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Welcome to BacTrack Wiki pages

BacTrack is an open-source multi platform java application intended to assist the researcher in tracking various organisms in sequences of images and obtaining and visualizing their quantitative data.

Motivation: A common task in today’s synthetic and systems biology studies is the analysis of various features of organisms using movies obtained through time-lapse microscopy.
This process consists of identifying organisms on a large number of images and measuring their features whilst keeping track of their lineage which is a very cumbersome and error prone task for the researcher.
To facilitate the analysis, various mostly automated tools and algorithms were developed in recent years but all of them targeting rather specific organisms and/or laboratory setups, since a general purpose automated solution to this detection problem is extremely hard if not impossible.

Solution: We've designed bactrack as a “platform”, that is as a collection of somewhat independent well defined modules working together. Such setup facilitates maintenance, customization and upgrades. This property is particularly useful for the tracking algorithms - in BacTrack it is possible to include multiple tracking algorithms (“best-of-breed approach”) and thus use the best fitted algoritm for the problem at hand.
It is even possible to mix-and-match algorithms in a way to segment one part of the movie with algorithm A and the other part with algorithm B.

BacTrack uses a semi-automated approach: it relies on the researcher to define the initial cells and all cell divisions. Other than that, the application tracks cells using a newly developed algorithm described here. At any point, a researcher can intervene and correct any unsatisfactory cell detections. We’ve tested on four different organisms and obtained promising results. The application enables configurable lineage tree visualization and data export for use in third party programs.

BacTrack provides the following features:

  • Easy to use GUI interface
  • Frame anlignment algorithm
  • Novel mycobacteria segmentation algorithm
  • Novel configurable lineage tree visualization
  • Automated acquisition of quantitative date
  • Relational database storage, SQL interface to data
  • Data export (CSV)


Example reports produced by BacTrack:

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