Segmentation propagation using a 3D embryo atlas for high-throughput MRI phenotyping: comparison and validation with manual segmentation.

Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine
Francesca C NorrisMark F Lythgoe

Abstract

Effective methods for high-throughput screening and morphometric analysis are crucial for phenotyping the increasing number of mouse mutants that are being generated. Automated segmentation propagation for embryo phenotyping is an emerging application that enables noninvasive and rapid quantification of substructure volumetric data for morphometric analysis. We present a study to assess and validate the accuracy of brain and kidney volumes generated via segmentation propagation in an ex vivo mouse embryo MRI atlas comprising three different groups against the current "gold standard"--manual segmentation. Morphometric assessment showed good agreement between automatically and manually segmented volumes, demonstrating that it is possible to assess volumes for phenotyping a population of embryos using segmentation propagation with the same variation as manual segmentation. As part of this study, we have made our average atlas and segmented volumes freely available to the community for use in mouse embryo phenotyping studies. These MRI datasets and automated methods of analyses will be essential for meeting the challenge of high-throughput, automated embryo phenotyping.

References

Apr 26, 1994·Proceedings of the National Academy of Sciences of the United States of America·B R SmithE Linney
Feb 13, 2001·Radiology·M R KausR Kikinis
Jun 13, 2001·Developmental Biology·M DhenainR E Jacobs
Oct 9, 2001·Nature Medicine·M R Capecchi
Dec 6, 2002·Nature·UNKNOWN Mouse Genome Sequencing ConsortiumEric S Lander
Oct 21, 2004·Birth Defects Research. Part C, Embryo Today : Reviews·Jürgen E Schneider, Shoumo Bhattacharya
Jan 5, 2005·International Journal of Radiation Oncology, Biology, Physics·Pierre-Yves BondiauNicholas Ayache
Aug 9, 2005·NeuroImage·X Josette ChenJeffrey T Henderson
Apr 28, 2006·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Nicholas A BockR Mark Henkelman
May 10, 2006·PLoS Genetics·John T JohnsonCharles Keller
Jan 16, 2007·Cell·Francis S CollinsWolfgang Wurst
Oct 19, 2007·NeuroImage·Jason P LerchR Mark Henkelman
Dec 1, 2007·Journal of Magnetic Resonance Imaging : JMRI·Edwin HeijmanGustav J Strijkers
Aug 21, 2008·Proceedings of the National Academy of Sciences of the United States of America·Alexandra E PetietG Allan Johnson
Mar 24, 2009·Alcoholism, Clinical and Experimental Research·Scott E ParnellKathleen K Sulik
Jul 15, 2009·NMR in Biomedicine·Jon O ClearyMark F Lythgoe
Oct 13, 2009·Computer Methods and Programs in Biomedicine·Marc ModatSébastien Ourselin
Dec 5, 2009·Methods in Molecular Biology·Alexandra Petiet, G Allan Johnson
Jun 1, 2010·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·Xiaoli ZhangR Mark Henkelman
Jul 6, 2010·NeuroImage·G Allan JohnsonJonathan Nissanov
Aug 5, 2010·Physiological Genomics·M ZamyadiJ G Sled
Oct 1, 2010·Journal of Magnetic Resonance Imaging : JMRI·Johannes RieglerMark F Lythgoe

❮ Previous
Next ❯

Citations

Sep 17, 2013·Trends in Genetics : TIG·Francesca C NorrisMark F Lythgoe
Oct 21, 2014·PloS One·Thomas A RobertsMark F Lythgoe
Jun 16, 2016·Circulation Journal : Official Journal of the Japanese Circulation Society·Samer S MerchantLuca Brunelli
Oct 16, 2016·Briefings in Bioinformatics·James M BrownAnn-Marie Mallon

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine
Francesca C NorrisMark F Lythgoe
Current Opinion in Genetics & Development
Brian J NiemanR M Henkelman
Developmental Dynamics : an Official Publication of the American Association of Anatomists
Gregory A AndersonR M Henkelman
© 2021 Meta ULC. All rights reserved