Code for implementing the Image Acquisition Pipeline
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01_Acquisition
02_SignalProcessing
03_Util
04_Demos
README.md

README.md

NeuBTracker Acquisition Software

Overview Website: NeuBtracker.org

Paper: DOI 10.1038/NMETH.4459

Contents

01_Acquisition/ - the acquisition routines
02_SignalProcessing/
    Registration/ - quality check and registration routines
    Tracking/ - tracking routines
03_Util/ - auxiliary routines
    external/ - external dependency sources from MathworksFileExchange
04_Demos/ - scrips for running the processing pipeline
    Data/ - datasets to be processed.

Example structure:
CAD/
    CAD_Fluor - magnified fluorescence images
    CAD_Refl - reflection images from tracking

Reference

Please cite our original publication in Nature Methods:

Symvoulidis P. et al. (2017) NeuBtracker – imaging neurobehavioral dynamics in freely bahaving fish. In: Nature Methods DOI: 10.1038/NMETH.4459

@Article{Symvoulidis2017,
author={Symvoulidis, Panagiotis
        and Lauri, Antonella
        and Stefanoiu, Anca
        and Cappetta, Michele
        and Schneider, Steffen
        and Jia, Hongbo
        and Stelzl, Anja
        and Koch, Maximilian
        and Perez, Carlos Cruz
        and Myklatun, Ahne
        and Renninger, Sabine
        and Chmyrov, Andriy
        and Lasser, Tobias
        and Wurst, Wolfgang
        and Ntziachristos, Vasilis
        and Westmeyer, Gil G.},
        title={NeuBtracker[mdash]imaging neurobehavioral dynamics in freely behaving fish},
        journal={Nat Meth},
        year={2017},
        month={Oct},
        day={02},
        publisher={Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
        volume={advance online publication},
        note={Brief Communication},
        issn={1548-7105},
        url={http://dx.doi.org/10.1038/nmeth.4459}
}

Contact

Corresponding Author: Gil G Westmeyer