Journal: bioRxiv

Article Title: An open source platform for analyzing and sharing worm behavior data

doi: 10.1101/377960

Figure Lengend Snippet: ( a ) To facilitate the sharing of tracking data, the OpenWorm Movement Database provides a web interface to search a database of worm videos by genotype, strain, and/or other discrete values. The interface includes interactive histograms, with sliders permitting users to filter results based on feature values, making it possible to find files with worms that are, for example, both fast and highly curved. The interface then connects to the video and feature data stored on Zenodo. Once downloaded, the video and feature data can be further analyzed or combined with data collected using other worm trackers through the Worm tracker Commons Object Notation (WCON), a human and machine readable JSON format for sharing tracking data. ( b ) Open-source repositories for tracking and analysis. Tierpsy Tracker segments and tracks worms, extracting the outline and skeleton of each animal then determining the head-tail orientation (Tierpsy is short for Tierpsychology, the German word for ethology). These data are saved in WCON. The Open Worm Analysis Toolbox is then used to extract the large set of behavioral features defined in Yemini et al . . WCON includes a flexible notation for adding custom features to the WCON file if desired.

Article Snippet: Tierpsy Tracker is at its core a multi-worm generalization of WormTracker 2.0 , a single-worm tracker, although it should be emphasized that the underlying software has been ported to Python from MATLAB and completely re-designed.

Techniques:

Journal: bioRxiv

Article Title: An open source platform for analyzing and sharing worm behavior data

doi: 10.1101/377960

Figure Lengend Snippet: A. Tracking results from video of a single L4 N2 analyzed with both Tierpsy Tracker (orange) and Worm Tracker 2.0 (green). Both trackers produce almost identical results except in a small segment where there was a head-tail identification error by Worm Tracker 2.0 (frames 5564 to 5678). The Tierpsy Tracker skeleton coordinates were rotated to align them with the Worm Tracker results prior plotting. This is because the coordinate system in Tierpsy matches the camera orientation, while in WT2.0, it matches the stage position. Left top , Root Square Mean Error (RMSE) between the skeletons output by each tracker. Left centre and bottom , y and x head coordinates over time. Right , midbody trajectory in space. Inset , example of the skeletonization results at frame 2500. B. Left , Cumulative distribution of the total fraction of skeletons with a given RMSE between the results of Worm Tracker 2.0 and Tierpsy Tracker. RMSE values are normalized by the worm length (L). The shaded blue region marks the threshold of 1/48 ≈ 0.021 and contains 99.2% of all the frames in RMSE switch . The inset shows an example of WT2.0 (red) and Tierpsy (cyan) with a RMSE of 0.02, which is at the border of the shaded region. 99.2% of skeleton agreements are as good or better than this. Right , videos sorted by the fraction of RMSE/L less than 1/48. See main text for more information.

Article Snippet: Tierpsy Tracker is at its core a multi-worm generalization of WormTracker 2.0 , a single-worm tracker, although it should be emphasized that the underlying software has been ported to Python from MATLAB and completely re-designed.

Techniques: