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-====== Welcome to BacTracke ​Wiki pages ======+====== Welcome to BactImAs ​Wiki pages ======
  
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-Unlike most approaches (REFS here), our aim is to build a general-purpose solution for tracking ​and analysis of various organisms. ​To that end, it is necessary to build a multi-platform, user-friendly application that is open to changes and additionsFurthermore,​ we believe it is important to enable ways for researchers to collaborate ​and easily exchange ​their analysis, ​so that they can reproduce other’s results ​and/​or ​take on a different perspective on existingalready processed data (movies)With that in mind, we’ve designed ​the application to be in some ways similar to movie editing software (e.g. LightWorks, Pinnacle Studioetc.) where the user is given full command of every step of the detection process ​(Fig 1). User can set or modify selections ​at any frameFor this purpose application leverages the ImageJ program ​an excellent open-source program well known to the biology community ​and heavily used in image processing ​and analysisBut unlike otherswe’ve taken the source code of ImageJ and incorporated it into our projectso that we can retain full control ​of our graphical user interface ​and program behaviourbehavior.  +**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  
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-{{:​segmentation.png|}} +Bactimas paper is published here: [[http://​dx.doi.org/​10.1186/​1471-2105-15-251|DOI:​10.1186/​1471-2105-15-251]] 
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-{{youtube>​xSpLbs5pe_Y?​large|Report video generated from the program }}+ 
 + 
 +**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 setupssince a general purpose automated solution to this detection problem is extremely hard if not impossible\\ 
 + 
 +**Solution:​** 
 +We've designed ​BactImAs as a "​platform",​ that is as a collection of somewhat independent well defined modules working togetherSuch setup facilitates maintenancecustomization and upgrades. 
 +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. 
 +  
 + 
 +BactImAs uses a semi-automated approach: it relies on the user to define the initial cells and all cell divisionsOther than that, the application tracks cells using a our newly developed algorithm. At any pointthe user can intervene and correct any unsatisfactory cell detections. 
 + 
 +BactImAs 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) 
 + 
 + 
 +---- 
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 +{{:​bactrack_main.png?400|}} 
 +{{:​btree.png?​400|}} 
 +{{:​frame.png?​400|}} 
 +{{:​segmentation.png?400|}} 
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 +---- 
 +Example reports produced by BactImAs: 
 + 
 +{{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) ​}}
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