3D Imaging

Capturing about 200 scans with 0.1 µm intervals from a semi-thick histological section, we can build 3-dimensional images of the nuclei in the section.

Overview

3D imaging process

Confocal laser scan microscopy has traditionally been used to create 3D images of cell and tissue specimens, but the method is limited to fluorescence. Our approach is to test a high resolution light microscope with penetrating light, combined with deconvolution and other image analysis techniques. We capture about 200 scans with 0.1 µm intervals, from a semi-thick histological section stained with the Feulgen-Schiff technique. Based on a section from the middle of the series, we segment and classify the nucleus and build 3-dimensional images based on the nucleus profile from all of the sections the nucleus is represented in. We have demonstrated that the technique works and have successfully produced several 3-dimensional images of nuclei.

Roadmap

The goal for this project is to create 3-dimensional analyses of nuclei, as well as visualize data in three dimensions. The first milestone will be to complete a DNA ploidy analysis on a set with 3-D reconstructed nuclei with an acceptable result (goal: CV on diploid nuclei < 7 %). To achieve this, the following tasks must be solved:

• Automate segmenting of the nucleus for all section profiles.
• Remove objects and light which are out of focus (haze removal).
• Define voxels (3-D pixels) in a functional way for analysis.
• Adapt IOD measurement to voxels.
• Optimize the method for uploading and time use.
• Optimize the texture properties and methods for analysis of chromatin structure in 3-D.