John Arne Nesheim

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Nucleotyping Work Station (NWS)

Digital imaging for chromatin studies in situ

NWS is an expansion of PWS with the same basic functionality. In addition, NWS processes 2D and 3D sections by localizing and segmenting nuclei that are not rinsed and placed in a monolayer, but instead are retained in place in the original tissue architecture.

NWS is one of our most frequently used research tools, often used to test new methods and concepts for image analysis. The NWS package performs a dual task, in which it both controls the parameters of the microscope robotically, and handles large amounts of imaging data for analysis.

FGrabber2D within the NWS package is used to generate images of the sections. The program ensures that the correct areas are photographed, based on input from the user. Focus points are either generated automatically or specified manually. Large volumes of data are generated through this process, where several gigabytes of images are saved per slide. In order to analyze these, a cluster of computers has been set up which enable us to perform time-consuming calculations quickly.

Nucleotyping has generated two complicated sub-projects that are of high priority for our institute and collaborations, segmentation and texture analyses.

Main features of the FGrabber software:

Monolayers in FGrabber

Classification is completed using rules contained in a rules set file. Different rules are used for different cell types and for monolayer and sections. The rules set makes it possible to store only the correctly segmented cells, and classify them in to galleries containing different cell types.

This text was last modified: 08.07.2016

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