Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation

Abstract

BackgroundWe present a visualization pipeline capable of accurate rendering of highly scattering fluorescent neocortical neuronal models. The pipeline is mainly developed to serve the computational neurobiology community. It allows the scientists to visualize the results of their virtual experiments that are performed in computer simulations, or in silico. The impact of the presented pipeline opens novel avenues for assisting the neuroscientists to build biologically accurate models of the brain. These models result from computer simulations of physical experiments that use fluorescence imaging to understand the structural and functional aspects of the brain. Due to the limited capabilities of the current visualization workflows to handle fluorescent volumetric datasets, we propose a physically-based optical model that can accurately simulate light interaction with fluorescent-tagged scattering media based on the basic principles of geometric optics and Monte Carlo path tracing. We also develop an automated and efficient framework for generating dense fluorescent tissue blocks from a neocortical column model that is composed of approximately 31000 neurons.ResultsOur pipeline is used to visualize a virtual fluorescent tissue block of 50 μm3 that is reconstructed from the somatosensory cortex of juvenile rat. The fluorescence optical model is qualitatively analyzed and validated against experimental emission spectra of different fluorescent dyes from the Alexa Fluor family.ConclusionWe discussed a scientific visualization pipeline for creating images of synthetic neocortical neuronal models that are tagged virtually with fluorescent labels on a physically-plausible basis. The pipeline is applied to analyze and validate simulation data generated from neuroscientific in silico experiments.

Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies

“…The resolution of the largest dimension of each volume is set to 8000 voxels. The area covered by the orange box in ( e ) represents the maximum volumetric extent that could be simulated in similar previous studies [ 28 , 29 ] …”

“…Note that we only voxelize a fraction of neurons to be able to visualize the volume, but in principle the volumes were created for all the neurons composing the circuit. Referring to previous studies [ 28 , 29 ], the scalability concerns addressed in this work has allowed the computational neuroscientists to extend the scale of their simulations from the size of the box colored in orange in Fig. 6 to an entire slice.…”

“…Building volumetric models of cortical tissue has been addressed in recent studies for the purpose of simulating microscopic experiments. Abdellah et al have presented two computational methods for modeling fluorescence imaging with low- [ 16 , 28 ] and highly-scattering tissue models [ 29 ]. The extent of their volumetric models was limited to tiny blocks of the cortical circuitry in the order of tens to hundreds of cubic micrometers.…”

Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies

“…Figure 3 shows the eventual shapes of the reconstructed somata of only 20 neurons. The progressive reconstruction of all the 55 exemplars is provided as a supplementary movie [Abd17].…”

“…A high resolution movie showing the somata reconstructed with our blenderbased mesh generation software for the 55 exemplars cells selected from the neocortical column [Abd17].…”