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Code for wall following in Xenopus laevis
These files are the analysis scripts to analyse the data for 'Wall following in Xenopus leaves'; the manuscript can be found on bioRxiv (see below).
The README file describes the packages and the versions used.
About half of the scripts (tankCornersLoop, trackingLoop, aviTrackingUtilities, findTankCorners, newThigmoTrackingFunctions, openCVtutorialUtils) were used to track the animals in the videos. Note, though, that the accompanying dataset contains tracked coordinates rather than the video files, because the video files are very large.
The other half of the scripts (plottingUtilities, tankSizeComparisons, saveExampleWarps, plotValuesSeveralAnimals, tentsComparison, bwComparison, frameCorrectionDictionary, IRcomparison, plottingLoop) concerns the analysis of the data after the x-y coordinates of the animals were obtained. Note that the accompanying dataset contains the x-y coordinates.
The README file describes the packages and the versions used.
About half of the scripts (tankCornersLoop, trackingLoop, aviTrackingUtilities, findTankCorners, newThigmoTrackingFunctions, openCVtutorialUtils) were used to track the animals in the videos. Note, though, that the accompanying dataset contains tracked coordinates rather than the video files, because the video files are very large.
The other half of the scripts (plottingUtilities, tankSizeComparisons, saveExampleWarps, plotValuesSeveralAnimals, tentsComparison, bwComparison, frameCorrectionDictionary, IRcomparison, plottingLoop) concerns the analysis of the data after the x-y coordinates of the animals were obtained. Note that the accompanying dataset contains the x-y coordinates.
Finally, there are two Matlab scripts that were used to read out the timestamps written into the first 4 pixels of the TIFF files by the camera.
Specifically, the graphs shown in the manuscript were generated using the following scripts:
- The panels in Figure 3 were produced from the plotValuesSeveralAnimals script.
- The panels in Figure 4 were produced from the tentsComparison script.
- The panels in Figure 5 were produced from the bwComparison and IRcomparison script.
- The panels in Figure 6 were produced from the tankSizeComparisons script.
For details and permissions please refer to the manuscript.
- The panels in Figure 4 were produced from the tentsComparison script.
- The panels in Figure 5 were produced from the bwComparison and IRcomparison script.
- The panels in Figure 6 were produced from the tankSizeComparisons script.
For details and permissions please refer to the manuscript.