Rigid and non-rigid registration of polarized light imaging data for 3D reconstruction of the temporal lobe of the human brain at micrometer resolution

Ali, Sharib; Amunts, Katrin; Eils, Roland; Wörz, Stefan; Rohr, Karl; Axer, Markus

doi:10.1016/j.neuroimage.2018.06.084

Journal Article

FZJ-2018-05013

Rigid and non-rigid registration of polarized light imaging data for 3D reconstruction of the temporal lobe of the human brain at micrometer resolution

Ali, S. (Corresponding author) ; Wörz, S. ; Amunts, K.FZJ* ; Eils, R. ; Axer, M.FZJ* ; Rohr, K. (Last author)

2018
Academic Press Orlando, Fla.

NeuroImage 181, 235-251 (2018) [10.1016/j.neuroimage.2018.06.084]

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Please use a persistent id in citations: http://hdl.handle.net/2128/19686 doi:10.1016/j.neuroimage.2018.06.084

Abstract: To understand the spatial organization as well as long- and short-range connections of the human brain at microscopic resolution, 3D reconstruction of histological sections is important. We approach this challenge by reconstructing series of unstained histological sections of multi-scale (1:3 μm and 64 μm) and multi-modal 3D polarized light imaging (3D-PLI) data. Since spatial coherence is lost during the sectioning procedure, image registration is the major step in 3D reconstruction. We propose a non-rigid registration method which comprises of a novel multi-modal similarity metric and an improved regularization scheme to cope with deformations inevitably introduced during the sectioning procedure, as well as a rigid registration approach using a robust similarity metric for improved initial alignment. We also introduce a multi-scale feature-based localization and registration approach for mapping of 1:3 μm sections to 64 μm sections and a scale-adaptive method that can handle challenging sections with large semi-global deformations due to tissue splits. We have applied our registration method to 126 consecutive sections of the temporal lobe of the human brain with 64 μm and 1:3 μm resolution. Each step of the registration method was quantitatively evaluated using 10 different sections and manually determined ground truth, and a quantitative comparison with previous methods was performed. Visual assessment of the reconstructed volumes and comparison with reference volumes conﬁrmed the high quality of the registration result.

Keyword(s): Health and Life (1st) ; Medicine (2nd)

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