Evaluating Registrations of Serial Sections With Distortions of the Ground Truths

Oleg Lobachev,Lars Knudsen,Simone Gaffling,Christian Muhlfeld,Jaan Toelen,Michael Guthe,David Haberthur,Roman Grothausmann,Ruslan Hlushchuk,Thomas Salaets,Alexander Pfaffenroth,Christoph Wrede,Reinhold Forster,Takuya Funatomi

doi:10.1109/access.2021.3124341

Abstract

Registration of histological serial sections is a challenging task. Serial sections exhibit distortions and damage from sectioning. Missing information on how the tissue looked before cutting makes a realistic validation of 2D registrations extremely difficult. This work proposes methods for ground-truth-based evaluation of registrations. Firstly, we present a methodology to generate test data for registrations. We distort an innately registered image stack in the manner similar to the cutting distortion of serial sections. Test cases are generated from existing 3D data sets, thus the ground truth is known. Secondly, our test case generation premises evaluation of the registrations with known ground truths. Our methodology for such an evaluation technique distinguishes this work from other approaches. Both under- and over-registration become evident in our evaluations. We also survey existing validation efforts. We present a full-series evaluation across six different registration methods applied to our distorted 3D data sets of animal lungs. Our distorted and ground truth data sets are made publicly available.

Highlights

M ICROSCOPY has a long tradition, and microscopic imaging is still one of the most frequently used and powerful tools in biomedical research
Our goal is to enable the evaluation of registration methods for serial sections with a ground truth from real biological data
A pair-wise evaluation is included in the supplementary material

Summary

Introduction

M ICROSCOPY has a long tradition, and microscopic imaging is still one of the most frequently used and powerful tools in biomedical research. From light microscopic (LM) techniques, including conventional fluorescent stainings, to transmission and scanning electron microscopic (EM) methods, the last two decades have witnessed substantial methodological progress in terms of resolution, speed, and automation. The use of serial sections remains an essential and cost-efficient tool to gain 3D insight into specimens for several reasons: Despite the progress in LM techniques the penetration depth of staining solutions, in particular fluorescent antibody staining, is limited, limiting the size of the sample that can be visualized. Modified organisms, such as mice, expressing fluorescent proteins.

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