​                            Volume Render Screen Recording

As per the screen recording below, the previously detailed steps (wk#20) are implemented.  The subsequent "aiNoise Attributes" screen shots compare the appearance of neuronal render outcomes which alter relevant parameters such as lacunarity, distortion, amplitude, and octaves. 

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       Plan for a 'Panning Resolution Schematized Animation'

The above render of a dendrite with obvious dendritic spines does have a modest degree of scientific accuracy, i.e. upon comparison to the hippocampal pyramidal cells as apparent in the previously reviewed neuroscience journals.  A primary concern with this process of modelling single neurons however, is the limited practical significance of animations focused on this level of resolution.   Specifically, neural circuits and networks attain a greater degree of practical behavioral and neuropsychological significance as they approach a meso-macro level of resolution.  Thus, on the left, in the pictorial summary of transition from the nano to meso to macro level of resolution (Saleeba et al, 2019), brief portrayal of single cell connections would primarily transition toward the macro level, i.e. the camera will zoom out and reveal portions of the neuroanatomical gross structure of relevance, not just individual hippocampal pyramidal cells, -but rather the full hippocampus itself.       

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    "Hollywood" Animation from the Internet 

The aforementioned summary of creating a neuronal surface that portrays both dendritic spines and a lacunar quality is aiming for a reasonable degree of scientific accuracy.  Neuronal animations available on the internet, such as the  video on the right from Brainquest Clinics (2017), frequently ignore neuroscientific realism and aim at generating more striking visuals.  My final effort will certainly acknowledge the visual appeal of animations aimed at optimizing an engaging visual, but will primarily respect neuroscientific photomicrographs as presented in prior blog entries (Benavides-Piccione et al., 2020).  

A Better Sense of the Real Brain … as an Animation

As presented in prior blog entries and above, typical Hollywood animations of neurons provide a poor sense of what it would be like to "wander" through the brain.  The brain is comprised of a dense mesh of neurons and supporting cells and the depictions frequently do not portray this effectively.   A better sense for what it might be like to "travel through the brain" -specifically at the nano and mesoscale level, is provided by the National Geographic special "Beautiful 3D Brain Scans Show Every Synapse" (2014).  Their 5 min mini-documentary is included as a link in the bibliography (below), but from their episode, I compiled a very brief crude "screen-shot animation" showing transition from nanoscale B+W ultra-thin brain slices highlighting one neuronal dendrite with all itz connections, through to a colored version of the neuron, which shows a single dendrite in red, as it would truly exist enmeshed in a tight covering of neuronal connections.  Take note that this will obviously provide a stark contrast to the neuron animations as typically depicted by Hollywood, or those available on the internet.   In brief, a notable problem with the depictions of neuronal circuits as presented in Hollywood movies is that brain parenchymal neurons do not generally exist in open spaces with isolated fibers projecting outward and connecting with other neurons almost as if in 'outer-space'.  The brain is a dense mesh of intertwined neurons.  The big open spaces between neurons, as depicted in Hollywood animations of the brain, in reality, are filled with a background neuropil matrix that is visible as dependent upon which histological stain is used to evaluate the neuronal sample.  A classic article by Maynard includes a glomerular section of a neuron shown with the top half stained by silver impregnation and bottom half by golgi staining (note B+W IMG below, on left); the bottom half appears to include big spaces, but the only difference (between the top and bottom halves) is the stain that was used for visualization  (1962).  This issue is partly, however, a function of the level of resolution at which the visualization is presented.   The Hollywood depictions are unrealistic, specifically in that they reveal several neuronal cell bodies within the same shot as separated by an expanse of space along the Z axis (i.e. in and out of the monitor screen). ​  At the level of resolution necessary to observe several full neurons within the same frame, there would be no apparent space surrounding the neuron so as to allow visualization of the next neuron.  In terms of genuinely visualizing neighboring neuron fibers in the same frame, most typically, several dendrities as opposed to full neurons, could be visible in the same frame, but even just this is certainly a function of how the tissue was prepared and the type of imaging technology used [note green IMG, on bottom right, and 2nd video clip  (Gao et al 2019)].  Otherwise, a real brain does include 'ventricular spaces' (filled w CSF), but these brain regions do not contain neurons!   

             Outstanding Issues: Additional Texturing, Lighting, and Pull Focus

In addition to plans to present a schematized animation that zooms across different levels of resolution and also addresses some degree of connectivity realism (within reason, obviously the National Geographic effort is not attainable in the next several days), issues for the final render that also require attention include generating a more intricate surface texture beyond that imparted simply with the aiNoise lacunarity option (Beane 2018), devising appropriate lighting for a scene inside the brain (SYIA Studios, 2018), and applying the pull focus skill from Blog wk#12.   

                      Houdini Lx#3, Terrains and Atmosphere


​This wk found Kelvin making a volcano.  The first part of the lecture involved the mountainous structure of the volcano, and the second part, the fog surrounding the volcano.  Of note, this lecture involved the use of geographic data from NASA, i.e. we used actual landscape data from an active volcano on the Kamchatka peninsula in Russia (a shot from the NASA website is the backdrop behind this paragraph).  I'm busy w neuronal modelling now, but will implement this Houdini algorithm over the summer break.  ​

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Bibliography

Beane A (2018). Maya: Advanced Texturing, https://www.linkedin.com/learning/maya-advanced-texturing/what-is-texture?u=57077561

Benavides-Piccione R, Regalado-Reyes M, Leon-Espinosa G, Rojo C, Insausti R, Segev I, Defelipe J (2020). Differential Structure of Hippocampal CA1 Pyramidal Neurons in the Human and Mouse, in Cerebral Cortex, pg 730-752. available at
doi: 10.1093/cercor/bhz122 ​

BrainQuest Clinics (2017). Animation of travelling through neurons in human brain,  avilable at:  https://youtu.be/ZSZ-JXI6oXE 

Gao R, Asano MS, Upadhyayula S, Pisarev I, Milkie DE, Liu TL, Singh V, Graves A, Huynh GH, Zhao Y, Bogovic J, Colonell J, Ott CM, Zugates C, Tappan S, Rodriguez A, Mosaliganti KR, Sheu SH, Pasolli HA, Pang S, Xu CS, Megason SG, Hess H, Lippincott-Schwartz J, Hantman A, Rubin GM, Kirchhausen T, Saalfeld S, Aso V, Boyden ES, Betzig E. (2019) “Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution.” Science. available at doi: 10.1126/science.aau8302

Malik P, (2018). Pluralsight Tutorial: Render Polygon Mesh as Volume.
https://app.pluralsight.com/player?course=arnold-maya-rendering-volumes-effects&author=pankaj-malik&name=56676bd2-eef2-4937-9e16-16976cc550ef&clip=0&mode=live

Maynard DM, (1962).  Organization of the Neuropil, Am Zoologist, 2:79-96.

National Geographic (2014).  Beautiful 3D Brain Scans Show Every Synapse.
https://video.nationalgeographic.com/video/magazine/00000144-91d5-d845-a9e4-f3d54e9a0000

Saleeba C, Dempsey B, Le S, Goodchild A, and McMullan S, (2019).  A Student's Guide to Neural Circuit Tracing, in Frontiers in Neuroscience.  available at doi: 10.3389/fnins.2019.00897

SYIA Studios (2018). Maya Lighting Tutorial: Volumetric Lighting with Arnold Renderer.  https://www.youtube.com/watch?v=Ve0Hs0v2qpA
 
Satellite data for the Volcano, ​https://worldview.earthdata.nasa.gov/