplices of high dimensional orders and even "cavities", such as the one illustrated here.
This publication generated a small buzz in the scientific community with over 90’000 views in two weeks and a lot of questions asked to BBP.
Max Nolte et al
Volumetric dataset illustrated
From a biological reference
Volumetric data of all sub-regions within the rat hippocampus, with a Nissl staining from an image stack that was the basis for calculating these volumes.
Aesthetic Merit, Seeing Life Science, EPFL 2018.
Close-up on tiophenol concentration in a 7Å gap
Published in Nature Nanotechnology
Cover of The Analytical Scientist
Molecular cavity optomechanics
Nano particles of gold are positioned to make a nano gap of about 7Å. When this gap is lit with a precise wavelength, tiophenol molecules react, "store" photons and scatter them soon after [Raman scattering]. Philippe Roelli et al described the inner workings of this phenomenon which resulted in a lot of attention in the scientific community and this will pave the way for new quantum technology.
- Nature Nanotechnology TOC Volume 11 Issue 2
- The Analytical Scientist #37
Tobias Kippenberg, Philippe Roelli et al.
Nicolas Antille © 2015-2020
About these scientific illustrations
Vision & work
I strive to make meaningful and aesthetic visuals for each and every project. As an engineer, I create tools, often based on open source ones, to process the data produced by the hard work of scientists. As an artist, I use these tools to reveal the complexity of research and its meaning in close collaboration with scientists.