Statistics of deformations in histology and application to improved alignment with MRI

Abstract

An exact registration of magnetic resonance images (MRI) with histological sections is impeded by local deformations resulting from histological preparation procedures. Therefore, it is desirable to know the probability density function of spatial deformations in order to estimate optimal global least-square transformation parameters from suitable landmarks. For this reason, the statistics of deformations is investigated. It is shown analytically that the frequency of occurrence of the absolute geometrical differences (deformations) are Rayleigh-Bessel distributed for anisotropic histological preparation procedures and Rayleigh distributed in the case of isotropic procedures. The probabilistic analysis is given in conjunction with an iterative optimization technique in order to ensure that the probability density function is within a threshold required for the application to experimental data. The application of the analytical model is investigated with real data. It is shown with this data that the extent of deformations varies with the size of the histological section. An individual threshold can be selected on the basis of a Rayleigh-function restricting local corrections to small parts of the image. Thus, global misalignment in each section can be avoided, resulting in an improved 3-D reconstruction of the volume, i.e., the transitions from one section to the next are more continuous.

Comprehensive Approach to Coregistration of Autoradiography and Microscopy Images Acquired from a Set of Sequential Tissue Sections

“…As previously reported in histopathologic image registration studies (18,19), tissue cutting and slide preparation induce in each collected tissue section unique characteristic nonlinear deformations (tissue stretching and warping, among others). Thus, deformable image registration is needed to correctly align the images obtained from sequential tissue sections.…”

Registration of in-vivo to ex-vivo MRI of surgically resected specimens: A pipeline for histology to in-vivo registration

“…Performing voxel-based registration allows for spatially local comparison of MRI and histology, and the scale of this analysis is dependent on the achievable registration accuracy. Many previous studies in MRI and histology registration (see Table 3 2004; Meyer et al, 2006;Lebenberg et al, 2010;Schormann et al, 1995;Yelnik et al, 2007;Osechinskiy and Kruggel, 2011;Bardinet et al, 2002), and furthermore many previous studies included evaluation on only one dataset (Malandain et al, 2004;Choe et al, 2011;Meyer et al, 2006;Schormann et al, 1995;Kim et al, 2000;Yelnik et al, 2007;Osechinskiy and Kruggel, 2011;Bardinet et al, 2002;Lazebnik et al, 2003). Of the studies that did report accuracy on more than one dataset, TRE ranged from sub-millimeter (Ceritoglu et al, 2010;Jacobs et al, 1999;Yang et al, 2012) to 3-5 mm (Liu et al, 2012;Singh et al, 2008).…”

“…The majority of these studies focused on primates (Dauguet et al, 2007;Malandain et al, 2004;Breen et al, 2005;Ceritoglu et al, 2010;Choe et al, 2011) or rodents (Jacobs et al, 1999;Humm et al, 2003;Meyer et al, 2006;Lebenberg et al, 2010;Yang et al, 2012;Liu et al, 2012). The few studies that registered human brain MRIto histology were performed on wholebrain (Schormann et al, 1995;Kim et al, 2000;Singh et al, 2008), or single hemisphere (Yelnik et al, 2007;Osechinskiy and Kruggel, 2011) post-mortem serially sectioned data (Amunts et al, 2013) created a 3D model of single subject's brain using post-mortem histological sections reconstructed at 20 m isotropic resolution and registered it to a T1 average atlas created from 24 subjects. Eriksson et al (2005) reported registering histology of neocortical specimens from anterior temporal lobectomies to in-vivo MRI; however, their approach only involved visually selecting the closest coronal MRI slice for each histology slide, and did not attempt to find a dense correspondence between each histology slide and its corresponding MRI slice.…”

Co‐registration of in vivo human MRI brain images to postmortem histological microscopic images

“…Previous work to co-register in-vivo MRIs to microscopically examined samples has been reported mostly for small animal studies [Jacobs et al 1999;Jiang et al 2004;Meyer et al 2006;Anderson et al 2006], a limited number of primates [Malandain et al 2004;Kaufman et al 2005;Dauguet et al 2007] and relatively few human studies [Schormann et al 1995;Mega et al 1997;Toga et al 1999;Kenwright et al 2003]. Most studies involve brain imaging.…”

“…A reported early human study [Schormann et al 1995] relied on a landmark based approach where histological sections were deformed to match local regions within the MRIs. Not only is it difficult to define landmarks in the histological sections, but warping the high-resolution histological images to match relatively low-resolution specific MRI regions introduces significant interpolation errors.…”