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Piecewise Affine Registration of Biological Images [chapter]

Alain Pitiot, Grégoire Malandain, Eric Bardinet, Paul M. Thompson
2003 Lecture Notes in Computer Science  
This manuscript tackles the registration of 2D biological images (histological sections or autoradiographs) to 2D images from the same or different modalities (e.g., histology or MRI).  ...  Finally, the pairs of sub-images are, independently, affinely registered and a hybrid affine/non-linear interpolation scheme is used to compose the output registered image.  ...  In particular, pair-by-pair registration of a series of 2-D biological images (histological sections or autoradiographs) enables the reconstruction of a 3D biological image.  ... 
doi:10.1007/978-3-540-39701-4_10 fatcat:kvyunrwtjzci3pb5l3p3snrify

Piecewise affine registration of biological images for volume reconstruction

Alain Pitiot, Eric Bardinet, Paul M. Thompson, Grégoire Malandain
2006 Medical Image Analysis  
This manuscript tackles the reconstruction of 3D volumes via mono-modal registration of series of 2D biological images (histological sections, autoradiographs, cryosections, etc.).  ...  Finally, the pairs of sub-images are, independently, affinely registered and a hybrid affine/non-linear interpolation scheme is used to compose the output registered image.  ...  Turnbull from the Skirball Institute at NYU for the mouse brain images.  ... 
doi:10.1016/j.media.2005.03.008 pmid:15963755 fatcat:qwss2qjzifasnaegdk3gycgece

Anatomically Guided Registration of Whole Body Mouse MR Images [chapter]

N. Kovacevic, G. Hamarneh, M. Henkelman
2003 Lecture Notes in Computer Science  
The registration algorithm is designed to remove postural differences between mice and thus enable meaningful comparisons between images.  ...  This approach is described in the context of a program to screen for mutant mouse phenotypes based on high resolution MR images of whole animals.  ...  The MR data used in the Results section, courtesy of Duke Center for In Vivo Microscopy (NCRR P41 05959, NCI R24 CA 92656).  ... 
doi:10.1007/978-3-540-39903-2_106 fatcat:e2gxo7g4zbhkbow5zut3ktbolm

病理顕微鏡画像のレジストレーション手法
Methods for Microscope Pathology Images

Hidekata HONTANI
2018 Medical Imaging Technology  
Med Imag Anal 38: 184-204, 2017 [12] Pitiot A, Bardinet E, Thompson PM, et al.: Piecewise affine registration of biological images for volume reconstruction.  ...  Med Imag Anal 10: 465-483, 2006 [13] Feuerstein M, Heibel H, Gardiazabal J, et al.: Reconstruction of 3D histology images by simultaneous deformable registration.  ...  Non-rigid registration of given 2D pathology images is required for the reconstruction of appropriate 3D microscope images.  ... 
doi:10.11409/mit.36.157 fatcat:bym4ygeeivdcxa6atcl2oucxoe

Nanometer-accuracy distance measurements between fluorophores at the single-molecule level

Stefan Niekamp, Jongmin Sung, Walter Huynh, Gira Bhabha, Ronald D. Vale, Nico Stuurman
2019 Proceedings of the National Academy of Sciences of the United States of America  
Here, we describe methods that utilize information about localization and imaging errors to measure distances between two different color fluorophores with ∼1-nm accuracy at distances >2 nm.  ...  Single-molecule Förster resonance energy transfer can measure intramolecular distance changes of single molecules in the range of 2 to 8 nm.  ...  Skokan for critical discussions of the manuscript and E. Jonsson for the kinesin plasmids and discussions about the kinesin distance measurements.  ... 
doi:10.1073/pnas.1815826116 pmid:30770448 pmcid:PMC6410877 fatcat:g75onbx5xrh5vfppkweih5undi

Large deformation diffeomorphic metric mapping registration of reconstructed 3D histological section images and in vivo MR images

Can Ceritoglu
2010 Frontiers in Human Neuroscience  
image volume from the aligned sections, (3) registration of reconstructed 3D histological volumes to the corresponding 3D MRI volumes using 3D affine transformation, (4) intensity normalization of images  ...  LDDMM improved the accuracy of the registration via decreased distances between GM/CSF surfaces after LDDMM (0.39 ± 0.13 mm) compared to distances after affine registration (0.76 ± 0.41 mm).  ...  affine (Pitiot et al., 2006) and adaptive piecewise affine registration algorithms (Dauguet et al., 2007) .  ... 
doi:10.3389/fnhum.2010.00043 pmid:20577633 pmcid:PMC2889720 fatcat:nn4rlus22vcmreo3mopexhsibu

A Review of Geometric Transformations for Nonrigid Body Registration

M. Holden
2008 IEEE Transactions on Medical Imaging  
This paper provides a comprehensive and quantitative review of spatial transformations models for nonrigid image registration.  ...  Index Terms-Fluid flow registration, linear elastic registration, nonrigid image registration, parametric transformation models, spatial transformations, spline based registration, wavelet based registration  ...  Piecewise Affine This is sometimes also termed block-matching, multiple or poly-affine registration.  ... 
doi:10.1109/tmi.2007.904691 pmid:18270067 fatcat:ij3xb2d4hfdfxa3dctj23mk4hm

Group-Wise Diffeomorphic Diffusion Tensor Image Registration [chapter]

