Neuroinformatics in The Netherlands

Research Groups

UVA - SILS Center for Neuroscience - Prof. dr. W.J. Wadman
details

RUN - Department of Biophysics - Prof C.C.A.M. Gielen
details, linkGielen

VUA - Center for Neurogenomics and Cognitive Research (CNCR), Department of Experimental Neurophysiology - Prof A.B. Brussaard, Dr. A. van Ooyen, Dr. N. Cornelisse, Dr. R. van Elburg
details, linkENF, linkBrussaard, linkVanOoyen, linkCornelisse

UU - RMI - Clinical Neuroscience - Prof N.F. Ramsey
details, linkRamsey

RUG - Department of Mathematics and Computer Graphics - Prof J.B.T.M. Roerdink
details, linkRoerdink, linkGroup, linkBCN, linkGVC, linkRealityCentre

VUA - Center for Neurogenomics and Cognitive Research - Department of Experimental Neurophysiology - Dr. Jaap van Pelt
details, linkVanPelt

RUN - F.C. Donders Center - Prof P. Hagoort
details, linkHagoort

RUG - Institute of Mathematics and Computing Science - Research group Intelligent Systems - Prof.dr.sc.techn. N. Petkov, Dr. M. Biehl, Dr M. Wilkinson
details, linkPetkov, linkImaging

UVA - Department of Psychology - Prof J. van der Pligt UVA - Psychonomics - Prof J. Raaijmakers, Prof V. Lamme, Prof. A. Kok UVA - Developmental Psychology - Prof M. van der Molen, Prof. H. van der Maas, Prof K.R. Ridderinkhof UVA - Psychological Methods - Prof P. Molenaar
details

TUE - Department of Biomedical Engineering - Group Biomedical Image Analysis - Prof B.M. ter Haar Romeny
details, linkTerHaarRomeny

NIN - Netherlands Institute for Neurosciences - KNAW - Retinal Signal Processing Group - Dr. M. Kamermans
details, linkKamermans

UT - Department of Biomedical Signals and Systems - Group Neurotechnology - Prof. Dr. W.L.C. Rutten
details, linkRutten

VUA - MEG Centrum VUMC - Dr. Jan C. de Munck
details

F.C. Donders Centre for Cognitive Neuroimaging - Dr. Ole Jensen - principal investigator with responsibility for the MEG/EEG facilities
details, linkJensen

Institute for Adaptive and Neural Computation (Edinburgh, U.K.) - Dr. Mark van Rossum
details, linkVanRossum

TUE - Department of Biomedical Engineering - Technische Universiteit Eindhoven - Dr. P.A.J. Hilbers, Dr. ir. H.M.M. ten Eikelder, N. Kuijpers
details, linkHilbers, linkTenEikelder

UMC-Utrecht - Structural Neuroimaging Group of the Departments of Psychiatry, Rudolf Magnus Institute of Neuroscience - Dr. Hugo Schnack
details, linkSchnack

UU - Functional Neurobiology, Helmholtz Institute, Faculty Biology, Utrecht University. Prof. Dr. A.V. (Bert) van den Berg, Dr. M.J.M. (Martin) Lankheet, Dr. R.J.A. (Richard) van Weezel.
details, linkGroup

TU Delft - Neuromuscular Control Group (NMC) - Prof. Dr Frans C.T. van der Helm, Dr DirkJan Veeger, Dr Ir Alfred C. Schouten, Dr Ir Erwin de Vlugt, Ir David A. Abbink, Drs Wendy W. de Graaf, Ir J. Schuurmans.
details, linkGroup

UU Utrecht - Large Distributed Databases Research Group - Prof. Dr. Arno Siebes
linkSiebes

Universiteit Leiden - Leiden Institute for Brain and Cognition - Dr. Frank van der Velde, Prof. dr. Mark van Buchem
details, linkGroup

Radboud Universiteit - Nijmegen - Department of Biological Psychology - Dr. C.M. (Tineke) van Rijn
details, linkGroup

University of Amsterdam - SILS Center for Neuroscience - Dr. Francesco P. Battaglia
details, linkBattaglia

Leiden University Medical Center - Department of Radiology - Division of Image Processing - Julien Milles, Ph.D., Assistant Professor, Section leader Neuro-Image Processing
details, linkMilles

