The Cortical Column Cajal Blue Brain Project 2014-08-28 | Visualization of the model cortical columnAuthors: Cajal Blue BrainVisit:http://cajalbbp.cesvima.upm.es
Simulation of a Random Sequential Adsorption (RSA) process in three dimensions Cajal Blue Brain Project 2014-08-28 | The simulation is performed using a sequential algorithm that first generates a random point that is the center of a sphere with a certain diameter. The diameters used in the simulations were randomly drawn from the probability distribution of the experimentally observed Feret’s diameters (Table 1). This distribution was found to be log-normal (Fig. 2). If the next simulated point with its corresponding Feret’s diameter does not overlap with previously generated points, then it is accepted. Otherwise it is rejected and another random point is generated. The process terminates when the desired number of points has been reached. (Published in Cereb Cortex. 2014 Jun;24(6):1579-88).Authors: Angel Merchán-Pérez, José-Rodrigo Rodríguez, Santiago González, Víctor Robles, Javier DeFelipe, Pedro Larrañaga and Concha BielzaVisit: http://cajalbbp.cesvima.upm.es
3D Reconstruction of structures visualized in FIB/SEM serial sections Cajal Blue Brain Project 2014-08-28 | Three-dimensional reconstruction of the extracellular Aß peptide, dystrophic neurites, and synaptic profiles found in the serial sections obtained with the FIB/SEM. Green objects, asymmetric synaptic junctions; red objects, symmetric synaptic junctions; brown objects, dystrophic neurites; yellow objects, extracellular Aß deposits. (Published in J Alzheimers Dis. 2013;34(4):995-1013).Authors: Lidia Blazquez-Llorca, Angel Merchan-Perez, Rodrigo Rodriguez, Jorge Gascon and Javier DeFelipeVisit: http://cajalbbp.cesvima.upm.es
Formation of a stack of serial sections obtained by FIB/SEM from the rat brain. Cajal Blue Brain Project 2014-08-28 | The video shows the formation of a stack of serial sections obtained by FIB/SEM from the neuropil of the rat somatosensory cortex (layer III). Synaptic junctions are then segmented and reconstructed. Asymmetric and symmetric synaptic junctions are shown in green and red respectively. The smallest spheres circumscribing the reconstructed synaptic junctions served to calculate the Feret’s diameters, which were used as an estimation of their size. An unbiased counting frame was also drawn to facilitate the quantification of the number of synapses per unit volume. The geometric centers or centroids of the synaptic junctions were also determined to indicate the spatial position of the synapses. The dimensions of the counting frame in this example were 7.16 x 4.58 x 3.98 µm. (Published in Cereb Cortex. 2014 Jun;24(6):1579-88).Authors: Angel Merchán-Pérez, José-Rodrigo Rodríguez, Santiago González, Víctor Robles, Javier DeFelipe, Pedro Larrañaga and Concha BielzaVisit: http://cajalbbp.cesvima.upm.es
Espina software for the segmentation of synaptic junctions from a stack of serial sections Cajal Blue Brain Project 2014-08-28 | In the main window the sections are viewed through the original plane of section, the x-y plane, as they were obtained by the dual-beam electron microscope (FIB/SEM). Other two windows show two alternative planes of section (x-z and y-z). A fourth window shows a 3D representation of the three orthogonal planes. The user can navigate within the image stack using the sliders located at the bottom of the window or by selecting the desired window and using the mouse wheel. In this example, two asymmetric synaptic junctions and one symmetric synaptic junction have been segmented and tagged. Some of their geometrical features, including their spatial position and Feret’s diameter, are determined by the same software. (Published in Cereb Cortex. 2014 Jun;24(6):1579-88).Visit: http://cajalbbp.cesvima.upm.esAuthors: Angel Merchán-Pérez, José-Rodrigo Rodríguez, Santiago González, Víctor Robles, Javier DeFelipe, Pedro Larrañaga and Concha Bielza
The Cortical Column Cajal Blue Brain Project 2014-08-28 | Flythrough visualization of the model juvenile rat cortical columnAuthors: Cajal Blue BrainVisit: http://cajalbbp.cesvima.upm.es
Rendered three dimensional reconstructions of synaptic profiles of rodent neocortex Cajal Blue Brain Project 2014-08-28 | Green objects represent asymmetric synaptic profiles and red objects symmetric synaptic profiles. All the objects shown were inside the counting brick or intersected one of the acceptance boundaries, without intersecting any of the exclusion planes. Note that every object can be individually identified and localized in the 3D space.Authors: Angel Merchán-Pérez, José-Rodrigo RodriguezVisit: http://cajalbbp.cesvima.upm.es
The Cortical Column Cajal Blue Brain Project 2014-08-28 | Visualization of the model activity of juvenile rat cortical columnAuthors: Cajal Blue BrainVisit:http: http://cajalbbp.cesvima.upm.es
Pyramidal cell and amyloid plaque in Alzheimers disease Cajal Blue Brain Project 2014-08-28 | Sequence of serial laser confocal images of an intracellular injected pyramidal cell (in red) and labeled amyloid plaque (in green) from the neocortex of a mouse model of Alzheimer's disease.Authors: Ruth Benavides-PiccioneVisit: http://cajalbbp.cesvima.upm.es
The Cortical Column Cajal Blue Brain Project 2014-08-28 | Visualization of the model juvenile rat cortical columnAuthors: Cajal Blue BrainVisit:http://cajalbbp.cesvima.upm.es
FIB SEM serial images of human brain from an Alzheimers disease patient Cajal Blue Brain Project 2014-08-28 | Sequence of 100 serial photomicrographs taken from a plaque located in layer IV of the frontal cortex of an Alzheimer's disease patient. The dominant feature is the presence of dystrophic neurites of different sizes and appearances. Synapses can be identified in the portions of the tissue not occupied by dystrophic neurites. Field width 17 µm, section thickness 20 nm. (Published in J Alzheimers Dis. 2013;34(4):995-1013).Authors: Lidia Blazquez-Llorca, Angel Merchan-Perez, Rodrigo Rodrıguez, Jorge Gascon and Javier DeFelipe.Visit: http://cajalbbp.cesvima.upm.es
Neuronize: A tool for building realistic neuronal cell morphologies Cajal Blue Brain Project 2013-04-15 | This tool presents a new technique for the generation of three-dimensional models for neuronal cells from the morphological information extracted through computed-aided tracing applications. The 3D polygonal meshes that approximate the cell membrane can be generated at different resolution levels, allowing balance to be reached between the complexity and the quality of the final model.Neuronize implements a novel approach to generate a realistic 3D shape of the soma from the incomplete information stored in the digitally traced neuron using a physical deformation technique.The addition of a set of spines along the dendrites completes the model, generating a final 3D neuronal cell suitable for its visualization in a wide range of 3D environments.
