Overview

TrakBox is a low cost tracking system to track (microscopic) nematodes under a microscope, for long periods of time, and to automatically analyse and report on their behaviour.

The system is made up of two parts; the low cost hardware which comprises an off the shelf USB microscope mounted on a tracking platform, and bespoke software that allows the tracking of single nematodes over long periods of time, and performs automatic analysis of behaviour.

TrakBox will accommodate dishes of various sizes (as well as multi-well plates), provides its own white (LED) light source and requires no external power as it is all powered from a single USB connection.

The software is written in Matlab and will run on a Windows or Mac platform – it requires that the Matlab run-time environment is downloaded and installed on the host computer – this is a free download available from the Mathworks website. All of the necessary drivers, and instructions for installation are included in the package.

How it works

TrakBox is kept low cost as it uses off the shelf hardware and bespoke 3D printed parts to perform the tracking. High precision servos, along with a USB microscope combine to allow an articulated arm with 2 degrees of freedom to track a (microscopic) nematode at the centre of the microscope’s field of view. Inverse kinematics are used to translate the nematode’s x & y coordinates to arm-angles and the arm is moved to keep the worm in the centre of  the field of view.

TrakBox: the base incorporates a built in (white) LED light, an articulated arm, a USB microscope and changeable dish holders for dishes of different sizes and diameters.

Images are captured at around 3 frames per second, and advanced image processing techniques are used to isolate the nematode on each frame and determine the location of the worm’s centre of mass. The worm’s absolute position is recorded and tracked, and when the worm attempts to move outside of a target area, the arm moves to keep the worm in the middle of the field of view. Advanced signal processing filters and corrects the worm position over time and constantly updates a series of behaviour parameters calculated ‘on the fly’. See a short video of this here.

TrakBox: C. elegans, with its centre of mass indicated by the red ‘*‘ is held within the focus (between the two concentric green rings). When the worm centre of mass moves out of the inner of the two rings the tracker moves to re-centre the camera/microscope on the worm position.

Behaviour monitoring

The TrakBox software records and derives a number of parameters over the course of the worm tracking. The maximum duration of the tracking is only really limited by hard disk storage space, and as the recorded worm parameters don’t occupy much space the recordings can be extremely long in practice. This means that nematode behaviour can be observed over long periods of time as the nematode exhibits different behaviour patterns.

TrakBox measures and displays the following parameters (over the entire duration of the recording):

  • x & y coordinates
  • instantaneous velocity
  • instantaneous direction of travel
  • dwelling and roaming times
  • number of reversals
The dwelling versus roaming plot which now shows the amount of time the worm spends in quiescent state too.

Reporting

Furthermore, TrakBox provides graphical, 2-Dimensional, reports of nematode behaviour over time, as a combination of x&y location, instantaneous velocity as well as locations of reversals.

TrakBox: On the left is a worm track that shows the worm position over time along with an arrow showing the amplitude and direction of the instantaneous velocity at each frame (so-called Featherplot). On the right, on the same worm track, each reversal is shown by the pink circle.

All data can be exported via a .CSV spreadsheet such that it can be used for further analysis/ graphing/ reporting in reports, papers, etc. Individual worm tracks can be saved and reanalysed at a later date, where different analysis parameters can be used to generate new results.

The TrakBox package

TrackBox is sold as a package consisting of:

  • The tracking base (which includes a built-in white LED light) with a plate for a 50 mm diameter dish.
  • The control box, which plugs into the two servo motors, the LED light (USB) and video microscope (USB) and which in turn plugs into the computer through a single USB connector.
  • The TrakBox tracking software, which includes all the necessary drivers and installation instructions for both Mac or Windows platforms.
  • The TrakBox analysis software that allows for the analysis of recorded worm tracks.
The complete TrakBox systems comprising the controller and the base unit.

 

Support

TrakBox is supported primarily through on-line/email support, if you need help please email us here or use our dedicated support page. At this stage, as EMbody is a small (but growing!) concern, we do not offer 24/7 support, but we will still do our very best to help you in a timely manner.

Cost

TrakBox is priced at an affordable level, each purchase comes with a unique license. We can provide a discount for multiple license purchases. Please contact us to request information on pricing for TrakBox.