Lab visits

Lab visit description

Are you interested in brain imaging and non-invasive brain stimulation, and would you like to broaden your horizon by joining a rich and diverse hands-on research experience? Using MRI and transcranial magnetic stimulation (TMS), we investigate the effects of motor learning and aging on the human brain. In close collaboration with your colleagues and the participants, you will support ongoing MRI and TMS research experiments, learn about various MRI research techniques, and get the chance to build a solid skillset in TMS. 

You will be working with Prof. dr. Koen Cuypers and his Ph.D. students at the university of Hasselt (REVAL) 

Scientific methods offered to the student

• Non-invasive brain stimulation (TMS, tDCS, tACS, etc)
• Magnetic Resonance Imaging techniques
• Advanced data analysis

Application details

Application has to contain the following documents:

• Recommendation letter
• Copy of passport
• Motivation letter

Applications will be evaluated based on the received information and an online interview. The decision will be based on information provided by the student, the ongoing research at the time of the planned visit, and the number of other internships in the lab. 

Be aware that the visit can only start after all administration has been finalized by the applicant and the sending/receiving university. 

Application to be sent via email to: 

koen.cuypers@uhasselt.be

Lab visit description

During this lab visit, you will 

(a) get familiar with the tools and methods developed by the APE Lab concerning:

1. simulations and models of spiking neural networks 
2. analysis of experimental data (ECoG, Ca-imaging, EEG) and of simulation outcome  

(b) validate and improve tools and methods, evaluate possible extensions and/or further application scopes, promote collaborations.

Scientific methods offered to the student

• DPSNN, the simulation engine developed by the APE LAB for distributed and plastic spiking neural network simulations

• Expertise with the NEST simulator (for the simulation of deep sleep and awake states)

• SWAP, the analysis pipeline developed by the APE LAB for the study of slow wave activity in deep sleep and anaesthesia states (Matlab, Python) using multi-electrode-array data and imaging data

• Inference methods for the prediction of cortical connectivity and data-constrained simulations

• Thalamo-cortical models of sleep-memory interactions

• Likelihood-based learning models in spiking neural networks

Application details

Application deadline: Reasonable notice (at least 1 week) with respect to the start date of the visit

Please include the following information in your application:

• Name, degree

• Name and contact details of current supervisor

• CV

• List of publications

• Short motivation letter for the lab visit, with description of current research topic and research interests

• Recommendation letter by supervisor/mentor, including why the lab visit is beneficial for the applicant

• Copy of passport

• Copy of highest university degree

Applications will be evaluated as received. The decision will be based on the information provided by the student; further action (as contacting the supervisor and/or requesting a Skype interview to assess interests and motivation) could be evaluated case by case.

Application to be sent via email to: 

Pier Paolucci 

pier.paolucci@roma1.infn.it, CC to Giula De Bonis giulia.debonis@roma1.infn.it; 

Subject Line: “HBP Lab Visits at APE Lab”

Lab visit description

Hands-on activities related to the HBP Brain Simulation Platform and cellular level model of the hippocampus.

Scientific methods offered to the student

• Computational neuroscience methods for cellular level modelling (NEURON, python)

• Tools and implementation strategies used within the HBP Brain Simulation Platform
   

Application details

Please include the following information in your application:

• Name of current supervisor

• CV

• List of publications

• Copy of passport

• Recommendation letter by supervisor/mentor

• Short motivation letter for choosing the lab

• Statement of funding availability for travel and subsistence costs during the visit

Applications will be evaluated as soon as they are received. The decision will be based on the information provided by the student, the requested period for the visit, and the number of concurrent visits, which cannot be more than 5 at the same time.

Application to be sent via email to:

Michele Migliore

michele.migliore@cnr.it, CC to Alessia Bonafede alessia.bonafede@cnr.it

Lab visit description

The visitor will get experience in one or more of the methods below and will collaborate with HBP on one of the following tasks:

1. neurophysiology of multisensory integration, episodic memory and object recognition in rodents;

2. generative models of cortical networks;

3. decoding of scene information in conscious and unconscious states or

4. data analysis, curation, and computing with recurrent networks. Our team will support the visitor with guidance throughout the techniques.

Scientific methods offered to the student (any or a combination of the following)

• Rodent behavioural training 

• In vivo chronic electrophysiological recordings

• Optogenetics

• 2-photon calcium imaging

• Computational modelling

• Advanced data analysis

Application details

Please include the following information in your application:

• Name of the applicant

• Name of institution of origin

• Name of current supervisor

• Publication list

• CV, diploma and motivation letter (in one PDF)

• 2 recommendation letters

• Grades list, courses and transcript

• Copy of passport

Applications will be evaluated as soon as they are received. The decision will be based on information provided by the student, the lab's research plan, and the number of other applicants. Administrative prearrangements prior to visit may take up to two months.

