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. 2013 Mar 30;4(Suppl):S10.
doi: 10.4103/2153-3539.109868. Print 2013.

Registration of histological whole slide images guided by vessel structures

Michael Schwier  1 , Tobias Böhler, Horst Karl Hahn, Uta Dahmen, Olaf Dirsch
Affiliations

Registration of histological whole slide images guided by vessel structures

Michael Schwier et al. J Pathol Inform. .

Abstract

Introduction: The registration of histological whole slide images is an important prerequisite for modern histological image analysis. A partial reconstruction of the original volume allows e.g. colocalization analysis of tissue parameters or high-detail reconstructions of anatomical structures in 3D.

Methods: In this paper, we present an automatic staining-invariant registration method, and as part of that, introduce a novel vessel-based rigid registration algorithm using a custom similarity measure. The method is based on an iterative best-fit matching of prominent vessel structures.

Results: We evaluated our method on a sophisticated synthetic dataset as well as on real histological whole slide images. Based on labeled vessel structures we compared the relative differences for corresponding structures. The average positional error was close to 0, the median for the size change factor was 1, and the median overlap was 0.77.

Conclusion: The results show that our approach is very robust and creates high quality reconstructions. The key element for the resulting quality is our novel rigid registration algorithm.

Keywords: Elastic registration; histology; rigid registration; vessel structure; whole slide images.

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Figures

Figure 1
Figure 1
Compute a transformation based on a double pair: (a) Original configuration. (b) Translate bk onto ai. (c) Pivot around ai to align aj and bl.
Figure 2
Figure 2
(a) A real histological slide of a rat liver. (b) A synthetic histological slide. (c) Corresponding label slide for automatic evaluation. Each vessel label in each slide has a unique ID throughout the whole dataset
Figure 3
Figure 3
Rigid registration errors: (a) Rotation error on rigid + elastic (top) and only rigid (bottom) deformed synthetic data. (b) Translation error (Euclidean distance) on rigid + elastic (top) and only rigid (bottom) deformed synthetic data
Figure 4
Figure 4
Boxplots of overall registration errors (red line = median, left/right end of box = lower/upper quartile, whiskers = 1.5 interquartile range (IQR)): (a) Relative inter-slice position error. (b) Size changes and inter-slice overlap changes
Figure 5
Figure 5
Some example slides that failed to be correctly registered due to severe disruptions
Figure 6
Figure 6
Example of six consecutive slides that have been registered successfully even though some rather difficult cases are apparent
Figure 7
Figure 7
(a) (b) Example cross sections of a registered histological dataset. Top: No registration. Middle: Only rigid registration. Bottom: Full registration (rigid + elastic)
See this image and copyright information in PMC

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