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The Bioinformatics and Computational Biosciences Branch hosts data prepared by NIAID researchers and collaborators for distribution to the research community at large.

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3D Swarms

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3D Reconstruction Via Stereoscopy for the Study of Mosquito Swarms

A detailed description of methods and some visualizations
Here you will find materials related to the stereoscopic analysis of video footage employed by Manoukis et al (2009) to study swarms of Anopheles gambiae.


Male mosquitoes swarm to find mates, but the characteristics of these swarms have not often been quantitatively analyzed in the field. This site includes information on a simple method used recently to localize individual Anopheles gambiae in a swarm via stereoscopic image analysis of video footage swarms recorded in Doneguebougou, Mali. The methods described here represent a streamlining of possibly the most basic method for localizing objects in space, in the hope that other researchers will be able to apply the method for studying fundamental questions about flying insects or other taxa.

To understand the method and its limitations, read "Description of a Method for Localizing Swarming Mosquitoes in 3D Space" and the original Manoukis et al. paper, "Structure and Dynamics of Male Swarms of Anopheles gambiae."


Manoukis et al, used various third-party programs to analyze our data. These are cited in the document below ("Description of a Method for Localizing Swarming Mosquitoes in 3D Space"), including URLs for download. The researchers also developed two programs to facilitate insect localization:

  1. An R function to calculate positions from stereo measurements, called calcxyz.R
  2. A convenience plugin for ImageJ, which may be used to gather these data easily (called StereoPointPicker, a small modification of PointPicker by Philippe Thevenaz

Download both the R function and the ImageJ plugin programs and a short explanation of how to use them.

Visualizations of Swarms

View supplementary materials resulting from the Manoukis et al. 2009 paper.

References and Citation

Manoukis NC. Description of a method for localizing swarming mosquitoes and other insects in 3D space with visualizations. Nat Precedings. 2008.

If you use the software distributed on this page to estimate 3D positions, cite Manoukis et al., referencing the following paper: Manoukis NC, Diabate A, Abdoulaye A, Diallo M, Dao A, Yaro AS, Ribeiro JMC, Lehmann T. Structure and dynamics of male swarms of Anopheles gambiae. J Med Entomol. 2009. In press.


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Content last reviewed on October 25, 2010