Application to be sent via email to: Cyriel M.A. Pennartz and Conrado Bosman Vitti

Lab visit description

Hands-on activities related to the HBP Neurorobotics Platform and spiking closed loop motor control of robots.

Scientific methods offered to the student
 

• Tools and implementation strategies used within the HBP Neurorobotics Platform

• Simulation of neuronal models in Nest and Nengo

• Machine learning

• Python programming
   

Application details

Please include the following information in your application:

• Current (HBP) research group, supervisor and activities within HBP

• Short description of programming experience

• Letter of motivation

• List of publications

• CV

Applications will be evaluated as soon as they are received. The decision will be based on the information provided by the student, the requested period for the visit, and the number of other applicants.

Application to be sent via email to:

Arne Rönnau

roennau@fzi.de

Lab visit description

The INM-1 focuses on the development of a three-dimensional model of the human brain based on cyto- and receptor architectonic, genetic and functional data as well as on information regarding connectivity between different brain regions. For further information visit the lab website.

Scientific methods offered to the student

• Lab visit – brain slicing, staining, labelling (receptor autoradiography) etc. (duration: 2 weeks)

• Cytoarchitectonic mapping (duration: 3 months)

• Polarized light imaging (duration: 3 months)

• Receptor architectonic mapping (duration: 4 months)

Application details

Please include the following information in your application:

• Name, degree

• Description of current research topic and motivation for the lab visit

• Name of the current supervisor

• Short statement by supervisor why lab visit is beneficial for the applicant

• CV

• Copy of highest university degree

• Copy of passport
   

Application to be sent via email to:

Julia Kämpfer

j.kaempfer@fz-juelich.de

Lab visit description

Techniques to record neuronal data from single neurons and population of neurons are rapidly improving. Meanwhile, recordings are possible from hundreds of channels simultaneously while animals perform complex tasks. Thus also the analysis of such data becomes increasingly challenging. In addition, progress in simulation technology and computer hardware enable the simulation of full-scale models to interpret such data. The lab visit aims at providing deeper insights in state-of-the-art analysis or simulation approaches. The course is addressed to excellent master and PhD students and young researchers who are interested in learning advanced techniques in data analytics and simulation and in getting hands-on experience in computational neuroscience.

Experienced researchers will help the visitor to learn how to operate one of two complex software packages of the HBP efficiently and safely. Participants will analyse provided data on their own using the tool box Elephant or will learn how to carry out neuronal network simulation with NEST.

Scientific methods offered to participants

• Neuronal network simulations with NEST. NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons. The student can also learn to extend the simulator according to need.

• Analysis of electrophysiological data with Elephant. Elephant is an open-source Python library that provides tools for the analysis of neuronal activity data, such as spike trains, local field potentials and intracellular data. Elephant focuses on generic tools that characterise the coordinated dynamics of large neural populations and methods that analyse the relationship of data recorded on multiple scales of observation. The student can also learn to extend the toolbox to need.
   

Application details

Please include the following information in your application:

• Short description of programming experience

• CV

• Letter of motivation

Applications are reviewed every 2 months and participants are selected according to qualification and success likelihood.
 

Application to be sent via email to:

Anne Elfgen

a.elfgen@fz-juelich.de

Lab visit description

The goal of the INM-7 is to obtain a more detailed characterisation of the organisation of the human brain and its inter-individual variability in order to better understand its changes in advanced age as well as neurological and psychiatric disorders. Based on this knowledge, new approaches for diagnosis and outcome prediction at the level of individual patients are developed. We pursue this objective by combining multi-modal MR imaging, detailed neuropsychological characterisation and innovative methods of data analysis and simulation. An important focus of the institute is to provide the developed tools and results to the scientific public in the form of software and data sets enabling the broad use of our research.

Further information

Scientific methods offered to the student (minimum stay 1-2 months)

• Neuroimaging analytics and brain-behaviour relationships

• Meta-analytics and data-base driven modelling of brain activation patterns

• Clinical neuroimaging and individual prediction of clinical states

• Simulation and modelling of brain dynamics

Application details

Please include the following information in your application:

• Name, degree

• Description of current research topic and motivation for the lab visit

• Name of the current supervisor

• Short statement by supervisor why lab visit is beneficial for the applicant

• CV

• Copy of highest university degree

• Copy of passport

Application to be sent via email to:

