Active projects

  • CeBMI: UNIVERSITY-INDUSTRY EDUCATIONAL CENTRE IN ADVANCED BIOMEDICAL AND MEDICAL INFORMATICS (KNOWLEDGE ALLIANCE) web
    • Funding agency: European Commission. Erasmus+
    • Duration: January 2020 - December 2022
    • Objective: Development of an educational Centre in advanced Biomedical and Medical Informatics. The centre will use new innovative cloud-based technology to support the creation and delivery of new courses in BMI, which is a very dynamic field undergoing rapid evolution and centrally featured in health reforms across Europe.
  • Human Brain Project web
    • Funding agency: European Commission. H2020 FET Flagship Project
    • Tasks: RUP 7.3.2, SGA1-T7.3.2, SGA1-T1.4.2, SGA2-T1.4.4, SGA2-T7.3.8, SGA2-T7.3.9
    • Duration:
      • RUP: September 2013 - March 2016
      • SGA1: April 2016 - March 2018
      • SGA2: April 2018 - March 2021
  • Cajal Blue Brain web
    • Funding agency: Ministerio de Ciencia e Innovación
    • Duration: 2009 - 2019
  • VIANA: VIsualización ANalítica Avanzada
    • Funding agency: Ministerio de Economía y Competitividad (MINECO)
    • Duration: Jan 2018 - Dec 2020

Recent past projects

  • NAVAN: Nuevos Avances en Visualización Analítica
    • Funding agency: Ministerio de Economía y Competitividad (MINECO)
    • Duration: Jan 2015 - Dec 2017 (Extended until Jun 2018)
  • RASimAs web

For a full list of past projects you can follow this link

Tools

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Pyramidal Explorer

A new tool to interactively explore and reveal the detailed organization of the microanatomy of pyramidal neurons.

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NeuroScheme

NeuroScheme is a tool that allows users to navigate through circuit data at different levels of abstraction using schematic representations.

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MSPViz

MSPViz is a new tool for for the analisys of structural plasticity models using abstract levels and a set of views composed by schematic representations on each level.

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NeuroTessMesh / NeuroLOTs

NeuroTessMesh / NeuroLOTs is a set of tools and libraries that allow creating neuronal meshes from a minimal skeletal description.

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ViSimpl

ViSimpl integrates a set of visualization and interaction tools that provide a multi-view visual analysis of brain simultation data.

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VMetaFlow

VMetaFlow is a web-based tool that integrates a meta-descriptive language and a visual environment for coordinated view application design.

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ClInt Explorer

ClInt Explorer is an application that uses supervised and unsupervised learning techniques to cluster neurobiological dataset.

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Vishnu

Vishnu tool provides information integration and storage from multiple sources, specimens and scales. Vishnu provides an interface to query, filter and extract the stored data to be explored with the integrated analysis applications: DC Explorer, Pyramidal Explorer and ClInt Explorer.

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Projectional Radiograph Simulator

This simulator provides a safe environment where the procedure can be rehearsed, reducing all kinds of radiological risk to the patient or even the radiographer.

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NeuroEditor

NeuroEditor is a software tool for the visualization and edition of morphological tracings that offers manual edition capabilities together with a set of algorithms that can automatically identify potential errors in the tracings.

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Neuronize

Neuronize is a software tool for the interoperability between neuronal mesh representation (Imaris) and tracing representation (Neurolucida)

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DeepSpineNet

DeepSpineNet is a GUI application for semiautomatic reconstruction of dendritic shafts and spines from microscopy images.

Libraries

  • FiReS: property management for Filtering, Retrieval and Search

    • Description: FiReS is a library that allow registering type-independent properties in objects. FiReS also provides tasks that can use the registered properties for filtering, search, sorting operations over a set of objects.
    • Links:

  • NeuroLOTs: Libraries and tools for generating neuronal meshes

    • Description: NeuroLOTs is a set of libraries and tools for generating neuronal meshes and for visualizing them at different levels of detail using GPU-based tessellation. Providing tools for the generation of 3D polygonal meshes that approximate the membrane of neuronal cells, from the morphological tracings that describe the morphology of the neurons. The 3D models can be tessellated at different levels of detail, providing either homogeneous or adaptive resolution along the model. The soma shape is recovered from the incomplete information of the tracings, applying a physical deformation model that can be interactively adjusted.
    • Links:

  • nsol: neuroscience objects library

    • Description: nsol is a library that provides data structures to handle basic neuroscientific data, mainly cortex morphologies and structures as Spine, Soma, Neuron, Colum, etc... It also provides some readers and writers to load and store dataset.
    • Links:

  • scoop: simple color palettes and mappers

    • Description: scoop is a library for color palettes and color mappers based on QColor.
    • Links:

  • ReTo: Render auxiliary Tools

    • Description: ReTo provides tools for Camera, Shader manager, Picking funcionallity, Object Loader, Spline navegation and a TextureManager.
    • Links:

