KESMBA: About

KESMBA
About

Overview

The KESM Brain Atlas (KESMBA) is a web-based, light-weight 3D volume viewer that serves large volumes (typically the whole brain) of high-resolution mouse brain images (~1.5 TB per brain, ~1 um resolution) from the Knife-Edge Scanning Microscope (KESM), invented by Bruce H. McCormick.

Whole brain scale (~1.5TB per brain)
High resolution (0.6 um x 0.7 um x 1.0 um voxel size)
Imaged using the Knife-Edge Scanning Microscope: Mayerich et al. (2008) based on US patent #US 6,744,572: Mccormick et al. (2004). [More publications...]

Atlas Technology

The KESMBA customizes and extends the Google Maps™ API, with support for overlaying transparent data slides for a quick and effective 3D visualization without the need for a high-end graphics card.

Modified Google Maps™ API
Image overlays for 3D rendering (see concept figure below)
Scale bars
3D navigation
Block download (in the works)
Source code available at SourceForge.

Figure: Image overlay for local 3D effect: Eng et al. (2008); Chung et al. (2011);

Data sets

Currently, KESMBA serves the following data sets:

Mouse: Whole-brain-scale Golgi (acquired 2008 spring): neuronal morphology: Choe et al. (2009)
Mouse: Whole-brain India Ink (acquired 2008 spring): vascular network: Choe et al. (2009); Mayerich et al. (2011);
Mouse: Whole-brain Golgi (acquired 2011 summer): neuronal morphology: Choe et al. (2011); Chung et al. (2011);
[More publications...]

The following data set has been acquired already and is under preparation to be included in the KESMBA:

Mouse: Whole-brain Nissl (acquired 2009-2010 winter): somata (Choe et al. 2010)

Publications

Please refer to the Publications page.