Peter Meijer - Seeing with sound - The vOICe
details, linkMeijer

Details

Research group:
UvA - SILS Center for NeuroScience
Prof. dr. Wytse J. Wadman
Postdoc: dr. Natalie Cappaert
AIOs: drs. Michiel Remme, drs. Hans Kager,
Foreign: Prof. dr. G.G. Somjen (Duke University, USA)

Research theme:
Regulation, plasticity and pathology of excitability in neurons and networks

Data resources and databases:

Patch-clamp data

Long term EEG and EP monitoring

Spike trains in-vivo and in-vitro

Voltage Sensitive dyes in-vitro

Ion concentrations

Gene array data

Acquisition and analysis tools:

Multi channel data recording and experimental control

Voltage Sensitive dyes for membrane voltage recordings

MATLAB, IGOR, pClamp

Home made universal experiment control software (C++, Modula)

Modeling tools:

NEURON, cellular, small network, glia-neuron interactions

PDP++, network models on learning (mainly for teaching)

MATLAB

Courses:

2nd year physics: membrane neurophysics

3rd year biology: Computational Neuroscience (3 weeks theory, 6 weeks simulation)

Master Neurobiology: Advanced Neuro Biology

Research group:
KUN - Department of Biophysics - Prof C.C.A.M. Gielen

Research theme:
Neuronal information processing in biological and artificial neural networks

Data resources and databases:

Action potentials from single-unit recordings in the monkey auditory system and oculomotor system (time of action potentials related to auditory/visual stimuli and eye/head movements)

Models and simulated responses of various types of neurons

Models and simulated responses of various types of neuronal networks

Acquisition tools:

Single-unit recordings in trained monkeys

Analysis tools:

Matlab

Software in C++

Modeling tools:

Software written in Matlab and C++

Research group:
VUA - Institute for Neurosciences, Department of Experimental Neurophysiology - Prof A.B. Brussaard

Research theme:
Electrophysiological research in brain slices
Synaptic vesicle release
Neural development, Neuronal form & function, Other lines.
Microcircuits for the Prefrontal Cortex, Part of the CASPAN (Computational Analysis of Spatiotemporal Patterns of Activity in Neuronal Networks) project

Data resources and databases:
Activity of synapses, neurons, microcircuits and neural networks

Ion currents and (sub)cellular morphology

Synaptic (plasticity) mechanisms

Voltage / current clamp data in Axon binary files

Mostly using using NeuroDB, ModelDB

Acquisition and analysis tools:

Pclamp / HEKA software (for Axon amplifiers and HEKA amplifiers

Modeling tools:

Research group:
UU - RMI - Clinical Neuroscience - Prof N.F. Ramsey

Research theme:
Clinical Neuroscience, Functional brain imaging in neurological (epilepsy) and psychiatric (schizophrenia) disorders. Research on mechanisms of fMRI, experimental and task design, neurophysiology of executive functions and language

Data resources and databases:

FMRI data sets and EEG data sets stored as raw data in LINUX data storage and processing systems

Acquisition tools:

MRI and direct cortical recording systems

Analysis tools:

Own programs in IDL, Matlab, C, Minc (Montreal), SPM, FSL toolbox

Modeling tools:

IDL and Matlab signal processing and image processing toolboxes

Task design: MEL, E-prime, Presentation

Research group:
RUG - Department of Mathematics and Computer Graphics - Prof J.B.T.M. Roerdink Participation in BCN via the Neuroimaging Centre of the University of Groningen.

Research theme:
Scientific Visualization and Computer Graphics, Computational Geometry and Geometric Modeling

Data resources and databases:

Type of data: 2D-3D image data (MRI, fMRI, PET, EEG, EMG).

Data acquired at the Neuroimaging Centre are stored and archived at the Storage Area Network of the Computing Centre of the University of Groningen.

Data acquired at the Academic Hospital Groningen are stored locally at the Department of Radiology and the Pet Centre

Acquisition tools:
At Academic Hospital Groningen:

Neuroimaging Centre of the University (3T Philips MRI scanner),

Department of Radiology (1.5 T MRI scanner)

PET Centre (several PET cameras)

Analysis tools:

General image processing software,

Signal analysis software,

Wavelet routines (Matlab tool boxes, IDL, ImageJ, in-house software in C++ and Java),

Volume rendering software (AVS, VTK, Amira),

Software for statistical analysis of functional neuroimaging data (SPM toolbox under Matlab, in-house software),

Brain imaging software (Brain Voyager), EEG analysis software (Besa).

