The course is focused on experimental and theoretical methods to study how the brain operates at the level of neuronal circuits. We cover various optical and electrophysiological concepts and techniques used currently in systems neuroscience from the basics to advanced topics on both theoretical and experimental grounds.
The course is designed to be a highly interactive, hands-on experience, reflecting the atmosphere of CSHL, Woods Hole or Champalimaud courses.
Typically, each course day will contain an extended lab session and several theoretical lectures.
Hard work will be combined with a few trips through the beautiful Transylvanian countryside.
The course is addressed to a graduate student/postdoc audience.
- Upinder Bhalla National Centre for Biological Sciences, India
- Florian Engert Harvard University, USA
- Winrich Freiwald Rockefeller University, USA
- Balázs Hangya IEM, Hungarian Academy of Sciences, Hungary
- Sonja Hofer Biozentrum, University of Basel, Switzerland
- Tomα Hromαdka Slovak Academy of Sciences, Slovakia
- Mark Hübener Max Planck Institute of Neurobiology, Germany
- Georg Keller Friedrich Miescher Institute, Switzerland
- David Kleinfeld - University of California, San Diego, USA
- Suhasa Kodandaramaiah University of Minnesota, USA
- Hannah Monyer DKFZ, University of Heidelberg, Germany
- Tom Mrsic-Flögel Sainsbury Wellcome Centre, University College London, UK
- Venkatesh Murthy Harvard University, USA
- Ruben Portugues Max Planck Institute of Neurobiology, Germany
- Botond Roska - Friedrich Miescher Institute, Basel, Switzerland
- Wolf Singer Max Planck Institute for Brain Research, Germany
- Chris Xu Cornell University, USA
- Tony Zador Cold Spring Harbor Laboratory, USA
- Raul Mureşan Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Adam Kampff Sainsbury Wellcome Centre, University College London, UK
- Florin Albeanu Cold Spring Harbor Laboratory, NY, USA
- Rob Campbell Biozentrum, University of Basel, Switzerland
- Federico Carnevale Cold Spring Harbor Laboratory, NY, USA
- Adriana Dăbâcan Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Elena Dreosti University College London, UK
- Medorian Gheorghiu Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Priyanka Gupta National Centre for Biological Sciences, Bangalore, India & CSHL, NY, USA
- Mitra Javadzadeh Biozentrum, University of Basel, Switzerland
- Leinweber Marcus Friedrich Mischer Institute, Basel, Switzerland
- Gonçalo Lopes Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal
- Fred Marbach Cold Spring Harbor Laboratory, NY, USA
- Vasile Moca Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Mehrab N. Modi Cold Spring Harbor Laboratory, NY, USA
- Jon Newman Massachusetts Institute of Technology, USA
- Marius Pachiţariu University College London, London, UK
- Bruno Pichler INSS (Independent NeuroScience Services)
- Nacho Sanguinetti Bernstein Center for Computational Neuroscience, Berlin, Germany
- Iuliu Vasilescu Politechnica University, Bucharest, Romania
- Jakob Voigts Massachusetts Institute of Technology, USA
- Petr Znamenskiy Biozentrum, University of Basel, Switzerland
- Basic Optics Diffraction and Resolution. Illumination Techniques. Numerical Aperture.
- Optical bench exercises Lenses, optical systems, illumination methods, basic microscopy techniques. How to custom build different kinds of microscopes.
- Noise measurements and photo-sensors Shot noise, optical detectors, amplifiers, NI-DAQ, CCD cameras, photodiodes, photo multiplier tubes (PMTs).
- Light and fluorescence microscopy Fluorescence, FRAP, photo-activation, photo-conversion. Point spread function measurements, basic image analysis (deconvolution, denoising, PCA).
- Fluorescence probes GFP, GFP based chromophores, organic calcium dyes, genetically encoded calcium dyes, pHluorins, voltage sensitive dyes.
- Intrinsic Optical Imaging Visual, auditory & barrel cortex; olfactory bulb. Students will build a custom wide field fluorescence and intrinsic optical imaging rig.
- Scanning microscopy Confocal and two-photon microscopy. Lasers. Students will build a two-photon microscope and write custom scanning and acquisition software in MATLAB and NI DAQmx. The ScanImage API.
- Viral approaches to label, monitor and alter neuronal circuits.
- Optogenetics Light activated ion channels and pumps. Patterned photo-stimulation techniques.
- Benchtop electronics and basic electrophysiology Impedence and Dipoles. Amplifiers. Extracellular and intracellular recordings. LFP; single unit, multi-unit extracellular recordings, tetrodes, electrode arrays; patch clamp.
- Awake head fixed and freely moving optical and electrophysiological recording strategies in rodents Microdrives. Fiber optic based systems. Open source systems. Open Ephys.
- Techniques for electrophysiological data analysis.
- Monitoring animal behavior Open Source tools for acquisition and analysis of video data. Intro to Bonsai and Arduino. Training Strategies. Closed loop systems.
- Neuronal functional connectivity and neuronal connectomics Serial electron-microscopy and trans-synaptic labeling methods.
- Synchrony and oscillations.
- Cortical attention, sparse neuronal codes.
- Decision making, uncertainty, neuro-modulatory systems.