MicroTracker

Overview

MicroTracker facilitates the correlation of results from methods such as DNA 2D ploidy and Nucleotyping to histopathological classification and grading - a comparative cell-by-cell analysis.

A single nucleus’ placement in the structure of the tumour tissue can be tracked and visualised. We can interconnect the results from, for example, a Nucleotyping analysis with other analytical methods for the same nucleus. In this way, we expose the connection between DNA 2D ploidy, texture analysis, Nucleotyping, Histotyping, Immunohistochemistry and HE-staining, CISH, - all from a single section.

Tracking and Visualization

MicroTracker allows the user to look at scans and detailed views at the same time. Here is an example where we see the Feulgen scan with some cells selected together with the results from a Ki67 analysis (+/-) in the background, and in front of this we see the microscope frame with a single cell (and its properties), grabbed from the exact same area.

Method

The MicroTracker software In the MicroTracker software each single nucleus placement in the structure of the tumor tissue can be tracked and visualized.

• First, the HE-stained section is scanned to provide a “map” of the tissue structure.
• The area of interest is delineated, either automatically by our AI-method, or manually by a pathologist.
• The original HE-section can be re-stained multiple times, with different IHC staining and Feulgen staining, and after each staining, the section will be re-scanned. We can scan the re-stained section either on a scanner or with a microscope system for even higher resolution.
• All scans and images are aligned, and we generate transformation matrices that let us match features on one scan/image to any other scan/image.
• For each scan/image, we can have different analyses, for example, IHC-analysis, Feulgen nuclei segmentation and texture features for nuclei.
• In the MicroTracker application, all data, both scans/images and results from the initial analyses, are organised as layers. These layers can be included in further analyses, and the MicroTracker application provides tools for combining and visualising results from the different analyses.
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Software

The MicroTracker application is developed in WPF/C# in Visual Studio and is created for Windows. The program is the result of tight collaboration between researchers, software developers and pathologists at the ICGI.