Visualization facilities include a CAVE Virtual Environment and a Reality Theater, located in the Visualization Center of the University.

Modeling tools:

Multidimensional signal processing,

Fourier and wavelet transforms,

Geometrical object modeling,

Mathematical morphology,

Pattern recognition,

Graph theory,

Network modeling,

Statistical models for brain activation.

Research group:
NIN - Netherlands Institute for Neurosciences - KNAW - Research Group Neurons & Networks - Dr. Jaap van Pelt, Dr. G.J.A. Ramakers, Dr. I. Vajda, Dr. R. Koene, Dr. M.A. Corner, Dr. R.E. Baker

Research theme:
Plasticity and information processing in neurons and networks

Data resources and databases:

Data sets of multi-electrode firing activity in cultured neuronal networks

High-resolution time-lapse video microscopy of outgrowing neurons in tissue culture

3D reconstructions of neuronal branching patterns of pyramidal and multipolar nonpyramidal rat cortical neurons

Acquisition tools:

Semi-automatic dendrite reconstruction system

Multi-electrode array action potential recording systems

High resolution time lapse video microscopy system

Analysis tools:

Home-made software tools (Fortran) for the reconstruction and analysis of dendritic branching patterns

Home-made software tools (Fortran, Matlab) for the analysis of multi-electrode spike trains

Modeling tools:

Home-made software tools (Fortran) for modeling the outgrowth and the geometry of dendritic branching patterns

Home-made software tools (C++) for modeling the firing dynamics and spatio-temporal patterning in neuronal networks

Home-made software tools (Neuron) for modeling the signal integration and action potential generation in neurons with specified geometries

Research group:
KUN - F.C. Donders Center - Prof P. Hagoort

Research theme:
Cognitive Neuroscience Functional brain imaging, focusing on cognition in perception, action, memory and language

Data resources and databases:

2D and 3D FMRI, EEG and MEG data sets obtained in experiments on perception, action, memory and language.

Advanced analysis tools for source localization

Models and simulated responses of various types of neuronal networks

Acquisition tools:

1.5 and 3.0 Tesla fMRI scanners

A whole-head, 151-channel MEG scanner

Three EEG laboratories

Integrated stimulus presentation facilities

Analysis tools:

General image processing software

Brain Voyager for analyzing brain imaging data.

EEG analysis software

Modeling tools:

Software written in Matlab and C++

Pattern recognition,

Neural Network modeling,

Statistical models for finding temporal structure in brain-imaging signals.

Research group:
RuG - Institute of Mathematics and Computing Science - Research group Intelligent Systems - prof.dr.sc.techn. N. Petkov, dr. M. Biehl, dr M. Wilkinson Links: www.cs.rug.nl/~petkov, www.cs.rug.nl/~imaging

Research theme:
Development of models of the visual cortex and their use in computer simulations and practical computer vision algorithms (Petkov). Fundamentals of neural networks and machine learning (Biehl).

Data resources and databases:

Database of natural images with associated subjectively defined object contour maps. This database can be used for performance evaluation of computer models of contour detection mechanisms.

Acquisition tools:
n.a.

Analysis tools:
n.a.

Modeling tools:

Computer programs (mostly in MatLab) for the simulation of populations of orientation selective visual neurons (simple, complex, and grating cells, augmented with non-classical receptive field modulation).

Computer algorithms for texture and contour detection.

