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Two individuals were also manually tracked using a VEMCO VR100 acoustic receiver coupled with a directional hydrophone, one in Norfolk Bay and the other in the Derwent Estuary (Fig. 1).
Cells were manually tracked using NIS Elements software (Nikon, Melville NY, USA).
Sporozoites were manually tracked using Imaris software and tracks overlapping with CD31+ vessels are colored orange, while tracks in between CD31+ vessels are white.
Individual cells were then manually tracked using the ImageJ™ cell tracking plugin, and the speed of random migration was calculated in μm moved/hour.
Images were projected into a single z-layer and the resulting two-dimensional data set was processed and manually tracked using Imaris software (Bitplane, Concord, MA, United States).
For each movie, at least 30 single cells were randomly selected and manually tracked using ImageJ 1.44m (National Institutes of Health, Bethesda, MD, USA).
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The corpus callosum was tracked using a single seed ROI from a manually delineated entire sagittal cross section (three slices thick, red on the eigenvector map, see Fig. 1C).
To compare crawling monocyte paths in different knockout animals and in in vivo blocking experiments in the mesenteric vessels, cells were tracked using the autoregressive-motion algorithm and filtered for a minimum track length of 30 μm from their origin and a minimum track duration of 3 min, then were manually assessed and edited for track continuity.
The dashed line represents the ground truth which is manually detected and the solid line represents the results of tracking using the Kalman filter.
Males were manually tracked and visualized using a 10X, 20X, or 40X long working distance objective.
For each time-lapse movie, mitochondria or autophagic vacuoles were manually tracked and transport parameters were generated using the ImageJ software plug-in Multiple Kymograph, submitted by J. Rietdorf and A. Seitz (European Molecular Biology Laboratory, Heidelberg, Germany).
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