TY - GEN
T1 - Fully automatic 3D reconstruction of histological images
AU - Baǧci, Ulaş
AU - Bai, Li
N1 - Copyright:
Copyright 2011 Elsevier B.V., All rights reserved.
PY - 2008
Y1 - 2008
N2 - In this paper, we propose a computational framework for 3D volume reconstruction from 2D histological slices using registration algorithms in feature space. To improve the quality of reconstructed 3D volume, first, intensity variations in images are corrected by an intensity standardization process which maps image intensity scale to a standard scale where similar intensities correspond to similar tissues. Second, a subvolume approach is proposed for 3D reconstruction by dividing standardized slices into groups. Third, in order to improve the quality of the reconstruction process, an automatic best reference slice selection algorithm is developed based on an iterative assessment of image entropy and mean square error of the registration process. Finally, we demonstrate that the choice of the reference slice has a significant impact on registration quality and subsequent 3D reconstruction.
AB - In this paper, we propose a computational framework for 3D volume reconstruction from 2D histological slices using registration algorithms in feature space. To improve the quality of reconstructed 3D volume, first, intensity variations in images are corrected by an intensity standardization process which maps image intensity scale to a standard scale where similar intensities correspond to similar tissues. Second, a subvolume approach is proposed for 3D reconstruction by dividing standardized slices into groups. Third, in order to improve the quality of the reconstruction process, an automatic best reference slice selection algorithm is developed based on an iterative assessment of image entropy and mean square error of the registration process. Finally, we demonstrate that the choice of the reference slice has a significant impact on registration quality and subsequent 3D reconstruction.
KW - Edgeness
KW - Elastic registration
KW - Entropy
KW - Histology
KW - Image reconstruction
UR - http://www.scopus.com/inward/record.url?scp=51049119205&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=51049119205&partnerID=8YFLogxK
U2 - 10.1109/ISBI.2008.4541165
DO - 10.1109/ISBI.2008.4541165
M3 - Conference contribution
AN - SCOPUS:51049119205
SN - 9781424420032
T3 - 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Proceedings, ISBI
SP - 991
EP - 994
BT - 2008 5th IEEE International Symposium on Biomedical Imaging
T2 - 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI
Y2 - 14 May 2008 through 17 May 2008
ER -