Two-photon imaging and analysis of neural network dynamics

The glow of a starry night sky, the smell of a freshly brewed cup of coffee or the sound of ocean waves breaking on the beach are representations of the physical world that have been created by the dynamic interactions of thousands of neurons in our brains. How the brain mediates perceptions, creates thoughts, stores memories and initiates actions remains one of the most profound puzzles in biology, if not all of science. A key to a mechanistic understanding of how the nervous system works is the ability to analyze the dynamics of neuronal networks in the living organism in the context of sensory stimulation and behaviour. Dynamic brain properties have been fairly well characterized on the microscopic level of individual neurons and on the macroscopic level of whole brain areas largely with the help of various electrophysiological techniques. However, our understanding of the mesoscopic level comprising local populations of hundreds to thousands of neurons (so called 'microcircuits') remains comparably poor. In large parts, this has been due to the technical difficulties involved in recording from large networks of neurons with single-cell spatial resolution and near- millisecond temporal resolution in the brain of living animals. In recent years, two-photon microscopy has emerged as a technique which meets many of these requirements and thus has become the method of choice for the interrogation of local neural circuits. Here, we review the state-of-research in the field of two-photon imaging of neuronal populations, covering the topics of microscope technology, suitable fluorescent indicator dyes, staining techniques, and in particular analysis techniques for extracting relevant information from the fluorescence data. We expect that functional analysis of neural networks using two-photon imaging will help to decipher fundamental operational principles of neural microcircuits.Comment: 36 pages, 4 figures, accepted for publication in Reports on Progress in Physic

Optical Recording of Neuronal Activity with a Genetically-Encoded Calcium Indicator in Anesthetized and Freely Moving Mice

Fluorescent calcium (Ca2+) indicator proteins (FCIPs) are promising tools for functional imaging of cellular activity in living animals. However, they have still not reached their full potential for in vivo imaging of neuronal activity due to limitations in expression levels, dynamic range, and sensitivity for reporting action potentials. Here, we report that viral expression of the ratiometric Ca2+ sensor yellow cameleon 3.60 (YC3.60) in pyramidal neurons of mouse barrel cortex enables in vivo measurement of neuronal activity with high dynamic range and sensitivity across multiple spatial scales. By combining juxtacellular recordings and two-photon imaging in vitro and in vivo, we demonstrate that YC3.60 can resolve single action potential (AP)-evoked Ca2+ transients and reliably reports bursts of APs with negligible saturation. Spontaneous and whisker-evoked Ca2+ transients were detected in individual apical dendrites and somata as well as in local neuronal populations. Moreover, bulk measurements using wide-field imaging or fiber-optics revealed sensory-evoked YC3.60 signals in large areas of the barrel field. Fiber-optic recordings in particular enabled measurements in awake, freely moving mice and revealed complex Ca2+ dynamics, possibly reflecting different behavior-related brain states. Viral expression of YC3.60 – in combination with various optical techniques – thus opens a multitude of opportunities for functional studies of the neural basis of animal behavior, from dendrites to the levels of local and large-scale neuronal populations

Die Rolle des menschlichen medialen frontalen Kortex in der Kognition untersucht mit Hilfe der funktionellen Magnetresonanztomographie.

In meiner Doktorarbeit untersuchte ich mit Hilfe der funktionellen Magnetresonanztomographie (fMRT) die funktionelle Anatomie des menschlichen medialen frontalen Kortex (MFC) während der Ausübung von drei kognitiven Aufgaben. Im ersten Experiment beobachtete ich die Aktivierung im Anterioren Cingulären Kortex (ACC) für erfolgreiche und fehlerhafte Antwortunterdrückungen während einer GoNogo Aufgabe. Hierzu benutzte ich eine neuartige fMRT Strategie, die es ermöglichte, Bilder mit achtfach höherer räumlicher Auflösung zu erstellen als herkömmliche Ansätze. Die Ergebnisse dieses Experimentes ließen auf eine bilaterale Verteilung von Fehlerprozessen im Anterioren Cingulum schließen, während erfolgreiche Unterdrückungen nur den ACC der rechten Hemisphäre aktivierten. Die Studie trägt zu einem besseren Verständnis der Mikroanatomie des ACC bei und demonstriert das Potential der fMRT, verschiedene kognitive Hirnregionen mit bisher unerreichter räumlicher Auflösung funktionell zu kartieren. In der zweiten Studie untersuchte ich die neuronal Grundlage für die Verarbeitung von Antwortkonflikten und Antizipation, mit besonderer Fokussierung auf den medialen frontalen Kortex. Bei herkömmlicher Auflösung waren sowohl Konflikt als auch Antizipationsprozesse mit überlappender Aktivierung im ACC assoziiert. Im Gegensatz dazu beobachtete ich eine differenzielle Aktivierung des Superioren Frontalen Gyrus (SFG) für beide Prozesse. Diese Ergebnisse stützen die Hypothese einer funktionellen Heterogenität innerhalb des MFC. SFG könnte eine Rolle in Prozessen spielen, die spezifisch für verschiedene Aufgaben sind, zum Beispiel die Unterdrückung von inkompatiblen Antworten um den Konflikt zwischen gegensätzlichen Handlungen aufzulösen. Diese Funktion stimmt mit Theorien überein, die SFG als höheres motorisches Areal beschreiben. Im Gegensatz dazu scheint ACC eine Rolle in abstrakteren und allgemeinen Verhaltensaspekten zu spielen. Im dritten Teil meiner Arbeit konnte ich mit Hilfe der Echtzeitauswertung von fMRT Daten zeigen, dass es Probanden möglich ist, die Aktivität einer kleinen, funktionell definierten Region innerhalb des ACC willentlich selbst zu modulieren. Diese Studie bildet die Grundlage für zukünftige Experimente in denen intentionale Regulierung von Aktivität in definierten Hirnregionen dazu beiträgt, kausale Zusammenhänge zwischen dem Areal und dessen Funktion als auch die Interaktion mit anderen Hirnstrukturen zu definieren