Some recent publications:
C. Grigorescu, N. Petkov, and M. A. Westenberg. Contour and boundary detection improved by surround suppression of texture edges, J. Image and Vision Computing, 2004, in press.
C. Grigorescu and N. Petkov. Distance sets for shape filters and shape recognition, IEEE Trans. on Image Processing, 2003, 12 (10) 2003, 1274-1286.
C. Grigorescu, N. Petkov, and M. A. Westenberg. Contour detection based on non-classical receptive field inhibition, IEEE Trans. on Image Processing, 12 (7) 2003, 729-739.
N. Petkov and M. A. Westenberg. Suppression of contour perception by band-limited noise and its relation to non-classical receptive field inhibition, Biological Cybernetics, 88, 2003, 236--246.
S.E. Grigorescu, N. Petkov and P. Kruizinga. Comparison of texture features based on Gabor filters, IEEE Trans. on Image Processing, Vol. 11, No. 10, pp.1160-1167, 2002.
P. Kruizinga and N. Petkov. Nonlinear Operator for Oriented Texture. IEEE Transactions on Image Processing, 8 (10), 1999, 1395-1407.
N. Petkov, and P. Kruizinga. Computational models of visual neurons specialized in the detection of periodic and aperiodic oriented visual stimuli: bar and grating cells, Biological Cybernetics, 76 (2), 1997, 83-96.

Research group:
UVA - Department of Psychology - Prof J. van der Pligt UVA - Psychonomics - Prof J. Raaijmakers, Prof V. Lamme, Prof. A. Kok UVA - Developmental Psychology - Prof M. van der Molen, Prof. H. van der Maas, Prof K.R. Ridderinkhof UVA - Psychological Methods - Prof P. Molenaar

Research theme:
Cognitive Processes, Arousal and Information Processing, Brain and Development, Developmental Processes.

Data resources and databases:

EEG, ERP, MEG, fMRI data sets obtained in experiments on perception, attention, memory, cognitive control

Tools for ERP source analysis, single trial and habituation analysis, adaptive signal analysis (for interaction between cortical areas)

Models and neural networks, simulation data

Acquisition tools:

fMRI (1.5 Sonata, 3T Philips)

EEG (Biosemi)

MEG (CTF)

TMS (magstim)

single en multi unit recordings equipment (custom build)

basic histological unit, Neural Networks (Python, C++)

64 channel BrainProducts EEG DC system

EEG (NeuroScan)

eye-tracking (iView)

ECG

integrated stimulus presentation facilities

Analysis tools:

ASA (Advanced Source Analysis, ANT Software)

Redux

Soft

dedicated software

Modeling tools:

Software in Matlab, C++, SPM, Python, BrainVoyager,

Transform techniques (Fourier, wavelet)

neural networks

recursive filtering techniques

Research group:
TUE - Department of Biomedical Engineering - Group Biomedical Image Analysis - Prof B.M. ter Haar Romeny

Research theme:
Medical imaging, pattern recognition and segmentation Computer vision

Data resources and databases:

Type of data: 2D, 3D, 4D and tensorial image data (CT, MRI, fMRI, PET, US, SPECT, DTI, 2-photon fluoroscopy and confocal microscopy);

We are connected by secure ftp to the clinical imaging database of the University Hospital Maastricht (access to several millions of images), the Eindhoven Maxima Medical Center and the Magnetic Resonance Laboratory of TUE

Acquisition tools:

MathVisionTools, our own library written in Mathematica;

EasyScil, Philips research libraries for medical workstation development

Volume rendering software: EasyVision, Vital Images, many own routines

Mathematica, for general symbolic and numerical calculations

Packages for wavelets, statistics, signal analysis, image processing

C++, Java, Matlab

Modeling tools:

Primarily Mathematica (www.wolfram.com)

Research group:
NIN - Netherlands Institute for Neurosciences - KNAW - Retinal Signal Processing Group - Dr. M. Kamermans

Research theme:
Retinal information processing

Data resources and databases:

Activity of retinal neurons, synaptic mechanisms, synaptic transfer functions, synaptic plasticity and retinal network behavior

Acquisition tools:

Single cell electrophysiology (patch-clamp, intracellular and extracellular) in retinal slices, isolated retinas, dissociated retinal neurons and cultured cells.

Multi-electrode recording in retinal slices and isolated retinas

Behavioral experiments

Morphology (EM, confocal)

Vital imaging (Ca-dyes)

Modeling tools:

Visual C++

Matlab

Research group:
University of Twente - Biomedical Signals and Systems - Neurotechnology, Prof. dr. W.L.C. Rutten

Research theme:
Live learning neural networks

Data resources and databases:

Time series of firing neurons in cultured networks of cortical rat neurons. Measured by planar MultiElectrode Arrays (home-built) with 61 electrodes (spacing 80 um). The network activity may be spontaneous or induced (training experiments). The layout of the network may be random (unpatterned networks) or patterned. The action potentials are detected by level detection or shape recognition and stored digitally as individual wave shapes, or as events (time stamping).

