BrainMaps.org consists largely of annotated, internet-accessible virtual slides and methods for navigating them and extracting data from them through a distributed server-client architecture. The infrastructure, consisting of web servers, relational databases, RAID arrays, and server-side scripts, has been developed (Mikula, Trotts, Stone, & Jones, 2007
) and tested over the past two years utilizing over 50 terabytes of virtual slides of largely histochemically-stained whole-brain sub-micron mouse and non-human primate brain material, but also including miscellaneous immunocytochemical, blockface, and in situ hybridization processed brain section series from myriad mammalian and avian species.
Multiresolution Images and Virtual Slides
The virtual slides at BrainMaps.org range from 100 megapixels, for rodent brain slices, to more than 10 gigapixels, for macaque brain slices. When working with massive images such as these, it is generally preferable and often necessary to break the image down into smaller pieces and to organize it as a multiresolution image. By 'multiresolution image', we mean that each image consists of a hierarchical image pyramid composed of small image tiles (). The multiresolution images we employ are divided into JPG image tiles, of maximum size equal to 256 × 256 pixels, organized as quad-trees (). A quad-tree models a two-dimensional region by recursively dividing it into quadrants. By doing this, it is possible to develop software for rapidly accessing just the portions of the multiresolution image that we are interested in, over the internet for example, and thereby bypassing the need to load the entire image into computer memory (RAM), which is oftentimes not technically possible.
Figure 1 Individual virtual slides are represented as multiresolution image pyramids composed of small image tiles, with a maximum size of 256 × 256 pixels. This allows for rapid online navigation because only the image tiles that are currently being viewed (more ...)
To date, more than 5000 virtual slides of primate and nonprimate brains, totaling over 16,033 gigapixels (or 48.1 terabytes, uncompressed) (), and scanned in at 0.46 microns per pixel, have been uploaded and are directly accessible from BrainMaps.org.
Figure 2 Total quantity of data scanned in, shown here as the distribution of image sizes at BrainMaps.org as of 06-18-2007 (a). The total size of the brain images is 16,435,723 MegaPixels, or 49.31 TeraBytes. The total number of images is 5264, with an average (more ...)
Online Navigation and Graphical User Interfaces
demonstrates navigation, using actual screenshots from a web browser using the AJAX GUI, through a Macaca mulatta dataset of Nissl-stained virtual slides at BrainMaps.org. The capability to interactively zoom in/out of and pan within individual virtual slides, and to rapidly jump to adjacent virtual slides, enables rapid navigation of virtual slides within a given dataset. Database integration permits both querying across datasets for various subsets that satisfy search query constraints and also for simple browsing of all available datasets, organized according to species or other criteria.
Figure 3 An example of navigation through virtual slides at BrainMaps.org using a Macaca mulatta Nissl dataset. All images are actual screenshots from a web browser and are what a visitor to BrainMaps.org would see. (a) An array of virtual slides for the dataset, (more ...)