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start [2013/12/21 21:09]
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start [2014/09/25 13:10] (current)
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-====== Welcome to BacTrack ​Wiki pages ======+====== Welcome to BactImAs ​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.  ​+**BactImAs ​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.  ​
  
 +Bactimas paper is published here: [[http://​dx.doi.org/​10.1186/​1471-2105-15-251|DOI:​10.1186/​1471-2105-15-251]]
  
-Motivation:+ 
 + 
 +**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. \\ 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. \\  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. \\ 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: +**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. +We've designed ​BactImAs ​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.  \\+This property is particularly useful for the tracking algorithms - in BactImAs ​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. 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.  ​+BactImAs ​uses a semi-automated approach: it relies on the user to define the initial cells and all cell divisions. Other than that, the application tracks cells using a our newly developed algorithm. At any point, ​the user can intervene and correct any unsatisfactory cell detections.
  
-BacTrack ​provides the following features:+BactImAs ​provides the following features:
  
   * Easy to use GUI interface ​   * Easy to use GUI interface ​
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   * Data export (CSV)   * Data export (CSV)
  
 +
 +----
  
  
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-Example reports produced by BacTrack:+Example reports produced by BactImAs:
  
 {{youtube>​xSpLbs5pe_Y?​medium|BW Report video generated from the program (black outline - computer, white - human) }}  {{youtube>​xSpLbs5pe_Y?​medium|BW Report video generated from the program (black outline - computer, white - human) }} 
 {{youtube>​GKMdunbu6CM?​medium|Color report video generated from the program (green outline - human, red - human) }} {{youtube>​GKMdunbu6CM?​medium|Color report video generated from the program (green outline - human, red - human) }}
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