Acquisition tools:

Home built 16- and 64-channel MEA electronic data-acquisition and stimulation systems under control of Labview.

Analysis tools:

Matlab, C

Modeling tools:

Matlab, Neuron, Ansys, Femlab

Courses and training:

Academic regular and individually tailored courses on Neurophysiology, Stochastic processes, Nonlinear modeling, Neurotechnology, Signal analysis, Electrophysiological Signals and Bioelectricity.

On site training in culturing of neurons, patterning of networks, cleanroom MEA-technology.

Research group:
VUA - MEG Centrum VUMC - Dr. Jan C. de Munck

Research theme:
Time series analysis of MEG/EEG, EEG/fMRI, MEG/EMG data

Data resources and databases:

Acquisition and Analysis tools:

MEG data (CTF system)

fMRI data (Simens Sonata 1.5 T)

simultaneous EEG/fMRI (MicroMED EEG system).

Modeling tools:

C/C++, MatLab, CTF software, a lot of tools are home-made

Courses:

brain imaging principles

time series analysis

MEG/EEG inverse modelling

Research group:
F.C. Donders Centre for Cognitive Neuroimaging - Dr. Ole Jensen - principal investigator with responsibility for the MEG/EEG facilities
http://oase.uci.ru.nl/~olejen

Research theme:
Measuring and modeling electromagnetic brain activity

Oscillatory brain activity in perception and motor action

The role of oscillatory brain activity in working memory and memory consolidation

Physiologically realistic computational models accounting for oscillatory activity.

Data resources and databases:

EEG and MEG data from humans. Type of storage: RAID + DVD

Acquisition and Analysis tools:

MEG: CTF, 151 sensors

EEG: Amplifiers from BrainVision, 32 - 128 channels (also 64 channels MR compatible EEG systems).

Modeling tools:
Various models written in Matlab for computational modeling.
Data analysis of EEG/MEG data: Locally written Matlab toolbox:
(See http://www.ru.nl/fcdonders/fieldtrip/ - Freely available, GPL)
Includes:

readers for common EEG/MEG systems

event-related responses

time-frequency analysis (wavelets, FFT)

beamforming techniques for source modelings (LCMV, DICS)

randomization statistics

various visualization tools

Courses:
At the F.C. Donders Centre we have the yearly courses:

Toolkit I (5 days, summer):
Basic neuroimaging (EEG, MEG, fMRI, PET, TMS, basic analysis)

Toolkit II (3 days, spring):
Advanced analysis of EEG/MEG data
We use our local Matlab toolbox, FieldTrip http://www.ru.nl/fcdonders/fieldtrip/
Includes time-frequency analysis, source modeling, randomization statistics, visualization)

Research group:
Edinburgh NeuroInformatics
Mark van Rossum

Research theme:
Computational neuroscience, Databases, NeuroEngineering
(Projects, People)

Data resources and databases:
Multiple

Acquisition and Analysis tools:
Multiple

Modeling tools:
Catacoomb, Flytrap, Neuron, NeuronC, Matlab, in house software

Courses:
We are running UK's Doctoral Training Centre Neuroinformatics. This is a 4 year PhD program, one year of which is training. Partial funding available for EU students.

Research group:
TUE - Department of Biomedical Engineering - Technische Universiteit Eindhoven - Dr. P. Hilbers, Dr. ir. H.M.M. ten Eikelder, N. Kuijpers

Data resources and databases:
None

Acquisition and Analysis tools:
C++ Programs, Matlab, Python

Modeling tools:
C++ simulator, Matlab, PumMa, Genesis

Research group:
UMC-Urecht - Structural Neuroimaging group of the Departments of Psychiatry, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht - Dr. Hugo Schnack.

Research theme:
Research on development and disease related changes of the human brain, in healthy people and psychiatric patients. Both patient-based research and methodological research are conducted. The group consists of psychologists, physicians (psychiatrists), medical biologists, physicists, computer scientists.

