Visualization of brain simulation (87TB dataset)

Bellow a few frames of the video I lead in the context of the Blue Brain project. The full video should soon be available on various channels. Stay tuned.

The video was produced using Brayns, the visualizer I created for visualizing high quality and neuroscience related large datasets.

The rendering technique is of course ray-tracing with a bit of global illumination to enhance the rendering of neuronal activity.

Visiting K Computer in Kobe

Many thanks to my good friend Syoyo for making it possible to visit the K Computer in Kobe. Great time, great people! Inspiring :)

Real-time raytracing of animated nD geometry

Let's face reality, 3D is dead, long live nD. Now that the Sol-R ray-tracer is more or less complete (for what it was initialy designed for anyway), it's time to move on to the next level. I added the Hypercube scene to the Sol-R viewer so that we can now play around with n dimensional hypercubes, thanks to the Delphi code, by cs_Forman (http://codes-sources.commentcamarche.net/source/33735-hypercubes).

Now that it's pretty clear that our world has more than 3 dimensions, I am hoping that Sol-R can now help understanding what n dimensional geometry looks like when it intersects our 3D world.

The code is there:

https://github.com/favreau/Sol-R

PS: The code was written while watching the inspiring Christopher Nolan Interstellar movie :-)

Sol-R, the speed of light OpenCL/CUDA ray-tracer is OpenSource!

Clone it, Fork it, Star it!
https://github.com/favreau/Sol-R
https://github.com/favreau/Sol-R-UI

Cool visualization of my github contributions

Those videos were rendered using this amazingly cool visualization tool

https://github.com/acaudwell/Gource

 

Deep learning and neuron visualization

Currently teaching my network to go from a simple representation of a neuron morphology to a more detailed and realistic representation. Here are the first (promising) results:

Global illumination / Volume rendering applied to molecular visualization

Global illumination / Volume rendering

Last night, I got inspired by the Exposure Render: An Interactive Photo-Realistic Volume Rendering Framework, and started adding global illumination to volume rendering in Brayns. The first results are the following ones, and the code is about to be merged :-)

When Virtual Drums meet Interactive Brain Visualization

Could not help it, had to synchronize my VDrums with Brayns, the large scale interactive brain visualizer I created at EPFL.

Components used for the demo:
- Mido: http://mido.readthedocs.io/en/latest/ 
- Brayns: https://github.com/BlueBrain/Brayns

In the insideHPC News!

 In this silent video from the Blue Brain Project at SC16, 865 segments from a rodent brain are simulated with isosurfaces generated from Allen Brain Atlas image stacks. The work is derived from the INCITE program’s project entitled: Biophysical Principles of Functional Synaptic Plasticity in the Neocortex.

I produced 2 sequences of that video using Brayns, the application I designed in the context of the Blue Brain Project.

Happy New Year!!!

Happy new year, best wishes to all, and ray-tracing forever!

Brayns for neuro-robotics

Last tuesday, I presented how Brayns could be used to render high quality images for our colleagues from the neuro-robotics team. Brayns is hardware agnostic and it takes no more than one command line argument to switch between OSPRay (CPU) and OptiX (GPU) backends. The following video shows Brayns in action, on a 24MPixel display wall! Brayns is running on 1 machine powered by 2 Quadro K5000 NVIDIA GPUs.

SIMD accelerated voxelizer

SIMDVoxelizer is a CPU-based voxalizer taking advantage of vectorization units to speed up creation of 8bit raw volumes.

usage: SIMDVoxelizer <voxel_size> <cutoff_distance> <input_file> <output_file>

Input file is a binary array of floats: x, y, z, radius and value of elements. Each voxel of the final volume contains the sum of all elements with a weight that correspond to the value of the element divided by its squared distance to the voxel. Note that in the final volume, values are normalized.

This is currently a brute force implementation that produces accurate 8bit volumes.

The <output_file> is suffixed by the size of the volume.

SIMDVoxelizer makes use of the Intel ISPC compiler and requires ispc to be in the PATH.

To build SIMDVoxelizer, simply run make in the source folder.

Source code available on github.