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Quality assurance for the 3D-PLI workflow

Background and Motivation

The Three-dimensional Polarized Light Imaging (3D-PLI) technology is used to capture high resolution images of thin post-mortem brain sections. The 3D-PLI raw data is processed in a complex reconstruction workflow to extract the orientations of the nerve fibers in the brain tissue.

After the slices have been prepared, they need to be stored until further processing can begin. However, over time, the composition of the stored tissue slowly changes. Such changes, as well as variations in the initial measurement quality, would propagate further down the processing pipeline unless identified at a sufficiently early stage. Delay in the identification of such problems can result in significantly more time spent on the processing pipeline, more changes in the tissue composition, as well as inefficient use of the high performance computing resources. It is therefore vital to have quality assurance procedures in place that can help identify issues early on.

Quality assurance for the 3D-PLI workflow

Figure 1: Illustration of the resulting fiber orientations after successful 3D-PLI reconstruction (left). Reconstruction based on an anatomically incorrect fiber orientation map (right). The root cause of the incorrect map is an error in one of the steps in the workflow.

Our approach

We have developed tools and algorithms that can detect potentially deficient measurements at an early stage in the workflow, as well as other errors during the execution of the workflow.

Our collaboration partners

This project is being conducted in collaboration with the Fiber Architecture group of the INM-1.

Related projects at the Simulation Laboratory Neuroscience