Publications

Latest publications

  • Aaron Sujar, Graham Kelly, Marcos García, Franck P. Vidal, "Interactive teaching environment for diagnostic radiography with real-time X-ray simulation and patient positioning", International Journal of Computer Assisted Radiology and Surgery, Volume 16, 2021, Pages 152, ISSN 1861-6410, https://doi.org/10.1007/s11548-021-02499-7
  • Sergio E. Galindo, Pablo Toharia, Óscar D. Robles, Eduardo Ros, Luis Pastor, Jesús Garrido, "Simulation, visualization and analysis tools for pattern recognition assessment with spiking neuronal networks", Neurocomputing, Volume 400, 2020, Pages 309-321, ISSN 0925-2312, https://doi.org/10.1016/j.neucom.2020.02.114
  • Diana Furcila, Marcos García, Cosmin Toader, Juan Morales, Antonio LaTorre, Ángel Rodríguez, Luis Pastor, Javier DeFelipe, Lidia Alonso-Nanclares "InTool Explorer: An Interactive Exploratory Analysis Tool for Versatile Visualizations of Neuroscientific Data", Frontiers in Neuroanatomy, Volume 13, 2019, DOI: https://doi.org/10.3389/fnana.2019.00028
  • Aaron Sújar, Graham Kelly, Marcos García and Franck P.Vidal "Projectional Radiography Simulator: an Interactive Teaching Tool", Computer Graphics and Visual Computing (CGVC) (2019, Sept), Eurographics Association, ISBN: 978-3-03868-096-3, DOI: https://doi.org/10.2312/cgvc.20191267
  • Isabel Vidaurre-Gallart, Aaron Sújar and Marcos García "Design and implementation of a volumetric merging tool", In Proceedings of the XXVIII Spanish Computer Graphics Conference (2018, June), Eurographics Association, ISBN: 978-3-03868-067-3, DOI: https://doi.org/10.2312/ceig.20181154
  • Aaron Sujar, Juan Jose Casafranca, Antoine Serrurier, Marcos Garcia, "Real-time animation of human characters’ anatomy", Computers & Graphics, Volume 74, 2018, Pages 268-277, ISSN 0097-8493, https://doi.org/10.1016/j.cag.2018.05.025
  • Juan J. Garcia-Cantero, Juan P. Brito, Susana Mata, Sofia Bayona and Luis Pastor. "NeurotessMesh: A tool for the Generation and Visualization of Neuron Meshes and Adaptive on-the-Fly Refinement". Front. Neuroinform., 22 June 2017. DOI: https://dx.doi.org/10.3389/fninf.2017.00038
  • Sergio E. Galindo, Pablo Toharia, Oscar D. Robles, Luis Pastor. "ViSimpl: Multi-View Visual Analysis of Brain Simulation Data". Front. Neuroinform., 07 October 2016. DOI: https://dx.doi.org/10.3389/fninf.2016.00044
  • Pablo Toharia, Oscar D. Robles, Isabel Fernaud-Espinosa, Julia Makarova, Sergio E. Galindo, Angel Rodriguez, Luis Pastor, Oscar Herreras, Javier DeFelipe and Ruth Benavides-Piccione. "PyramidalExplorer: A New Interactive Tool to Explore Morpho-Functional Relations of Human Pyramidal Neurons". Front. Neuroanat., 06 January 2016. DOI: https://dx.doi.org/10.3389/fnana.2015.00159
  • Pablo Toharia, Juan Morales, Octavio de Juan, Isabel Fernaud, Angel Rodríguez, and Javier DeFelipe "Musical Representation of Dendritic Spine Distribution: A New Exploratory Tool. Neuroinformatics. 2014; 12(2): 341–353. 2014 Jan 7. DOI: 10.1007/s12021-013-9195-0
An exhaustive list of publications can be found here

People

  • Luis Pastor

    Professor. ETSII-URJC, CCS

  • Sofía Bayona

    Faculty. ETSII-URJC, CCS.

  • Marcos García

    Faculty. ETSII-URJC, CCS

  • Susana Mata

    Faculty. ETSII-URJC, CCS.

  • Óscar David Robles Sánchez

    Faculty. ETSII-URJC, CCS.

  • Ángel Rodríguez

    Faculty. ETSIINF-UPM. CCS

  • Pablo Toharia

    Faculty. ETSIINF-UPM, CCS.

  • Juan Pedro Brito Méndez

    Postdoctoral researcher. CCS

  • Francisco González de Quevedo

    Project Manager. URJC

  • José Miguel Espadero

    System admin. URJC.

  • Aaron Sujar Garrido

    Assistant Professor

  • Cristian Rodíguez Bernal

    PhD Student. URJC

  • Gonzalo Bayo Martínez

    PhD Student.URJC

  • Isabel Vidaurre

    PhD Student. URJC

  • Cosmin Toader

    PhD Student. URJC

  • Iván Velasco

    PhD Student. URJC

  • Sergio E. Galindo Ruedas

    PostDoctoral external collaborator

  • Juan José García Cantero

    PostDoctoral external collaborator