Persistent Identifiers and the openBIS Research Data Management System

Scientists face increasing requirements to publish data according to the FAIR (Findable, Accessible, Interoperable and Reusable) principles. To achieve this, every step of the research process needs to be accurately documented, and data needs to be securely stored, backed up, and annotated with sufficient metadata to make it re-usable and re-producible. The use of an integrated research data management system and Electronic Lab Notebook (ELN) can help researchers towards this goal. openBIS is such a system that has been developed by ETH Scientific IT Services for over 10 years. Data stored in openBIS are immutable and have internally unique and persistent identifiers (PIDs). In an ongoing collaboration with the Swiss Supercomputing Center (CSCS), they are working towards linking the internal openBIS identifiers to global PIDs provided by the ePIC consortium via the CSCS. The presentation will give an overview of the openBIS data management system and report on current progress of the integration with the ePIC PID service

Steady or changing? Long-term monitoring of neuronal population activity

Stability and flexibility are both hallmarks of brain function that allow animals to thrive in ever-changing environments. Investigating how a balance between these opposing features is achieved with a dynamic array of cellular and molecular constituents requires long-term tracking of activity from individual neurons. Here, we review in vivo chronic extracellular recording studies and recent long-term two-photon calcium-imaging investigations that address the question of stability and plasticity of neuronal population activity in the mammalian brain. Overall, spiking activity is heterogeneously distributed among neurons in local populations and largely remains stable for individual cells over time. Tuning properties appear more flexible and may be adaptively stabilized, possibly by neuromodulators, to encode reliably and specifically salient stimuli or behaviors

Keep calm and manage your data. Research data management education for scientists in Switzerland.

Researchers at Higher Education Institutions in Switzerland generate large amounts of data of various types in their daily work. In order to ensure their usability in the long term and to meet the requirements of investors, they depend on efficient data management, including the creation of data management plans (DMPs). The latter became particularly relevant following the announcement by the Swiss National Science Foundation (SNSF) that a DMP must be drawn up and submitted for each project application from October 2017 onwards. By managing one’s data, even if a funding body does not call for it, the research funds can be used optimally through avoidance of unnecessary duplicate work and streamlining of the work process. Additionally, proper data management is a key prerequisite for effective data sharing and publishing, which in turn increases the visibility of one’s scholarly work and thus is likely to increase citation rates. In order to support Swiss researchers, the libraries of ETH Zurich and EPF Lausanne, together with the ETH Zurich Scientific IT Services have been leading the efforts to provide consulting and training services in the field of research data management at their institutions. Together with partners of the national Data Life Cycle Management (DLCM) project (http://www.dlcm.ch), the services are constantly being expanded and adapted to the latest requirements. The offer ranges from individual consultation of individual researchers to the consultation of research groups, from short coffee lectures to full-day workshops, providing insight on data management planning and active research data management, as well as publishing and long-term preservation of research data. In addition to regular training courses and workshops, personalised lectures and events for groups are available on request

Research Data Management Services at ETH Zurich

Research Data Management (RDM) is an integral part of scientific practice. The responsibility for RDM therefore lies with individual researchers, but service units of universities can support researchers’ efforts with appropriate service offers. From the point of view of the institution, this helps to streamline operations towards effective and efficient solutions. We outline here the RDM services provided to researchers at ETH Zurich by ETH Scientific IT Services and ETH Library. We comment on current experiences and open issues