FastTrack: An open-source software for tracking varying numbers of deformable objects

Abstract

Analyzing the dynamical properties of mobile objects requires to extract trajectories from recordings, which is often done by tracking movies. We compiled a database of two-dimensional movies for very different biological and physical systems spanning a wide range of length scales and developed a general-purpose, optimized, open-source, cross-platform, easy to install and use, self-updating software called FastTrack. It can handle a changing number of deformable objects in a region of interest, and is particularly suitable for animal and cell tracking in two-dimensions. Furthermore, we introduce the probability of incursions as a new measure of a movie’s trackability that doesn’t require the knowledge of ground truth trajectories, since it is resilient to small amounts of errors and can be computed on the basis of an ad hoc tracking. We also leveraged the versatility and speed of FastTrack to implement an iterative algorithm determining a set of nearly-optimized tracking parameters—yet further reducing the amount of human intervention—and demonstrate that FastTrack can be used to explore the space of tracking parameters to optimize the number of swaps for a batch of similar movies. A benchmark shows that FastTrack is orders of magnitude faster than state-of-the-art tracking algorithms, with a comparable tracking accuracy. The source code is available under the GNU GPLv3 at https://github.com/FastTrackOrg/FastTrack and pre-compiled binaries for Windows, Mac and Linux are available at http://www.fasttrack.sh.

Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability

“…We thus ignore the fine structure of the swimming events, such as the amplitude of the tail deflection or beating frequency [ 20 , 21 ] but examine their resulting heading reorientation and linear displacements. The center of mass coordinates and orientation of each larva in every frame were extracted using FastTrack [ 22 ] (see “ Methods ” section). For each identified swim bout, we computed three scalar parameters (Fig.…”

“…Larvae were tracked offline using the open-source FastTrack software [ 22 ]. It generates a text file containing the position of each fish’s center of mass and body angle across frames until they leave the defined ROI.…”

Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability

“…We thus ignore the fine structure of the swimming events, such as the amplitude of the tail deflection or beating frequency [21, 22], but examine their resulting heading reorientation and linear displacements. The center of mass coordinates and orientation of each larva in every frame were extracted using FastTrack [23] (see Methods). For each identified swim bout, we computed three scalar parameters (Figure 2A) whose statistics control the fish spatio-temporal exploration [19]: (i) the interbout interval (IBI), δt n , is the idle time following the bout event, (ii) the displacement, d n , is the travelled distance associated with the bout, and (iii) the reorientation angle, δθ n , denotes the change in heading direction.…”

“…Batches of 10 zebrafish larvae aged 5-7 days were video-monitored at 25 frames/second for periods of 30 minutes as they freely swam in a rectangular 100×45×4.5mm 3 pool at a constant and uniform temperature (figure 1A, see Methods). For each batch, we successively imposed up to 5 values of temperature (18,22,26,30 and 33 • C) in a random order. This thermal range spans the non-lethal conditions for larval zebrafish, and has been shown to be effectively encountered by the animal in its natural habitat [19].…”

“…Tracking and basic analysis Larvae were tracked offline using the open-source FastTrack software [23], https://www.fasttrack.sh). It generates a text file containing the position of each fish's center of mass and body angle across frames until they leave the defined ROI.…”