In order to visualize and manipulate and analyze the collected data, we developed new tools, since no existing tools provide the necessary features for multi-brain region analysis. The main tools are: a data warping and submission tool; a 3D database browser; and a set of analysis tools for performing different quantitative studies across multiple data sets. They are all avaliable for download.

Visualization Tool (MorphMLViewer)

We created this tool to visualize  3D cellular and anatomical data of the rat brain collected at multiple levels and from multiple brain regions generated in multiple laboratories. The tool now is able to render  fully reconstructed cells as well as spatial organizations and show them at their exact location in the rat brain. The tool can directly use our database as well as open data files located on the user computer. More details here.

Clustering Tool

For quantification and statistical analysis of cell clusters we implemented an algorithm that determines the number of cell bodies within a spherical volume around each neuron. If the total number of cells contained increases linearly with the diameter of spheres, the cell population is considered to be homogeneously distributed (Null hypothesis). In contrast, any deviation from the linear function is an indicative of clusters (alternative hypothesis). The critical diameters and cell counts at which deviations occur represent the critical density and cluster size. Applying the critical density and cluster size as thresholds, the program is able to select and visualize neurons which are part of a putative cluster. The user also have the ability to detect spatial overlap between a found cluster and any given cell population. The tool can work in batch mode allowing users to call the algorithm from scripts or other programs (e.g. Matlab). More details here

Warping Tool (E-Brain Builder)

The E-Brain Builder (Warping) Tool allows data files to be loaded and 'warped' into the global coordinate system of the reference brain. It supports Microbrightfield's Neurolucida files and MDPlot's Accustage files. The warping algorithm requires several markers, uniquely identifiable points, to be labeled in both the data file and the reference, or scaffold brain, and produces an affine transformation which transform the data file into the reference coordinate space. These warp points are specified by clicking on particular markers in the data set and the corresponding points in the reference brain, both of which are displayed on screen at the same time. The warped data is stored in the database using the XML-based MorphML format; the tool also works in an off-line mode, for working on datasets on the local file system. More details here

Overlapping Analysis Tool

The overlapping analysis method is suited for comparison of density and overlap between two or more cell populations. The program divides the brain volume occupied by the datasets into boxes of a given size and counts the cell types within each box. If the cell number of each population within a box are equal or above a certain threshold the program shows this box in a different color indicating the spatial segregation or overlap. Similar approach has been used by He et al.,(1993), Alloway et al.,(1999) and Leergard et al.,(2000).  More details here