Electrophysiology lab automation: a case study

Abstract

Event Abstract Back to Event Electrophysiology lab automation: a case study Rembrandt Bakker1*, Dirk Schubert2 and Paul Tiesinga1 1 Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Netherlands 2 Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Netherlands A major hurdle for sharing neuroscientific data is the effort to annotate it with meta data: the parameters that describe the circumstances relevant to the recorded data. Traditionally, meta data is distributed over a lab journal (parameters that change often) and the experimenter's personal memory (constant parameters). To get the meta data in electronic form, one needs to design an ontology that covers all parameters that are relevant to the experiments, and then extract these parameters from the lab journal and personal memory. We present a case study from an electrophysiology lab to show that carrying out these steps is a rewarding investment that not only enables data sharing but also the construction of automated analysis pipelines. Our database concerns in vitro Multi Electrode Array (MEA) and single cell patch clamp measurements from the rat barrel cortex. The meta data ontology is implemented as a relational database scheme, available at http://mealab.science.ru.nl/main/scheme.php. We created a MySQL database according to this scheme, and populated it with thousands of MEA experiments. For the analysis pipeline, we rely on three associated web services: (1) A meta data search wizard (http://mealab.science.ru.nl/main/search_wizard.php) to find experiments that meet certain criteria; the available choices are inferred from the database scheme. (2) An interactive webpage that groups and displays key properties and images of recordings, with links to detailed info (see figure). Each entry contains a field 'Quality', where one can assign a quality rating to the experiment. (3) An SQL query service that returns tables in JSON format. This allows web-based access to the database without the need to install drivers. Keywords: Electrophysiology, Neuroscience, meta data, ontology, multi electrode array Conference: 5th INCF Congress of Neuroinformatics, Munich, Germany, 10 Sep - 12 Sep, 2012. Presentation Type: Poster Topic: Neuroinformatics Citation: Bakker R, Schubert D and Tiesinga P (2014). Electrophysiology lab automation: a case study. Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2014.08.00023 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 21 Mar 2013; Published Online: 27 Feb 2014. * Correspondence: Dr. Rembrandt Bakker, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Donders, Netherlands, r.bakker@donders.ru.nl Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Rembrandt Bakker Dirk Schubert Paul Tiesinga Google Rembrandt Bakker Dirk Schubert Paul Tiesinga Google Scholar Rembrandt Bakker Dirk Schubert Paul Tiesinga PubMed Rembrandt Bakker Dirk Schubert Paul Tiesinga Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.