Nicolas Antille

Engineer, designer.

Modern scientific illustration with complex digital data.

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.

Tools
Shaker (Python lib I developed), Blender, Cycles raytracer modification.

Astrocytes in blue, neurons in yellow and blood vessels in red
Science owner
Eleftherios Zisis
Publications

Neuronal connectivity reveals patterns

Illustration showing connectivity patterns – such as the "rich club" in the middle – found in simulations of neuronal activity within what appears to be a chaotic forest.

Publication
Nature Neuroscience TOC, July 17
Tools
Blender, Sverchok, Cycles.
Science owner
Eyal Gal

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.

Publication
Front. Neurosci., 25 September 2018
Science owner
Corrado Cali

Inside the neocortical microcircuit

Scientific illustration selected by Cell journal to make the cover for a major BBP publication about the microcircuitry of the brain. I also contributed other figures to this publication.

Publications
Award
Aesthetic Merit, Seeing Life Science, EPFL 2018.
Science owner
Henry Markram et al.
Framing [Science] SNSF image competition selection, Zürich

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.

Publication
Award
2nd place award, professional illustrators category
AEIMS 18 medical illustration congress
Science owner
Eleftherios Zisis et al.

Particle simulation for an astrocyte

On top of automatically creating the 3D models for this illustration, I proposed a way to illustrate perivascular end feet – the parts that wrap around red tubes – with particle simulations that extend and flow over the capillaries.

This shows how astrocytes interact structurally with blood vessels. The figure below illustrates in more details what happens at a molecular level.

Publication
  • Scientific poster, SfN 2017
  • Le grand Atlas du cerveau, 2018
Science owner
Eleftherios Zisis

Energy supply between cells in the brain

Illustration about noradrenergic modulation of energy supply in the neuro-glial-vascular ensemble or in less barbarious terms, how molecules flow and interact between blood vessels, astrocytes and neurons.

Publication
Front. Neurosci., 25 September 2018
Science owner
Jay Coggan 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.

Publication
  • Scientific poster, SfN 2017
  • Le grand Atlas du cerveau, 2018
Science owner
Eleftherios Zisis
Technical note

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.

Award
2nd place award, professional illustrators category
AEIMS 18 medical illustration congress
Tools
Shaker (meshing algo), Blender, Cycles.
Science owner
Henry Markram et al.

The tree of thought

Illustration of algebraic topology applied to neuronal simulations. This is an artistic interpretation.

Publication
Link to Neurotop workshop 2018
and the EPFL event page.
Science owner
Kathryn Hess Group

Topology, a tool to understand the brain

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.

Publication
Frontiers news
Science owner
Max Nolte et al
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. This paves the way for new technology.

Publication
  • Nature Nanotechnology TOC Volume 11 Issue 2
  • The Analytical Scientist #37
Science owner
Tobias Kippenberg, Philippe Roelli et al.
Nicolas Antille © 2015-2018
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.

Award
Aesthetic Merit, Seeing Life Science, EPFL 2018.
Science owner
Armando Romani
Neurons in CA1

To a digital circuit of neurons

A digital circuit of the hippocampus CA1, a collaboration with engineer Cyrille Favreau using the open-source visualiser "Brayns".

Publication
Blue Brain Project's contribution to HBP, a separate entity.

Hippocampi and thalami

Distribution of neurons cores in thalami (yellow-orange regions) and hippocampi (blue regions) in the rat brain.

Science owners
Christian O'Reilly and Armando Romani

The delicate structure of the mouse brain

Complex datasets are often filtered by sampling/reducing the amount of visible elements. Here I tried to reveal all brain regions at once, with a work on transparency.

Using 3D surface reconstructions of all regions of the mouse brain, this was an attempt to reveal this intricate organ that measures a mere 1.3cm in length.

Science owner
Open source data by Allen Brain Institute Atlas

Layers of neocortical neurons

A frontal view of a thousand neurons in a circuit. They are coloured according to their position within the six layers of the neocortex with an approximate height of 2.2 millimetres.

Publications
Science owner
Eilif Muller et al.

A grant for neuroplasticity

Synapses evolve over time. While connections are formed and strengthened, others dissolve.

This illustration was requested to show research on neuroplasticity which got a grant of 100M core hours offered by ALCF (Argonne, USA) to Blue Brain in order to run simulations to study plasticity in the neocortex.

Science owner
Guiseppe Chindemi

Somatosensory cortex simulation

This is one of the largest simulations of the neocortex that BBP produced in mid 2017. The simulation is 87 Terrabyte large for a mere 217’000 neurons. A collaboration with engineer Cyrille Favreau.

Science owner
Guiseppe Chindemi et al.

Cell cores densities

Illustration of neocortical densities of neurons (red), astrocytes (green) and blood vessels (blue). Intricate details appear close-up. The denser layer 4 is clearly visible in this illustration.

Publications
Science owner
Eleftherios Zisis

About these scientific illustrations


"How do you do that?"

A vast majority of the artworks here were created with Blender & Cycles. Automatic 3D reconstruction of neurons, glia and blood vessels were carried out with Python & Shaker, a peer-reviewed Blender plug-in I developed at that Blue Brain Project. Of course not everything is automated. I make the tools do the necessary work of consuming data and then the artistic and design parts take over.

"What are these artworks for?"

These artworks are produced for scientific publications and public communication alike. They are the results of collaborations with scientists and sometimes engineers. Making an illustration very often helps in improving the digital model by visual debugging. All illustrations here are made with real data consumed with code.