Data resources and databases:
Magnetic resonance imaging (MRI) scans of the whole brain (several types, a.o., high-resolution anatomical scans and diffusion tensor imaging (DTI) scans). The scans are saved as three-dimensional image files on hard-disk and magneto-optical disk / cdrom / dvd. Several data formats are supported, the main format being MINC.

Acquisition and Analysis tools:
The data are acquired on MRI scanners (Philips); The data are processed with in-house developed software and software from collaborating sites (mainly image processing programs).

Modeling tools:
Structural Equation Modeling: Mx.

Courses and training:
Workshop on MRI brain image processing and data analysis for researchers in, e.g., psychiatry groups.

Research group:
UU - Functional Neurobiology, Helmholtz Institute, Faculty Biology, Utrecht University Prof. Dr. A.V. (Bert) van den Berg, Dr. M. J.M. (Martin) Lankheet, Dr. R.J.A. (Richard) van Wezel.

Research theme:
Our research concerns perception of spatial relationships and how that is supported by active exploration of eye, head and body movement. Our research methods cover all neurobiological and behavioural methods, besides mathematical and biophysical theory and simulation studies.

Data resources and databases:
data from single unit (multi-electrode) recordings in cortical areas - fMRI data - eye movement data - human psychophysical data - VEP

Acquisition and Analysis tools:
(multi-) electrode single unit recordings and behavioural control - eye-movement recordings - psychophysical techniques - haptic force feed-back

Modeling tools:
Matlab - Mathematica - C

Courses and training:
Bachelor level: - Computational Animal Biology - Neuroscience - Functional Neurobiology Master level: -Biophysics of Perception and Action

Research group:
TU Delft - Neuromuscular Control group (NMC) - Prof. Dr Frans C.T. van der Helm; Dr DirkJan Veeger (associate); Dr Ir Alfred C. Schouten (postdoc); Dr Ir Erwin de Vlugt (postdoc); PhD students: Ir David A. Abbink, Drs Wendy W. de Graaf, Ir J. Schuurmans
http://www.3mE.TUDelft.nl/nmc

Research theme:
At the Delft Neuromuscular Control group (NMC) system identification and modelling techniques are combined in an attempt to reveal the neural control properties of the human motor system. Mechanical perturbation experiments and techniques used in the field of control engineering are used to identify and quantify spinal reflex pathways. Modelling includes linear and non-linear lumped parameter models as well as detailed neural models in closed loop with musculoskeletal models. The techniques are applied to studying the mechanisms of neuromuscular disorders like Parkinson's disease, CVA and CRPS.

Data resources and databases:
Datasets from 1 DOF and 2 DOF mechanical perturbation experiments on shoulder, wrist and ankle. Measured variables: user applied force/torque, disturbance force/torque, position, sEMG, microneurography.

Acquisition and Analysis tools:
Acquisition:
2 DOF shoulder manipulator (hydraulic)
1 DOF shoulder manipulator (hydraulic)
1 DOF ankle manipulator (electric)
1 DOF wrist manipulator (electric)
Delsys sEMG
DSPACE
Analysis:
MATLAB identification routines for Spectral analysis, Parameter estimation, Wavelet analysis

Modeling tools:
Custom simulation software in MATLAB, Simulink, NEURON (rarely)

Courses and training:
M.Sc courses relevant to this field:
System Identification and Parameter Estimation
The Human Controller
Human Movement Control

Research group:
Leiden Institute for Brain and Cognition. Contact neuroinformatics: Dr. F. van der Velde

Research theme:
Computational Cognitive Neuroscience on perception, memory, action, language. Functional and structural brain imaging. Information processing in neural networks.

Data resources and databases:
FMRI and MRI data, EEG data. FMRI and MRI imaging data (format: dicom, converted to NIFTI for post processing purpose). Storage: on hard disks (high safety level), automatic daily back up on mirror hard disk.

Acquisition and Analysis tools:
Neuroimaging with 1.5T and 3T Philips MRI scanner (7T Philips MRI scanner in near future), SPM, FSL Analysis Software, Brainvoyager.

Modeling tools:
C++ software for neural models.

