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BisQuit: Open-Source Interactive Tool for Image Sequence Analysis

O. Mariani, V. Uhlmann, D. Sage, M. Unser

Second Swiss Image-Based Screening Conference (SIBSC'13), Lausanne VD, Swiss Confederation, June 10-11, 2013.



BisQuit (bacterial image-sequence quantification interactive tool) is a semi-automated interactive analysis tool designed in particular for time-lapse biomicroscopy image sequences. It integrates different image processing tools into an efficient pipeline for the tracking and segmentation of sequences featuring elongated objects such as rod-shaped bacteria.

The algorithm's main steps include image preprocessing, object ridge tracing, tracking and finally segmentation. The tracing and tracking steps are interactive and therefore allow editing and automatic propagation of manual corrections. Several measurements comprising among others phylogenetic trees and image-based information can be outputted by the program. BisQuit is designed as plugin for ImageJ and is therefore free and open-source.


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