Bactimas bactimas_wiki https://homer.zpr.fer.hr/bactimas/index.php?title=Main_Page MediaWiki 1.40.0 first-letter Media Special Talk User User talk Bactimas Bactimas talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk 0 1 26 25 2023-07-18T10:42:10Z Igor 1 26 wikitext text/x-wiki == 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: [[http://dx.doi.org/10.1186/1471-2105-15-251|DOI:10.1186/1471-2105-15-251]] '''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) ---- [[File:bactrack_main.png|400px]] [[File:btree.png|400px]] [[File:frame.png|400px]] [[File:segmentation.png|400px]] ---- === Example reports produced by BactImAs: === * BW Report video generated from the program (black outline - computer, white - human <youtube>xSpLbs5pe_Y</youtube> * Color report video generated from the program (green outline - human, red - human) <youtube>GKMdunbu6CM</youtube> qqpnuuycaip9ikvx3vhvi5a7sessrgx