Introduction

Imaging and analyzing the locomotion behavior of small animals such as Drosophila larvae or C. elegans worms has become an integral subject of biological research. In the past we have introduced FIM, a novel imaging system feasible to extract high contrast images. This system in combination with the associated tracking software FIMTrack is already used by many groups all over the world. However, so far there has not been an in-depth discussion of the technical aspects. Here we elaborate on the implementation details of FIMTrack and give an in-depth explanation of the used algorithms. Among others, the software offers several tracking strategies to cover a wide range of different model organisms, locomotion types, and camera properties. Furthermore, the software facilitates stimuli-based analysis in combination with built-in manual tracking and correction functionalities. All features are integrated in an easy-to-use graphical user interface. To demonstrate the potential of FIMTrack we provide an evaluation of its accuracy using manually labeled data. The source code is available under the GNU GPLv3 at https://github.com/i-git/FIMTrack and pre-compiled binaries for Windows and Mac are available at http://fim.uni-muenster.de.

Publications

  1. FIMTrack: An open source tracking and locomotion analysis software for small animals.
    Cite this
    Risse B, Berh D, Otto N, Klämbt C, Jiang X, 2017-05-01 - PLoS Computational Biology
  2. FIM, a novel FTIR-based imaging method for high throughput locomotion analysis.
    Cite this
    Risse B, Thomas S, Otto N, Löpmeier T, Valkov D, Jiang X, Klämbt C, 2013-01-01 - PloS one

Credits

  1. Benjamin Risse
    Developer

    School of Informatics, University of Edinburgh, United Kingdom of Great Britain and Northern Ireland

  2. Dimitri Berh
    Developer

    Faculty of Mathematics and Computer Science, University of Münster, Germany

  3. Nils Otto
    Developer

    Department of Behaviour and Neuronal Biology, University of Münster, Germany

  4. Christian Klämbt
    Developer

    Department of Behaviour and Neuronal Biology, University of Münster, Germany

  5. Xiaoyi Jiang
    Investigator

    Faculty of Mathematics and Computer Science, University of Münster, Germany

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Summary
AccessionBT003686
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByXiaoyi Jiang