Hippocampus 3D Model – Availability of Data

            Supplementary data for Ropireddy D, Bachus SE, Ascoli GA (2012) Non-Homogeneous Stereological Properties of the Rat Hippocampus from High-Resolution 3D Serial Reconstruction of Thin Histological Sections. Neuroscience (http://dx.doi.org/10.1016/j.neuroscience.2011.12.055)


The data files corresponding to the high resolution three dimensional (3D) structure of the rat hippocampus that we reconstructed from histological sections can be downloaded from our server. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files.


Links to download the files


All the files are uploaded into a common folder that can be accessed here. Within this parent folder there are five sub-folders (NisslImages, Tracings, VoxelDB, VRML, and 3DHippocampusMovie).



Hippocampus Nissl Images


The high resolution histological Nissl images obtained at 16 μm inter-slice distance for the Long-Evans rat hippocampus can be downloaded here. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files (part1.rar, part2.rar, part3.rar, part4.rar, part5.rar, part6.rar, part7.rar).



Hippocampus Layer Tracings


The seven hippocampus layers ‘ML, ‘GC’, ‘HILUS’ in DG and ‘LM’, ‘RAD’, ‘PC’, ‘OR’ in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded here. In order to open and view the XML tracing files, decompress all the Nissl rar archives and the zipped tracings in one directory and open the master Reconstruct file (Series_10.ser) in Reconstruct. The instructions for using this tool are also provided at Synapse web.


Hippocampus VoxelDB


The 3D hippocampus reconstructed is volumetrically transformed into 16 μm sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file archive file can be downloaded here (Hippocampus-VoxelDB.txt


The details of the organization of this voxel database file are discussed in this README file.


3D Surface Renderings


Surface rendering (or triangulation) VRML files of the DG and CA layers can be downloaded here. This is a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene.


3D Hippocampus Movie


   This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites. This movie can be downloaded here.