IGEM:IMPERIAL/2008/Prototype/Drylab/Data Analysis/Track Software

= Tracking Software = ImageJ was used primarily to analyse images. Various plugins were tested, such as SpotTracker and Particle Tracker, but both failed to producing any form of convincing result. Microscopy videos were captured using Volocity software, which also provided a cell tracking function. Thus analysis of synthetic videos was done manually and using 64-Bit Volocity analysis software. The synthetic video shown to the right was used as an input for the tracking of synthetic cells.

Volocity
Volocity 64-Bit was used to analyse synthetic videos created. The following protocol was followed:


 * 1) Filter images using SD intensity of lower limit -100 and upper limit -35. This is to select cells which have a dark cell body.
 * 2) Set tracking method to trajectory variation
 * 3) Check the box "Ignore Stationary Objects" to disable tracking of the image border
 * 4) Set displacement estimation to automatic
 * 5) Begin tracking using Ctrl-U

Manual Tracking
Synthetic cells were tracked using ImageJ via the Manual Tracking Plugin. The following protocol was followed:


 * 1) Save .avi movie as an image sequence and then import image sequence.
 * 2) Start Manual Tracking Plugin.
 * 3) Identify the cell of interest and start new track.
 * 4) Click on the centroid of the cell of interest. This will cause the image to advance to the next frame. Continue till the cell exits field of view
 * 5) Once tracking is complete, end track and save results with a .xls extension.