Correcting spatial distortion in histological images

Breen, Michael S.; Lancaster, Tanya L.; Wilson, David L.

doi:10.1016/j.compmedimag.2005.04.006

Cited by 18 publications

(24 citation statements)

References 27 publications

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“…This ''floating out'' phase introduces substantial distortion (in addition to the macroscopic distortion caused by initial wax-embedding). Breen et al 5,6 have used sophisticated 2D methods to correct the distortion introduced when serial thin sections are cut from wax-embedded skeletal muscle 5 and brain 6 specimens. As in this study, extrinsic corner markers and intrinsic tissue features were imaged before processing (photographically or with MRI) and used to control the registration process.…”

Section: Imaging Registration and Correctionmentioning

confidence: 99%

“…Tissue images in 3D have been reconstructed using wax-embedded segments. 5,6,18 However, unlike the SIM method, images have typically been acquired from serial thin sections cut with a microtome, fixed to glass slides, de-waxed, hydrated and stained using a variety of histological techniques. This ''floating out'' phase introduces substantial distortion (in addition to the macroscopic distortion caused by initial wax-embedding).…”

Section: Imaging Registration and Correctionmentioning

confidence: 99%

“…These occur during cutting and mounting, and are nonlinear, variable, and unpredictable. 8,32 Image slices must also be registered to preceding and subsequent images, 6,18 typically using established 2D registration methods. 7,23,34 Current trends are to combine the strengths of multiple imaging modalities.…”

Section: Introductionmentioning

confidence: 99%

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Three-Dimensional Cardiac Tissue Image Registration for Analysis of In Vivo Electrical Mapping

et al. 2010

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A method is presented for registering 3D cardiac tissue images to reference data, for the purpose of analyzing recorded electrical activity. Following left-ventricular in vivo electrical mapping studies in pig hearts, MRI is used to define a reference geometry in the tissue segment around the recording electrodes. The segment is then imaged in 3D using a high-resolution serial imaging microscopy technique. The tissue processing required for this introduces segment-wide distortion. Piecewise-smooth maps are used to correct the tissue distortion and register the 3D images with the reference MRI data. The methods are validated and techniques for identifying the preferred maps are proposed. Recorded electrical activation is shown to map reliably onto cardiac tissue structure using this registration method.

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Section: Imaging Registration and Correctionmentioning

confidence: 99%

Section: Imaging Registration and Correctionmentioning

confidence: 99%

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Three-Dimensional Cardiac Tissue Image Registration for Analysis of In Vivo Electrical Mapping

et al. 2010

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“…In the past two decades, there have also been many studies specifically dealing with in-vivo brain MRI to post-mortem histology. 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.…”

Section: Introductionmentioning

confidence: 99%

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

Goubran

Ribaupierre

Hammond

et al. 2015

Journal of Neuroscience Methods

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h i g h l i g h t s• We present a protocol for registration of in-vivo to ex-vivo brain specimens.• This protocol completes a registration pipeline for histology to in-vivo MRI.• A TRE of 1.35 ± 0.11 mm (neocortex) and 1.41 ± 0.33 mm (hippocampus) was found.• Deformable registration significantly improved the registration accuracy.• This pipeline allows for the assessment of pathological correlates in MRI. a r t i c l e i n f o t r a c tBackground: Advances in MRI have the potential to improve surgical treatment of epilepsy through improved identification and delineation of lesions. However, validation is currently needed to investigate histopathological correlates of these new imaging techniques. The purpose of this work is to develop and evaluate a protocol for deformable image registration of in-vivo to ex-vivo resected brain specimen MRI. This protocol, in conjunction with our previous work on ex-vivo to histology registration, completes a registration pipeline for histology to in-vivo MRI, enabling voxel-based validation of novel and existing MRI techniques with histopathology. New method: A combination of image-based and landmark-based 3D registration was used to register in-vivo MRI and the ex-vivo MRI from patients (N = 10) undergoing epilepsy surgery. Target registration error (TRE) was used to assess accuracy and the added benefit of deformable registration. Results: A mean TRE of 1.35 ± 0.11 and 1.41 ± 0.33 mm was found for neocortical and hippocampal specimens respectively. Statistical analysis confirmed that the deformable registration significantly improved the registration accuracy for both specimens.Comparison with existing methods: Image registration of surgically resected brain specimens is a unique application which presents numerous technical challenges and that have not been fully addressed in previous literature. Our computed TRE are comparable to previous attempts tackling similar applications, as registering in-vivo MRI to whole brain or serial histology. Conclusion: The presented registration pipeline finds dense and accurate spatial correspondence between in-vivo MRI and histology and allows for the spatially local and quantitative assessment of pathological correlates in MRI.

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“…The spin probe used for the EPRI was a carbon centered trityl radical, OX063 (methyl-tris[8-carboxy-2,2,6,6-tetrakis[(2-hydroxyethyl]benzo[1,2-d:4,5-d′] bis [1,3]dithiol-4-yl] trisodium salt), injected IV. A 1.6-cm diameter loop-gap resonator was used for EPRI at 250 MHz (FOV = 3.96 cm, matrix size = 64 × 64 × 64).…”

Section: Demonstration Of Mri-epri and Mri-histology Registrationmentioning

confidence: 99%

Immobilization using dental material casts facilitates accurate serial and multimodality small animal imaging

Haney

Fan

Parasca

et al. 2008

Concepts Magn Reson

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Custom disposable patient immobilization systems that conform to the patient's body contours are commonly used to facilitate accurate repeated patient setup for imaging and treatment in radiation therapy. However, in small-animal imaging, immobilization is often overlooked or done in a way that is not conducive to reproducible positioning. This has a negative impact on the potential for accurate analysis of serial or multimodality imaging. We present the use of vinyl polysiloxane dental impression material for immobilization of mice for imaging. Four different materials were examined to identify any potential artifacts using magnetic resonance techniques. A water phantom placed inside the cast was used at 4.7 T with magnetic resonance imaging and showed no effect at the center of the image when compared with images without the cast. A negligible effect was seen near the ends of the coil. Each material had no detectable signal using electron paramagnetic resonance imaging at 9 mT. The use of dental material also greatly enhances the use of fiducial markers that can be embedded in the mold. Therefore, image registration is simplified as the immobilization of the animal and fiducials together helps in translating from one image coordinate system to another.

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Correcting spatial distortion in histological images

Cited by 18 publications

References 27 publications

Three-Dimensional Cardiac Tissue Image Registration for Analysis of In Vivo Electrical Mapping

Three-Dimensional Cardiac Tissue Image Registration for Analysis of In Vivo Electrical Mapping

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

Immobilization using dental material casts facilitates accurate serial and multimodality small animal imaging

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