Interactive Exploration of Large Remote Micro-CT Scans

1
Interactive Exploration of Large Remote Micro-CT
Scans

• Prohaska, Hutanu, Kähler, Hege (Zuse Institut
  Berlin)

2
Motivation

• Large medical datasets (10 100 GB)
• Centrally (remotely) stored image data
• Interactive exploration

3
Design Overview

• Goal efficient external data access
• Interface to regular grid data
• multidimensional array of data elements
• subblocks at various resolutions can be accessed.
• Asynchronous access using a background thread
• Under the hood HDF5 as data container

4
HDF5 and Data Layout

• HDF5 supports
• subblock/ hyperslab selection
• external I/O drivers
• only synchronous I/O ?
• Data is stored at highest resolution using a
  chunked layout (blocksize 256KB 2MB)
• In addition, a low-res preview version of data
  is generated (adds 15 of data)

5
HDF5 and Remote Data Access

• When handling remote data, the external I/O
  driver should know which high-level function it
  serves (virtual data access layer).
• GridFTP was chosen as underlying client-server
  data access architecture.

6
Rendering

• Hierarchical multi-resolution approach
• Spherical ROI visualized in high-res, other data
  displayed at coarser resolution
• Octree structure used as multilevel
  representation of data volume, to find blocks
  intersecting ROI.
• 3D texture based volume rendering (octree based
  back-to-front rendering)

7
Results

• Measurements
• Responsiveness (time to load one block) latency
  block size/ bandwidth
• Throughput
• Data server dual Xeon 1.7GHz with 170GB storage
  (at 15MB/s read rate)
• Network latency 0.2ms (LAN), 360ms (WAN)

8
Results (Contd.)

• Dataset 2048 x 2048 x 1024, 2 bytes per voxel,
  8GB of data.
• Preprocessing (generation of preview version)
  takes 25 minutes and adds 2GB of extra data.
• Block sizes used 128 x 128 x 64 (2MB), 64 x 64 x
  32 (256KB)

9
Actual Results

• Responsiveness
• 2MB block 1.9s/blk (WAN), 0.7s/blk (LAN)
• 256K block 1.4s/blk (WAN), 0.1s/blk (LAN)
• Throughput
• 2MB block 8.3 MBit/s (WAN), 23MBit/s (LAN)
• 256K block 1.4MBit/s (WAN), 20MBit/s (LAN)
• Basically, as expected. Trade off between
  responsiveness and throughput.