Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images.

PloS One
Alfredo RodriguezSusan L Wearne

Abstract

A fundamental challenge in understanding how dendritic spine morphology controls learning and memory has been quantifying three-dimensional (3D) spine shapes with sufficient precision to distinguish morphologic types, and sufficient throughput for robust statistical analysis. The necessity to analyze large volumetric data sets accurately, efficiently, and in true 3D has been a major bottleneck in deriving reliable relationships between altered neuronal function and changes in spine morphology. We introduce a novel system for automated detection, shape analysis and classification of dendritic spines from laser scanning microscopy (LSM) images that directly addresses these limitations. The system is more accurate, and at least an order of magnitude faster, than existing technologies. By operating fully in 3D the algorithm resolves spines that are undetectable with standard two-dimensional (2D) tools. Adaptive local thresholding, voxel clustering and Rayburst Sampling generate a profile of diameter estimates used to classify spines into morphologic types, while minimizing optical smear and quantization artifacts. The technique opens new horizons on the objective evaluation of spine changes with synaptic plasticity, normal developm...Continue Reading

References

Sep 1, 1990·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·J R Glaser, E M Glaser
Jan 1, 1989·Trends in Neurosciences·J R Naegele, C J Barnstable
Jan 1, 1969·Experimental Brain Research·F Valverde, A Ruiz-Marcos
Apr 1, 1970·The American Journal of Anatomy·A Peters, I R Kaiserman-Abramof
Jun 1, 1997·Current Opinion in Neurobiology·H BitoR W Tsien
Mar 31, 1999·Proceedings of the National Academy of Sciences of the United States of America·T Schikorski, C F Stevens
Jun 22, 2000·Nature Neuroscience·R YusteK Holthoff
Aug 25, 2001·Annual Review of Neuroscience·R Yuste, T Bonhoeffer
Dec 26, 2001·Nature Reviews. Neuroscience·H Hering, M Sheng
Feb 5, 2002·Annual Review of Physiology·Esther A NimchinskyKarel Svoboda
Feb 8, 2002·Neuron·Knut HolthoffRafael Yuste
May 22, 2002·Neural Computation·Ingrid Y Y KohKarel Svoboda
May 29, 2002·Brain Research·Jeffrey L KrichmarGiorgio A Ascoli
Jun 22, 2002·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Khalid A Al-KofahiBadrinath Roysam
Sep 12, 2002·Network : Computation in Neural Systems·Geert J Streekstra, Jaap van Pelt
Dec 20, 2002·Nature·Jaime GrutzendlerWen-Biao Gan
Jul 10, 2003·Trends in Neurosciences·Haruo KasaiHiroyuki Nakahara
Aug 7, 2003·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Wenyun HeBadrinath Roysam
Jun 29, 2004·Trends in Neurosciences·Qiang Zhou, Mu-ming Poo
Jan 25, 2005·Neuron·Anthony J G D HoltmaatKarel Svoboda
Nov 8, 2005·Science·Brenda L Bloodgood, Bernardo L Sabatini
Jun 23, 2006·Nature·Anthony HoltmaatKarel Svoboda
Nov 23, 2006·Neuron·Fidel SantamariaGeorge J Augustine
Feb 7, 2007·Annual Review of Neuroscience·Veronica A Alvarez, Bernardo L Sabatini
Apr 25, 2007·Current Opinion in Neurobiology·Brenda L Bloodgood, Bernardo L Sabatini
May 15, 2007·Current Opinion in Neurobiology·Jennifer Bourne, Kristen M Harris
Jul 17, 2007·Journal of Neuroscience Methods·Jie ChengSteven T C Wong

❮ Previous
Next ❯

Citations

Oct 10, 2014·Medical Image Analysis·Clemens BlumerThomas G Oertner
Feb 19, 2013·Brain Structure & Function·Sarah E Crowe, Graham C R Ellis-Davies
Aug 20, 2014·Nature Communications·Katherine L EalesSonia A L Corrêa
Jun 12, 2014·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Karolina SzczesnaManel Esteller
Feb 9, 2010·Cerebral Cortex·Rebecca M ShanskyJohn H Morrison
Mar 10, 2010·Brain Structure & Function·Dara L DicksteinPatrick R Hof
Aug 12, 2010·Journal of Cell Science·Agnès BellyYves Goldberg
Oct 22, 2010·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Hugo H HansonGreg R Phillips
Feb 11, 2011·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Sophie Scotto-LomasseseIsabelle Caillé
Apr 26, 2011·RNA·Eun Joo LeeKenneth S Kosik
Jun 28, 2011·Science·Daniel BusheyChiara Cirelli
Oct 5, 2012·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Joseph M AmatrudoJennifer I Luebke
Nov 2, 2012·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Laura Beth J McIntireTae-Wan Kim
Feb 27, 2013·PloS One·Ignacio JausoroAlfredo Caceres
Jul 5, 2013·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Xiaoting WangMarina E Wolf
Oct 4, 2013·BMC Bioinformatics·Aruna JammalamadakaKenneth S Kosik
Jul 12, 2012·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Daniel J ChristoffelScott J Russo
Jun 30, 2012·Bioinformatics·Boguslaw ObaraMark D Fricker
Feb 12, 2013·Bioinformatics·Brian E RuttenbergAmbuj K Singh
Aug 24, 2010·Nature Neuroscience·Quincey LaPlantEric J Nestler
Jun 19, 2014·Molecular and Cellular Neurosciences·Mikko KoskinenPirta Hotulainen
Sep 12, 2012·The Journal of Cell Biology·Mado LemieuxPaul De Koninck
Nov 4, 2015·The Journal of Cell Biology·Joerg SchreiberRonald E Van Kesteren
Apr 8, 2016·Cellular Logistics·Sharon A SwangerJeremy H Herskowitz
Jan 23, 2016·Frontiers in Molecular Neuroscience·Francesca Pischedda, Giovanni Piccoli
Apr 3, 2013·Neurobiology of Disease·Jarin HongpaisanDaniel L Alkon

❮ Previous
Next ❯

Methods Mentioned

BETA
electron microscopy
light microscopy

Software Mentioned

AutoNeuron
ISODATA
Octree
NeuronStudio
Rayburst
Neurolucida
NeuroZoom
Windows

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.