BIOMEDICAL IMAGING GROUP (BIG)
Laboratoire d'imagerie biomédicale (LIB)

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. 

@INPROCEEDINGS(http://bigwww.epfl.ch/publications/mariani1301.html,
AUTHOR="Mariani, O. and Uhlmann, V. and Sage, D. and Unser, M.",
TITLE="{BisQui}t: {O}pen-Source Interactive Tool for Image Sequence
	Analysis",
BOOKTITLE="Second Swiss Image-Based Screening Conference ({SIBSC'13})",
YEAR="2013",
editor="",
volume="",
series="",
pages="",
address="Lausanne VD, Swiss Confederation",
month="June 10-11,",
organization="",
publisher="",
note="")
© 2013 EPFL. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from EPFL. This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.