Simon Eickhoff

S.Eickhoff@fz-juelich.de

Lab visit description

Observation of experiments
 

Scientific methods offered to the student

• MRI in nonhuman primates

• Behavioural experiments in nonhuman primates

• Electrophysiology in nonhuman primates

• Electrical microstimulation and optogenetics in nonhuman primates

Application details

Please include the following information in your application:

• Name of current supervisor

• CV

• Skills list

• Recommendation letter

• Copy of passport

• Recent TB test (< 6 months old, needs to be negative)

Application to be sent via email to:

Wim Vanduffel

wim.vanduffel@kuleuven.be

Scientific methods offered to the student

• Human brain imaging

• Data analysis

• Statistics

• Machine learning

• Python programming
   

Application details

Please include the following information in your application:

• Letter of motivation

• CV

For long stays, the administrative application may take 2 to 3 months.
 

Application to be sent via email to:

Bertrand Thirion

bertrand.thirion@inria.fr

Lab visit description

Observation of scRNA-Seq experiments. For more information regarding the lab please visit the website: https://www.dzne.de/en/research/precise/

Scientific methods offered to the student (any or a combination of the following)

• scRNA-Seq: SeqWell, Smart-Seq2

Application details

Please include the following information in your application:

• Name

• Description of current research topic and motivation for lab visit

• Name of supervisor

• Short statement by supervisor why lab visit is beneficial for the applicant

• CV

• Copy of highest university degree

• Copy of passport
   

Applications will be evaluated as soon as they are received. The decision will be based on information provided by the student, the lab's research plan, and the number of other applicants. Administrative prearrangements prior to visit may take 2 months.
 

Application to be sent via email to:

Kristian Händler

kristian.haendler@dzne.de

Lab visit description

The SimLab Neuroscience at Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich is an interdisciplinary team of scientists and engineers with complementary backgrounds and skills, dedicated to supporting neuroscientists in using high-performance computing (HPC) and data resources for their research. Expertise in both neuroscience and HPC is based on in-house research and development, as well as collaborative joint projects with the Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, and other national and international partners. It is an active Partner in multiple HBP Work Packages. JSC is also one of the Fenix hosting sites.

The SimLab offers students an insight into the world of HPC and how HPC can be efficiently used for neuroscience research, from modelling and simulation to data analysis and neuroimaging. Visiting students should have some programming skills, e.g. in C, C++ or Python, to be able to use their visit for a (first) project with HPC and/or data resources. Short-term visits allow a student to join SimLab experts in their everyday work; longer-term stays offer the opportunity to actively contribute to one of the SimLab projects or to work on an own project.

JSC offers a number of (free) training courses throughout the year. A Lab Visit could be combined with the attendance of one or multiple courses, e.g. an introduction to the supercomputing resources at the institute or an introduction to GPU programming.
 

The SimLab Neuroscience experts also supervise Bachelor and Master projects. Students who are searching for a hosting lab for their thesis, should mention this in their application.
 

One of the SimLab Neuroscience teams takes care of coordination, management and dissemination of projects, e.g. for the HBP Work Package 6 (EBRAINS Computing Services) and the Interactive Computing E-Infrastructure (ICEI) project, which is creating the Fenix Infrastructure for the HBP and other science communities. Interested Students should mention their interest to work with this team in their application.
 

Scientific methods offered to the student

A detailed list of the research topics and projects of the SimLab Neuroscience can be found on our website.

• High Performance Computing
• Simulators and simulation engineering, e.g.

• Development of the simulators Arbor, NEST, The Virtual Brain
• Structural plasticity
• Parameter exploration
• Modular science: complex interactive workflows on supercomputers

• Data analysis and visualisation, e.g.

• Visualisation-guided interactive graph analysis
• Interactive steering and visualisation
• Visual connectivity generation

• Neuroimaging pipelines, e.g.

• Deep Learning for brain extraction from MRI scans
• Deep Learning for image segmentation of 3D-PLI images
   

Application details

Please include the following information in your application:

• Name
• Current supervisor, if any*
• Short description of programming skills
• Short description of current project
• Motivation for the lab visit
• List of publications, if any
• Preferred timeframe for the lab visit, e.g. “up to 4 weeks in July-September 2021”

*Students who currently do not have a supervisor can nevertheless apply
 

Please include the following documents in your application:

• Letter of motivation
• CV
• Short statement by supervisor why a lab visit is beneficial for the applicant

Applications are reviewed as they arrive.

The SimLab team leaders will review every application together to identify one or multiple SimLab teams that the student could visit, and check if these teams have enough manpower to supervise a visiting student in the envisaged timeframe. If a lab visit can be offered, the SimLab will then get in contact with the student to sort out the details of the stay.

Application to be sent via email to:

Prof. Dr. Abigail Morrison
slns@fz-juelich.de