@tutor: Neuropixels @edition: 1st -->
This is the @edition edition of this workshop, jointly organised by the VIB and ELIXIR Belgium.
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This workshop dives into Neuropixels recordings, a powerful technique for capturing neural activity from freely moving animals over extended periods. Researchers of all experience levels will learn the entire workflow, from Neuropixels technology basics to data analysis, gaining expertise from leading experts in the field. By attending, you can expand your research capabilities to study complex behaviors and track brain disorders in a more natural setting, while joining a collaborative community to accelerate your discoveries.
Technical personel, PhD, PostDoc, Industry
The participants;
will be able to recall the fundamental principles of Neuropixels technology. will demonstrate comprehension of the methods and challenges involved in performing acute electrophysiological recordings in awake, freely moving animals. will be able to learn current techniques for chronic implants using Neuropixels probes. will analyze data obtained from long-term chronic implants to identify patterns and anomalies, utilizing the provided analysis primer.
Software: Python (basic)
Kilosort (https://github.com/MouseLand/Kilosort) Neuropixels Trajectory Explorer (https://github.com/petersaj/neuropixels_trajectory_explorer) Herbs (https://github.com/Whitlock-Group/HERBS) Pinpoint (https://github.com/VirtualBrainLab/Pinpoint) Spikeglx (https://billkarsh.github.io/SpikeGLX/) Openephys (https://open-ephys.org/) EMD (https://github.com/janelia-TDHarrisLab/Yuan-Neuron_Tracking) Unitmatch (https://github.com/janelia-TDHarrisLab/Yuan-Neuron_Tracking)
Cagatay Aydin - Nerf Expert Unit Member Asli Ayaz - Nerf Expert Unit Member Kacper Kondrakiewicz - Haesler Lab Shahriar Hosseinjany - Bonin Lab Practical info Date
9 October 2024
Imec tower (visits) Remisebosweg 1 3001 Leuven Belgium More info
Room
Imec tower room 1A
Course Description
This course consist of short tutorials related to current state of art using Neuropixels technology following with our interactive hands-on course about how to visualize electrophysiological data.
Hardware Overview
Neuropixels' recording hardware is modular, with key components including probe (shank and base), headstage, neuropixels module
For more details, check the Neuropixels Manual.
More details about hardware requirements can be found in the SpikeGLX system requirements.
Software Overview
SpikeGLX
Open Ephys
Level: Beginner
License: Creative Commons Attribution 4.0 International License
Funding: This project has received funding from the ELIXIR Programme 2022-2023.
Time estimation: 120 minutes
Supporting Materials:
Requirements: The (technical) installation requirements are described in the installations section.
Acknowledgement:
PURL:
@orcid(Asli Ayaz) @orcid(Kacper Kondrakiewicz) @orcid(Asli Ayaz)
Please cite as:
- ...
Here are some great tips for learning and to get inspired for writing your own pipelines:
- Nextflow's official documentation (link)
- Reach out to the community on Slack (link)
- Curated collection of patterns (link)
- Workshop focused on DSL2 developed by CRG Bioinformatics Core (link)
- Tutorial exercises (DSL1) developed by Seqera (link)
- Curated ready-to-use analysis pipelines by NF-core (link)
- Model example pipeline on Variant Calling Analysis with NGS RNA-Seq data developed by CRG (link)
- Tutorial by Andrew Severin (link)
- Nextflow community basic training (link)
About ELIXIR Training Platform
The ELIXIR Training Platform was established to develop a training community that spans all ELIXIR member states (see the list of Training Coordinators). It aims to strengthen national training programmes, grow bioinformatics training capacity and competence across Europe, and empower researchers to use ELIXIR's services and tools.
One service offered by the Training Platform is TeSS, the training registry for the ELIXIR community. Together with ELIXIR France and ELIXIR Slovenia, VIB as lead node for ELIXIR Belgium is engaged in consolidating quality and impact of the TeSS training resources (2022-23) (https://elixir-europe.org/internal-projects/commissioned-services/2022-trp3).
The Training eSupport System was developed to help trainees, trainers and their institutions to have a one-stop shop where they can share and find information about training and events, including training material. This way we can create a catalogue that can be shared within the community. How it works is what we are going to find out in this course.
About VIB and VIB Technologies
VIB is an entrepreneurial non-profit research institute, with a clear focus on groundbreaking strategic basic research in life sciences and operates in close partnership with the five universities in Flanders – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel and Hasselt University.
As part of the VIB Technologies, the 12 VIB Core Facilities, provide support in a wide array of research fields and housing specialized scientific equipment for each discipline. Science and technology go hand in hand. New technologies advance science and often accelerate breakthroughs in scientific research. VIB has a visionary approach to science and technology, founded on its ability to identify and foster new innovations in life sciences.
The goal of VIB Technology Training is to up-skill life scientists to excel in the domains of VIB Technologies, Bioinformatics & AI, Software Development, and Research Data Management.
Editorial team for this course
Authors: @orcid(Alexander Botzki), @orcid(Bruna Piereck)
Technical Editors: Alexander Botzki
License: 