Citing VidSync
The preferred citation for use of VidSync is:
Neuswanger, J. R., Wipfli, M. S., Rosenberger, A. E., and Hughes, N. F. 2016. Measuring fish and their physical habitats: versatile 2D and 3D video techniques with user-friendly software. Canadian Journal of Fisheries and Aquatic Sciences 73(12): 1861–1873.
The paper describes the mathematical methods, calibration approach, and performance tests underlying the software. If your institution lacks access, you may contact Jason Neuswanger or download the accepted manuscript.
Example citation in a Methods section
Video measurements were made with VidSync version [version] (Neuswanger et al. 2016).
The macOS version normally does not need to be reported.
Reporting a VidSync study
A Methods section should tell readers what was measured, identify the software and camera system, and summarize the evidence that the measurements were suitable for the study. Detailed processing and project-organization information can usually be placed in an appendix or supplement. This keeps the main text concise while preserving the information needed for exact reproduction or detailed review.
Information for the main Methods section
- Software: the VidSync version and the citation above.
- Measurements: the major observations recorded in VidSync, such as 2-D or 3-D positions, lengths, tracks, velocities, event times, counts, or behavioral classifications. State the units and explain the principal variables derived from them.
- Camera system: the number and model of cameras, recording resolution, and frame rate. For cameras with interchangeable or adjustable lenses, report the lens and focal length. For GoPros and similar action cameras, report the Digital Lens, field-of-view, or zoom setting, such as Wide, Linear, or Narrow, because it determines the effective field of view and focal length.
- Camera arrangement: for spatial measurements, briefly report camera separation, convergence angle or general orientation, approximate subject range, and whether filming occurred in air, through an aquarium wall, or underwater through housings.
- Calibration: state that nonlinear optical distortion was corrected and that the camera system was calibrated with a known reference object or two-plane calibration frame, as applicable.
- Validation: if known targets or another validation procedure were used, report the target, tested distances or conditions, error or precision statistic, result, and any correction subsequently applied to the measurements.
- Measurement rules: summarize any sampling, eligibility, exclusion, or observer rules that could materially affect the results.
Information for an appendix or supplement
A short reproducibility appendix is often the best place for the following details:
- complete camera settings, stabilization or cropping modes, housings, and preprocessing details;
- the transcoding procedure, software or command used, and any changes to resolution, frame rate, timing, or compression;
- distortion-correction and calibration procedures, calibration-frame dimensions, node arrangement, coordinate definitions, and treatment of poor or obscured nodes;
- refraction handling, including material thicknesses, refractive indices, or other inputs supplied to VidSync;
- the synchronization cue, time offsets, and method used to align clips;
- the Object, Event, and Point hierarchy, including operational definitions, codes, expected point order, and relationships among records;
- the export format, field definitions, units, data transformations, and software used for subsequent analysis;
- observer training, quality-control procedures, outlier handling, adjudication, and the full validation protocol.
When a technical detail belongs in the main text
Move an appendix item into the main Methods section when it directly affects interpretation of the results. Synchronization should be described there when timing, speed, or simultaneous behavior is central. Refraction handling should be included when an unusual optical interface could influence accuracy. Transcoding belongs there when it altered temporal or spatial sampling. Object and Event definitions should be included when they define the biological response being analyzed.
Example main-Methods template for a GoPro stereo study
Three-dimensional positions, lengths, and swimming tracks were measured manually with VidSync version [version] (Neuswanger et al. 2016). Videos were recorded with two GoPro [model] cameras at [resolution and frame rate] using the [Digital Lens or field-of-view setting], mounted [separation] apart with approximately [angle] of convergence. Nonlinear distortion was corrected separately for each camera, and the system was calibrated with a two-plane frame. Measurements of known-length targets over the study range produced [validation statistic and result]. Complete camera settings, synchronization, calibration, project organization, and export procedures are provided in Appendix [number].