An animal-actuated rotational head-fixation system for 2-photon imaging during 2-d navigation, bioRxiv, 2018-03-02

AbstractUnderstanding how the biology of the brain gives rise to the computations that drive behavior requires high fidelity, large scale, and subcellular measurements of neural activity. 2-photon microscopy is the primary tool that satisfies these requirements, particularly for measurements during behavior. However, this technique requires rigid head-fixation, constraining the behavioral repertoire of experimental subjects. Increasingly, complex task paradigms are being used to investigate the neural substrates of complex behaviors, including navigation of complex environments, resolving uncertainty between multiple outcomes, integrating unreliable information over time, andor building internal models of the world. In rodents, planning and decision making processes are often expressed via head and body motion. This produces a significant limitation for head-fixed two-photon imaging. We therefore developed a system that overcomes a major problem of head-fixation the lack of rotational vestibular input. The system measures rotational strain exerted by mice on the head restraint, which consequently drives a motor, rotating the constraint system and dissipating the strain. This permits mice to rotate their heads in the azimuthal plane with negligible inertia and friction. This stable rotating head-fixation system allows mice to explore physical or virtual 2-D environments. To demonstrate the performance of our system, we conducted 2-photon GCaMP6f imaging in somas and dendrites of pyramidal neurons in mouse retrosplenial cortex. We show that the subcellular resolution of the system’s 2-photon imaging is comparable to that of conventional head-fixed experiments. Additionally, this system allows the attachment of heavy instrumentation to the animal, making it possible to extend the approach to large-scale electrophysiology experiments in the future. Our method enables the use of state-of-the-art imaging techniques while animals perform more complex and naturalistic behaviors than currently possible, with broad potential applications in systems neuroscience.

biorxiv neuroscience 200-500-users 2018

fastp an ultra-fast all-in-one FASTQ preprocessor, bioRxiv, 2018-03-02

AbstractMotivationQuality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming, and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g., Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and IO inefficient.ResultsWe developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality cutting, and many other operations with a single scan of the FASTQ data. It also supports unique molecular identifier preprocessing, poly tail trimming, output splitting, and base correction for paired-end data. It can automatically detect adapters for single-end and paired-end FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools.Availability and ImplementationThe open-source code and corresponding instructions are available at <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsgithub.comOpenGenefastp>httpsgithub.comOpenGenefastp<jatsext-link>Contactchen@haplox.com

biorxiv bioinformatics 100-200-users 2018

 

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