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== Welcome to BactImAs Wiki pages ==


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== Getting started ==
'''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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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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'''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 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 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 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.
 
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)
 
 
----
 
 
{{:bactrack_main.png?400|}}
{{:btree.png?400|}}
{{:frame.png?400|}}
{{:segmentation.png?400|}}
 
 
 
 
 
 
----
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) }}

Revision as of 10:28, 18 July 2023

Welcome to BactImAs Wiki pages

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: [[1]]


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 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 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 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.

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)




Bactrack main.png?400 Btree.png?400 Frame.png?400 Segmentation.png?400





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) }}