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Title: Serial Section Registration of Axonal Confocal Microscopy Datasets for Long-Range Neural Circuit Reconstruction

Abstract

In the context of long-range digital neural circuit reconstruction, this paper investigates an approach for registering axons across histological serial sections. Tracing distinctly labeled axons over large distances allows neuroscientists to study very explicit relationships between the brain's complex interconnects and, for example, diseases or aberrant development. Large scale histological analysis requires, however, that the tissue be cut into sections. In immunohistochemical studies thin sections are easily distorted due to the cutting, preparation, and slide mounting processes. In this work we target the registration of thin serial sections containing axons. Sections are first traced to extract axon centerlines, and these traces are used to define registration landmarks where they intersect section boundaries. The trace data also provides distinguishing information regarding an axon's size and orientation within a section. We propose the use of these features when pairing axons across sections in addition to utilizing the spatial relationships amongst the landmarks. The global rotation and translation of an unregistered section are accounted for using a random sample consensus (RANSAC) based technique. An iterative nonrigid refinement process using B-spline warping is then used to reconnect axons and produce the sought after connectivity information.

Authors:
; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1045096
Report Number(s):
PNNL-SA-88916
Journal ID: ISSN 0165-0270; JNMEDT; WN0219080; TRN: US201214%%924
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Journal of Neuroscience Methods
Additional Journal Information:
Journal Volume: 207; Journal Issue: 2; Journal ID: ISSN 0165-0270
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; DISEASES; MICROSCOPY; ORIENTATION; ROTATION; TARGETS; image registration

Citation Formats

Hogrebe, Luke, Paiva, Antonio R., Jurrus, Elizabeth R., Christensen, Cameron, Bridge, Michael, Dai, Li, Pfeiffer, Rebecca, Hof, Patrick, Roysam, Badrinath, Korenberg, Julie, and Tasdizen, Tolga. Serial Section Registration of Axonal Confocal Microscopy Datasets for Long-Range Neural Circuit Reconstruction. United States: N. p., 2012. Web. doi:10.1016/j.jneumeth.2012.03.002.
Hogrebe, Luke, Paiva, Antonio R., Jurrus, Elizabeth R., Christensen, Cameron, Bridge, Michael, Dai, Li, Pfeiffer, Rebecca, Hof, Patrick, Roysam, Badrinath, Korenberg, Julie, & Tasdizen, Tolga. Serial Section Registration of Axonal Confocal Microscopy Datasets for Long-Range Neural Circuit Reconstruction. United States. doi:10.1016/j.jneumeth.2012.03.002.
Hogrebe, Luke, Paiva, Antonio R., Jurrus, Elizabeth R., Christensen, Cameron, Bridge, Michael, Dai, Li, Pfeiffer, Rebecca, Hof, Patrick, Roysam, Badrinath, Korenberg, Julie, and Tasdizen, Tolga. Fri . "Serial Section Registration of Axonal Confocal Microscopy Datasets for Long-Range Neural Circuit Reconstruction". United States. doi:10.1016/j.jneumeth.2012.03.002.
@article{osti_1045096,
title = {Serial Section Registration of Axonal Confocal Microscopy Datasets for Long-Range Neural Circuit Reconstruction},
author = {Hogrebe, Luke and Paiva, Antonio R. and Jurrus, Elizabeth R. and Christensen, Cameron and Bridge, Michael and Dai, Li and Pfeiffer, Rebecca and Hof, Patrick and Roysam, Badrinath and Korenberg, Julie and Tasdizen, Tolga},
abstractNote = {In the context of long-range digital neural circuit reconstruction, this paper investigates an approach for registering axons across histological serial sections. Tracing distinctly labeled axons over large distances allows neuroscientists to study very explicit relationships between the brain's complex interconnects and, for example, diseases or aberrant development. Large scale histological analysis requires, however, that the tissue be cut into sections. In immunohistochemical studies thin sections are easily distorted due to the cutting, preparation, and slide mounting processes. In this work we target the registration of thin serial sections containing axons. Sections are first traced to extract axon centerlines, and these traces are used to define registration landmarks where they intersect section boundaries. The trace data also provides distinguishing information regarding an axon's size and orientation within a section. We propose the use of these features when pairing axons across sections in addition to utilizing the spatial relationships amongst the landmarks. The global rotation and translation of an unregistered section are accounted for using a random sample consensus (RANSAC) based technique. An iterative nonrigid refinement process using B-spline warping is then used to reconnect axons and produce the sought after connectivity information.},
doi = {10.1016/j.jneumeth.2012.03.002},
journal = {Journal of Neuroscience Methods},
issn = {0165-0270},
number = 2,
volume = 207,
place = {United States},
year = {2012},
month = {6}
}