8K Brain Tour: Interactive 3D visualization of terabyte-sized nanoscale brain images at 8K resolution

Kaori Kikuchi, Nickolaos Savidis, Yosuke Bando, Kazuhiro Hiwada, Mika Kanaya, Takahito Ito, Shoh Asano, Edward Boyden

8K Brain Tour is a visualization system for terabyte-scale, three-dimensional (3D) microscopy images of brains.  High resolution (8K or 7680 x 4320 pixels), large format (85” or 188 cm x 106 cm), and touch-sensitive interactive rendering allows the viewers to dive into massive datasets capturing a large number of neurons and to investigate nanoscale and macroscale structures of the neurons simultaneously.

The image shown on the 8K display is a rendering of a slice of the part of the mouse brain called hippocampus. The specimen was physically expanded by 4.5-fold using Expansion Microscopy before being imaged under the light sheet microscope, resulting in a 3D image consisting of 25,000 x 14,000 x 2,000 voxels each representing a volume of around 50 x 50 x 200 nanometers. The dataset size is 5 terabytes.

A high-resolution, large-scale dataset like this calls for high resolution visualization, as otherwise the viewers would have to choose to either zoom into a small area of the data to see it in detail or zoom out to look at the entire data at a low resolution. With 8K rendering, this trade-off is significantly relaxed. As an example, suppose the entire image above is shown on an 8K display. Without zooming in, the small region in the yellow rectangle reveals details as shown below. Therefore, the viewers can observe microscopic thorny structures (called dendritic spines, which are where synapses are located) without losing sight of the macroscopic layered structures of neurons in the hippocampus.

In order to realize interactive visualization of terabytes of data at a high resolution, we developed a volume renderer, named BrainTour, that takes full advantage of graphics processing units (GPUs) and solid-state drives (SSDs) by optimizing data transfer from SSDs to keep feeding data to GPUs. As a result, BrainTour requires only a single desktop computer with commodity hardware as listed below.

  • 1x CPU with 6 cores at 3.0 GHz
  • 2x GPUs each with 11 GB video memory
  • 128 GB RAM
  • NVMe SSDs

The BrainTour renderer is a Windows application that can read 3D images in TIFF format. It first converts data into a preprocessed format offline and then performs interactive visualization.

Here is another specimen example, showing the entire brain of a fruit fly, expanded and captured using a lattice light sheet microscope. This 11-terabyte dataset consists of 15,000 x 28,000 x 6,600 voxels at a voxel size of 24 x 24 x 44 nanometers. A fly-through movie was created using the BrainTour renderer.

Research Topics
#data #neurobiology #imaging