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Norbert Vischer: ObjectJ: Non-destructive marking and linked results used in bacterial molecular cytology

Abstract

The critical parameters in bacterial images include morphometrical properties such as cell length, cell diameter, and constriction site. In addition to these, parameters that describe intensity and spatial distribution of fluorescent objects inside the cell are also important. The information for an individual cell is typically extracted from a phase contrast and one to three fluorescence images organized in a hyperstack. In order to acquire and manage this multitude of parameters in context, we use ImageJ in combination with the ObjectJ plug-in. ObjectJ handles the organization of image-analysis tasks by using a project file that integrates all related components: a user-defined palette for non-destructive markers, color-coded vector objects across many images that are linked to the project, qualifiers for creating subsets of results, and the macros that are in use. At any time the user has the flexibility to extract different sets of results from existing markers such as intensities and spatial parameters.

ObjectJ helps to keep the desktop clean; in many cases, graphs and numerical output can transiently be created from the newest data set without sending additional files to an external (spreadsheet) program, which would break the interconnection of cell data and their link to the images. We demonstrate a project that in a first step automatically traces bacteria and detects cell axes and diameters. In the second step, the type, number, and local positions of fluorescent objects, as well as the longitudinal fluorescence distribution in their respective channels, are determined. The user can inspect the output by quickly navigating from cell to cell or by jumping back-and-forth between images and related results. This makes the chain of processing steps transparent and helps to detect analysis artifacts. In situations where automatic algorithms are unreliable or do not exist at all, markers can also interactively be set, edited or deleted. This project is one of the examples that are documented and available for download from:

http://simon.bio.uva.nl/objectj/

Keywords

non-destructive marking, vector objects, ObjectJ, image analysis

Administrative data

Presenting author: Norbert Vischer
Organisation: Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam

co-authors: Stelian Nastase, Tanneke den Blaauwen

Type: Poster (portrait)

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