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Related Experiment Video

Updated: Oct 11, 2025

Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools
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QuickPIV: Efficient 3D particle image velocimetry software applied to quantifying cellular migration during

Marc Pereyra1, Armin Drusko2, Franziska Krämer3

  • 1Frankfurt Institute for Advanced Studies (FIAS) and Goethe Universität Frankfurt am Main, Ruth-Moufang-Straße 1, 60438, Frankfurt am Main, Germany. pereyra@fias.uni-frankfurt.de.

BMC Bioinformatics
|December 5, 2021
PubMed
Summary

We developed quickPIV, a fast and efficient 3D Particle Image Velocimetry (PIV) software package for analyzing biological image data. This open-source tool accelerates the study of dynamic 3D biological processes and cellular migration.

Keywords:
3D image analysisCollective cell migrationJuliaLight-sheet fluorescence microscopyParticle image velocimetryTribolium castaneum

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Area of Science:

  • Life Sciences
  • Biophysics
  • Developmental Biology

Background:

  • Advanced imaging techniques enable high-resolution 3D recording of living samples.
  • Analyzing large 3D datasets of developing organisms requires efficient, automated pipelines.
  • Particle Image Velocimetry (PIV) is a robust, segmentation-free method for quantifying collective cellular migration.

Purpose of the Study:

  • To present quickPIV, an efficient 3D PIV package implemented in Julia.
  • To optimize CPU performance and ensure robustness for biological image data analysis.

Main Methods:

  • Implementation of a 3D PIV package in the Julia programming language.
  • Utilized zero-normalized and normalized squared error cross-correlations.
  • Incorporated sub-pixel/voxel approximation and multi-pass processing.

Main Results:

  • quickPIV demonstrates a threefold speed increase over Python-based openPIV for both 2D and 3D analyses.
  • Achieved accuracy comparable to established literature values on synthetic data.
  • Successfully recapitulated cellular migration during Tribolium castaneum embryogenesis.

Conclusions:

  • quickPIV provides a fast, open-source solution for 3D PIV in biological research.
  • The software offers comprehensive analysis and visualization tools, including 3D vector field visualization in Paraview.
  • Addresses the need for efficient quantitative analysis of dynamic biological processes.