A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth
Three-dimensional (3-D) image analysis techniques provide a powerful means to rapidly and accurately assess complex morphological and functional interactions between neural cells. Current software-based identification methods of neural cells generally fall into two applications: (1) segmentation of...
Main Authors: | , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2015-07-01
|
Series: | Frontiers in Neuroanatomy |
Subjects: | |
Online Access: | http://journal.frontiersin.org/Journal/10.3389/fnana.2015.00087/full |
id |
doaj-9aab4c722f4d4b39a18f7f3c9d829339 |
---|---|
record_format |
Article |
spelling |
doaj-9aab4c722f4d4b39a18f7f3c9d8293392020-11-24T22:38:01ZengFrontiers Media S.A.Frontiers in Neuroanatomy1662-51292015-07-01910.3389/fnana.2015.00087151904A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowthJames D. Ross0James D. Ross1D. Kacy eCullen2D. Kacy eCullen3James Patrick Harris4James Patrick Harris5Michelle C. LaPlaca6Michelle C. LaPlaca7Stephen P. DeWeerth8Stephen P. DeWeerth9Georgia Institute of Technology / EmoryGeorgia Institute of TechnologyUniversity of PennsylvaniaPhiladelphia Veterans Affairs Medical CenterUniversity of PennsylvaniaPhiladelphia Veterans Affairs Medical CenterGeorgia Institute of Technology / EmoryGeorgia Institute of TechnologyGeorgia Institute of Technology / EmoryGeorgia Institute of TechnologyThree-dimensional (3-D) image analysis techniques provide a powerful means to rapidly and accurately assess complex morphological and functional interactions between neural cells. Current software-based identification methods of neural cells generally fall into two applications: (1) segmentation of cell nuclei in high-density constructs or (2) tracing of cell neurites in single cell investigations. We have developed novel methodologies to permit the systematic identifica-tion of populations of neuronal somata possessing rich morphological detail and dense neurite arborization throughout thick tissue or 3-D in vitro constructs. The image analysis incorporates several novel automated features for the discrimination of neurites and somata by initially classi-fying features in 2-D and merging these classifications into 3-D objects, the 3-D reconstructions automatically identify and adjust for over and under segmentation errors. Additionally, the plat-form provides for software-assisted error corrections to further minimize error. These features attain very accurate cell boundary identifications to handle a wide range of morphological com-plexities. We validated these tools using confocal z-stacks from thick 3-D neural constructs where neuronal somata had varying degrees of neurite arborization and complexity, achieving an accuracy of ≥ 95%. We demonstrated the robustness of these algorithms in a more complex are-na through the automated segmentation of neural cells in ex vivo brain slices. The novel methods surpass previous research improving the robustness and accuracy by: (1) the ability to process neurites and somata, (2) bidirectional segmentation correction, and (3) validation via software-assisted user input. This 3-D image analysis platform provides valuable tools for the unbiased analysis of neural tissue or tissue surrogates within a 3-D context, appropriate for the study of multi-dimensional cell-cell and cell-extracellular matrix interactions.http://journal.frontiersin.org/Journal/10.3389/fnana.2015.00087/fullconfocalfluorescent microscopyimage processingsegmentationneural constructs |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
James D. Ross James D. Ross D. Kacy eCullen D. Kacy eCullen James Patrick Harris James Patrick Harris Michelle C. LaPlaca Michelle C. LaPlaca Stephen P. DeWeerth Stephen P. DeWeerth |
spellingShingle |
James D. Ross James D. Ross D. Kacy eCullen D. Kacy eCullen James Patrick Harris James Patrick Harris Michelle C. LaPlaca Michelle C. LaPlaca Stephen P. DeWeerth Stephen P. DeWeerth A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth Frontiers in Neuroanatomy confocal fluorescent microscopy image processing segmentation neural constructs |
author_facet |
James D. Ross James D. Ross D. Kacy eCullen D. Kacy eCullen James Patrick Harris James Patrick Harris Michelle C. LaPlaca Michelle C. LaPlaca Stephen P. DeWeerth Stephen P. DeWeerth |
author_sort |
James D. Ross |
title |
A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth |
title_short |
A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth |
title_full |
A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth |
title_fullStr |
A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth |
title_full_unstemmed |
A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth |
title_sort |
three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Neuroanatomy |
issn |
1662-5129 |
publishDate |
2015-07-01 |
description |
Three-dimensional (3-D) image analysis techniques provide a powerful means to rapidly and accurately assess complex morphological and functional interactions between neural cells. Current software-based identification methods of neural cells generally fall into two applications: (1) segmentation of cell nuclei in high-density constructs or (2) tracing of cell neurites in single cell investigations. We have developed novel methodologies to permit the systematic identifica-tion of populations of neuronal somata possessing rich morphological detail and dense neurite arborization throughout thick tissue or 3-D in vitro constructs. The image analysis incorporates several novel automated features for the discrimination of neurites and somata by initially classi-fying features in 2-D and merging these classifications into 3-D objects, the 3-D reconstructions automatically identify and adjust for over and under segmentation errors. Additionally, the plat-form provides for software-assisted error corrections to further minimize error. These features attain very accurate cell boundary identifications to handle a wide range of morphological com-plexities. We validated these tools using confocal z-stacks from thick 3-D neural constructs where neuronal somata had varying degrees of neurite arborization and complexity, achieving an accuracy of ≥ 95%. We demonstrated the robustness of these algorithms in a more complex are-na through the automated segmentation of neural cells in ex vivo brain slices. The novel methods surpass previous research improving the robustness and accuracy by: (1) the ability to process neurites and somata, (2) bidirectional segmentation correction, and (3) validation via software-assisted user input. This 3-D image analysis platform provides valuable tools for the unbiased analysis of neural tissue or tissue surrogates within a 3-D context, appropriate for the study of multi-dimensional cell-cell and cell-extracellular matrix interactions. |
topic |
confocal fluorescent microscopy image processing segmentation neural constructs |
url |
http://journal.frontiersin.org/Journal/10.3389/fnana.2015.00087/full |
work_keys_str_mv |
AT jamesdross athreedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT jamesdross athreedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT dkacyecullen athreedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT dkacyecullen athreedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT jamespatrickharris athreedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT jamespatrickharris athreedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT michelleclaplaca athreedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT michelleclaplaca athreedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT stephenpdeweerth athreedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT stephenpdeweerth athreedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT jamesdross threedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT jamesdross threedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT dkacyecullen threedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT dkacyecullen threedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT jamespatrickharris threedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT jamespatrickharris threedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT michelleclaplaca threedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT michelleclaplaca threedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT stephenpdeweerth threedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth AT stephenpdeweerth threedimensionalimageprocessingprogramforaccuraterapidandsemiautomatedsegmentationofneuronalsomatawithdenseneuriteoutgrowth |
_version_ |
1725715070005018624 |