Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines

TL;DR

This paper introduces a fuzzy set theory-based method to incorporate prior knowledge into large-scale 3D+t microscopy image analysis, enhancing accuracy and efficiency without sacrificing result quality.

Contribution

It presents a novel approach for estimating and propagating uncertainty in image analysis operators using fuzzy set theory, improving large-scale bioimage processing pipelines.

Findings

Enhanced detection and segmentation accuracy in microscopy data

Validated on simulated and real zebrafish embryo datasets

Applicable to various linear image processing pipelines

Abstract

Many automatically analyzable scientific questions are well-posed and offer a variety of information about the expected outcome a priori. Although often being neglected, this prior knowledge can be systematically exploited to make automated analysis operations sensitive to a desired phenomenon or to evaluate extracted content with respect to this prior knowledge. For instance, the performance of processing operators can be greatly enhanced by a more focused detection strategy and the direct information about the ambiguity inherent in the extracted data. We present a new concept for the estimation and propagation of uncertainty involved in image analysis operators. This allows using simple processing operators that are suitable for analyzing large-scale 3D+t microscopy images without compromising the result quality. On the foundation of fuzzy set theory, we transform available prior knowledge into a mathematical representation and extensively use it enhance the result quality of various processing operators. All presented concepts are illustrated on a typical bioimage analysis pipeline comprised of seed point detection, segmentation, multiview fusion and tracking. Furthermore, the functionality of the proposed approach is validated on a comprehensive simulated 3D+t benchmark data set that mimics embryonic development and on large-scale light-sheet microscopy data of a zebrafish embryo. The general concept introduced in this contribution represents a new approach to efficiently exploit prior knowledge to improve the result quality of image analysis pipelines. Especially, the automated analysis of terabyte-scale microscopy data will benefit from sophisticated and efficient algorithms that enable a quantitative and fast readout. The generality of the concept, however, makes it also applicable to practically any other field with processing strategies that are arranged as linear pipelines.