Courses and training:
In preparation

Research group:
Radboud University Nijmegen, NICI, Department of Biological Psychology.
Head of the department: Prof Dr. AML Coenen; Senior researchers: Dr ELJM van Luijtelaar, Dr JHR Maes, Dr E Maris, Dr CM (Tineke) van Rijn (formal contact: rijn@nici.ru.nl); Junior researcher: Dr MLA Jongsma; PhD students: Drs JM Knippenberg, Drs EY Sitnikova, Drs IA Westmijse.

Research theme:
Cognitive electro-physiological research in rats and in humans. The main research questions are related to cognitive functions in relation to attention, learning and memory. The themes have in common that they are covered by the phrases 'interactions within neuronal circuits' and 'plasticity'. Human and animal research is complementary.

Data resources and databases:
In freely moving rats: invasive techniques, multichannel recordings, depth electrodes. In humans: multichannel EEG recordings. Long term (days in rats) EEG and Event Related Potential recordings. Cognitive manipulations. Simultaneous recordings psychological variables (rats: skinner boxes) and physiological variables (EEG/ERP) Neuropharmacological manipulations.

Acquisition and Analysis tools:
Data acquisition in Rats: Windaq; in Humans: Neuroscan;
Data analysis: Brain Vision.

Modeling tools:
Software written in Matlab and C++ (wavelet denoising, by R Quian Quiroga; Granger causality, modeling hidden variables, unraveling temporal relations, by the groups of Saratov Sate University, Russia).

Research group:
Dr. Francesco P. Battaglia - Assistant Professor
SILS Center for Neuroscience, University of Amsterdam,
Kruislaan 320 - 1098SM Amsterdam, the Netherlands
(E) battagli@science.uva.nl; (Ph) +31-(0)20-5257968; (F) +31-(0)20-5257709

Research theme:
Cortico-hippocampal communication
Dynamics of slow wave sleep
Representations of space in rodents
Models of memory consolidation

Data resources and databases:
In vivo recordings of ensembles of 20-100 neurons in cerebral cortex (mostly prefrontal) and hippocampus in behaving rats and mice
Local Field potentials from same recordings sessions as above tracking of behavior

Acquisition and Analysis tools:
multi-electrode/multi-tetrode recording from freely moving rats and mice
Signal processing code in Python/C/C++ (for spike sorting in particular)
Home-written MATLAB analysis tools for neural ensemble data and local field potentials, with several C/C++ extensions
Analysis database
Experiment database (in MySQL) covering from data acquisition to analysis (under development)
GUI for spike sorting (Python/QT, under development)

Modeling tools:
Models of hippocampal place cells/entorhinal grid cells in Matlab/C/C++
Models of memory consolidation inspired to machine learning and computational linguistics

Research group:
Julien Milles, Ph.D. Assistant Professor
Section leader Neuro-Image Processing - Division of Image Processing
Department of Radiology, 1-C2S
Leiden University Medical Center
Albinusdreef 2, PO Box 9600, 2300 RC Leiden, the Netherlands
(T) +31 (0)71 526 5342; (F) +31 (0)71 526 6801
(E) J.Milles@lumc.nl; (URL) http://www.lkeb.nl

Research group:
LUMC - Division of Image Processing (LKEB)
Prof. J.H.C. Reiber, Dr. J.R. Milles (contact), Dr. L. Ferrarini, Prof. M.A. van Buchem

Research theme:
Medical image processing, functional biomarkers, complex networks theory, neurodegenerative diseases

Data resources and databases:
MRI, DTI and fMRI data, originating from scanners with field strength ranging from 1.5 to 7T. Access to the ADNI database.

Acquisition and Analysis tools:
Neuroimaging with 1.5T, 3T and 7T Philips MRI scanner, SPM, FSL Analysis Software, locally developed software packages.

Modeling tools:
Locally developed software packages, primarily developed in Matlab and C/C++

Company:
Seeing with sound - The vOICe
Peter Meijer, Ph.D.
(E) feedback@artificialvision.com
(URL) http://www.artificialvision.com/

Research theme:
Artifial Vision for the Totally Blind
Together with research partners around the world investigate adult neural plasticity, particularly in relation to human vision and human blindness.
Sensory substitution, Computer vision, Artificial neural networks, Augmented reality, Neural plasticity, Nonlinear modeling and Analog circuit simulation.

Acquisition, Analysis and Modeling tools:
Dynamic neural networks, augmented reality software, etc.