Xiujuan Geng, Hong Gu, Wanyong Shin, Thomas J. Ross, Yihong Yang
2010 Lecture Notes in Computer Science  
We propose an unbiased group-wise diffeomorphic registration technique to normalize a group of diffusion tensor (DT) images.  ...  The performance of the proposed method is compared with reference-based diffusion tensor imaging (DTI) registration methods.  ...  This work was sponsored by the National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health.  ... 
doi:10.1007/978-3-642-15705-9_73 fatcat:6nsjl5kkpzfxhlnk3gffoh3nmq

High accuracy measurements of nanometer-scale distances between fluorophores at the single-molecule level [article]

Stefan Niekamp, Jongmin Sung, Walter Huynh, Gira Bhabha, Ronald D Vale, Nico Stuurman
2017 bioRxiv   pre-print
Here, we describe methods that utilize information about localization and imaging errors to measure distances between two different color fluorophores with ~1 nm accuracy at any distance >2 nm, using a  ...  These new methods enable high-accuracy distance measurements of single-molecules that can be used over a wide range of length scales.  ...  Skokan for critical discussions of the manuscript. We are grateful to E. Jonsson for the kinesin plasmids and discussions about the kinesin distance measurements.  ... 
doi:10.1101/234740 fatcat:jfm5bdqtbzdwraevv3nvmm235q

FEATURE CURVE-GUIDED VOLUME RECONSTRUCTION FROM 2D IMAGES

Yunhao Tan, Jing Hua, Ming Dong
2007 2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
Histology slices are first scanned into computer as a sequence of image files with a histology film scanner.  ...  An initial 3D alignment of the images is obtained through the histological similarity matching between neighboring slices.  ...  Although informative itself, histology provides little information of the overall 3D biological structures and physical attributes.  ... 
doi:10.1109/isbi.2007.356952 dblp:conf/isbi/TanHD07 fatcat:3nzylx3i3ngthbd5o44pirs4zm

Image Registration: A Review of Elastic Registration Methods Applied to Medical Imaging

Asmita AMoghe, Jyoti Singhai
2013 International Journal of Computer Applications  
Such mapping of coordinates of the image that has undergone transformation on account of one or a combination of these factors calls for hybrid registration.  ...  Image registration is mapping different images of the same scene which have undergone changes due to time, position or inherent changes in the image.  ...  P.K Dave, MD, DRM, Radiologist, Kamla Nehru Gas Relief Hospital Bhopal, India, for his support and authorities of Jawaharlal Nehru Cancer Hospital and Research Center Bhopal, India, for providing the images  ... 
doi:10.5120/11972-7827 fatcat:z27kolxx6fgavfc5qtrmsfcqy4

Numerical methods for polyline-to-point-cloud registration with applications to patient-specific stent reconstruction

Claire Yilin Lin, Alessandro Veneziani, Lars Ruthotto
2017 International Journal for Numerical Methods in Biomedical Engineering  
We present novel numerical methods for Polyline-to-Point-Cloud Registration and their application to patient-specific modeling of deployed coronary artery stents from image data.  ...  The key contributions of the present paper are to represent the stent efficiently as a polyline (defined in [30] as piecewise linear objects consisting of vertices and edges) and develop new numerical  ...  Boyi Yang for his help in preparing the data set and invaluable feedback as well as the Core Lab in the Interventional Cardiology of the Emory University Hospital (H. Samady, B.  ... 
doi:10.1002/cnm.2934 pmid:29073332 fatcat:gvv64lcumbabbcnv7646yea5fe

Simple Methods for Scanner Drift Normalization Validated for Automatic Segmentation of Knee Magnetic Resonance Imaging - with data from the Osteoarthritis Initiative [article]

Erik B Dam
2017 arXiv   pre-print
The combined effects are particularly challenging for automatic image analysis methods used in longitudinal studies.  ...  The validation included a total of 1975 scans from both high-field and low-field MRI.  ...  The OAI is a public-private partnership comprised of five contracts (N01-AR-2-2258; N01-AR-2-2259; N01-AR-2-2260; N01-AR-2-2261; N01-AR-2-2262) funded by the National Institutes of Health, a branch of  ... 
arXiv:1712.08425v1 fatcat:odpdasxcurhhpjgpi67oitoxxi

IEEE Transactions on Medical Imaging

1986 IEEE Transactions on Medical Imaging  
This paper provides a comprehensive and quantitative review of spatial transformations models for nonrigid image registration.  ...  Index Terms-spatial transformations, nonrigid image registration, linear elastic registration, fluid flow registration, parametric transformation models, wavelet based registration, spline based registration  ...  Piecewise affine This is sometimes also termed block-matching, multiple or poly-affine registration.  ... 
doi:10.1109/tmi.1986.4307730 fatcat:r64bsavyq5dyti3ntc3dr7ta24

IEEE Transactions on Medical Imaging

1984 IEEE Transactions on Medical Imaging  
This paper provides a comprehensive and quantitative review of spatial transformations models for nonrigid image registration.  ...  Index Terms-spatial transformations, nonrigid image registration, linear elastic registration, fluid flow registration, parametric transformation models, wavelet based registration, spline based registration  ...  Piecewise affine This is sometimes also termed block-matching, multiple or poly-affine registration.  ... 
doi:10.1109/tmi.1984.4307643 fatcat:4hawzsfkvbci7e3vedmslszbjq
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