Search Results - "neuron segmentation"

Quantifying morphologies of developing neuronal cells using deep learning with imperfect annotations

Authors: Amir Masoud Nourollah Hamid Hassanpour Amin Zehtabian

Source: IBRO Neurosci Rep
IBRO Neuroscience Reports, Vol 16, Iss, Pp 118-126 (2024)

Subject Terms: Neuron Segmentation, 0301 basic medicine, Imperfect Annotation, 0206 medical engineering, Neurosciences. Biological psychiatry. Neuropsychiatry, 500 Naturwissenschaften und Mathematik::570 Biowissenschaften, Biologie::570 Biowissenschaften, Biologie, 02 engineering and technology, Neuronal Morphologies, 03 medical and health sciences, Fluorescence Microscopy, Deep Learning, Weak Supervision, RC321-571, Research Paper

Access URL: https://pubmed.ncbi.nlm.nih.gov/38282758
https://doaj.org/article/65317f08c7a24bb193b878b7f45ccef9

Neuronal Mesh Reconstruction from Image Stacks Using Implicit Neural Representations

Authors: Xiaoqiang Zhu Yanhua Zhao Lihua You

Source: Mathematics, Vol 13, Iss 8, p 1276 (2025)

Subject Terms: implicit neural representations, SDF, deep learning, neuronal morphology, representation learning, neuron segmentation, Mathematics, QA1-939

Relation: https://www.mdpi.com/2227-7390/13/8/1276; https://doaj.org/toc/2227-7390; https://doaj.org/article/2d708fa5e8b747d48dd1b802ce0bf9de

Availability: https://doi.org/10.3390/math13081276
https://doaj.org/article/2d708fa5e8b747d48dd1b802ce0bf9de

A modular framework for multi-scale tissue imaging and neuronal segmentation

Authors: Cauzzo S. Bruno E. Boulet D. et al.

Contributors: Cauzzo S. Bruno E. Boulet D. et al.

Subject Terms: Neuron segmentation, algorithm, image processing, dense-packed microstructure, imaging framework

File Description: ELETTRONICO

Relation: info:eu-repo/semantics/altIdentifier/pmid/38778027; info:eu-repo/semantics/altIdentifier/wos/WOS:001229525900027; volume:15; issue:1; numberofpages:17; journal:NATURE COMMUNICATIONS; https://hdl.handle.net/11568/1241429

Availability: https://hdl.handle.net/11568/1241429
https://doi.org/10.1038/s41467-024-48146-y
https://www.nature.com/articles/s41467-024-48146-y.pdf

DDeep3M+ : adaptive enhancement powered weakly supervised learning for neuron segmentation

Authors: Xiao, R Zhu, L Liao, J et al.

Contributors: Xiao, R Zhu, L Liao, J et al.

Subject Terms: Convolutional neural network, Hessian matrix, Image segmentation, Neuron segmentation, Weakly supervised deep learning

Relation: http://hdl.handle.net/10397/109677; 10; 035003; OA_Scopus/WOS

Availability: http://hdl.handle.net/10397/109677
https://doi.org/10.1117/1.NPh.10.3.035003

Quantifying morphologies of developing neuronal cells using deep learning with imperfect annotations

Authors: Nourollah, Amir Masoud Hassanpour, Hamid Zehtabian, Amin

Subject Terms: Neuronal Morphologies, Fluorescence Microscopy, Neuron Segmentation, Deep Learning, Imperfect Annotation, Weak Supervision, ddc:570

File Description: 9 Seiten; application/pdf

Availability: https://refubium.fu-berlin.de/handle/fub188/42772
https://doi.org/10.17169/refubium-42488
https://doi.org/10.1016/j.ibneur.2023.12.009

NeuroSeg-II: A deep learning approach for generalized neuron segmentation in two-photon Ca2+ imaging

Authors: Zhehao Xu Yukun Wu Jiangheng Guan et al.

Source: Front Cell Neurosci
Frontiers in Cellular Neuroscience, Vol 17 (2023)

Subject Terms: 0301 basic medicine, 0303 health sciences, 03 medical and health sciences, hybrid training, deep learning, Neurosciences. Biological psychiatry. Neuropsychiatry, attention mechanism, two-photon Ca2+ imaging, generalized neuron segmentation, RC321-571, Neuroscience

Access URL: https://pubmed.ncbi.nlm.nih.gov/37091918
https://doaj.org/article/34bba380bc1e4757a76c044b916e632e

Real-Time Image Processing Toolbox for All-Optical Closed-Loop Control of Neuronal Activities

Authors: Weihao Sheng Xueyang Zhao Xinrui Huang et al.

Source: Frontiers in Cellular Neuroscience, Vol 16 (2022)

Subject Terms: calcium imaging, closed-loop optogenetic stimulation, image registration, neuron segmentation, fast image processing, image alignment, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fncel.2022.917713/full; https://doaj.org/toc/1662-5102

Access URL: https://doaj.org/article/c5b185fab370484985fedd6df45ea2df

Mosaic: A Python Tool for the Instance Segmentation of Immunofluorescent Neuron Images

Authors: Lam, Dylan Christopher

Subject Terms: Bioinformatics, Neurosciences, Instance Segmentation, Neuron Segmentation, Python, Segmentation, Spatial Transcriptomics, Subcellular Spatial Transcriptomics

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/87z766h5
https://escholarship.org/content/qt87z766h5/qt87z766h5.pdf

Watershed Merge Forest Classification for Electron Microscopy Image Stack Segmentation

Authors: Liu, Ting Seyedhosseini, Mojtaba Ellisman, Mark et al.

Subject Terms: Machine learning, neuron segmentation, watershed, random forest, neural circuit reconstruction

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/3j09m4ww
https://escholarship.org/content/qt3j09m4ww/qt3j09m4ww.pdf

TED: A Tolerant Edit Distance for segmentation evaluation

Authors: Jan Funke Francesc Moreno-Noguer Jonas Klein et al.

Contributors: Jan Funke Francesc Moreno-Noguer Jonas Klein et al.

Source: UPCommons. Portal del coneixement obert de la UPC
Universitat Politècnica de Catalunya (UPC)
Recercat. Dipósit de la Recerca de Catalunya
instname
Digital.CSIC. Repositorio Institucional del CSIC

Subject Terms: FOS: Computer and information sciences, 0301 basic medicine, Informàtica::Automàtica i control [Àrees temàtiques de la UPC], Computer Vision and Pattern Recognition (cs.CV), Computer Science - Computer Vision and Pattern Recognition, Pattern Recognition, Automated, Machine Learning, Mice, 03 medical and health sciences, Segmentation, Àrees temàtiques de la UPC::Informàtica::Automàtica i control, 11. Sustainability, Electron microscopy, Image Processing, Computer-Assisted, Learning, Animals, Humans, Evaluation, Neuron segmentation, Cerebral Cortex, Neurons, Analysis of Variance, 0303 health sciences, Classificació INSPEC::Pattern recognition::Computer vision, Microscopy, Electron, Drosophila melanogaster, 13. Climate action, Computer vision, Pattern recognition::Computer vision [Classificació INSPEC]

File Description: application/pdf

Access URL: http://arxiv.org/pdf/1503.02291
https://pubmed.ncbi.nlm.nih.gov/28108198
http://arxiv.org/abs/1503.02291
http://hdl.handle.net/2117/115439
http://hdl.handle.net/10261/167081
https://core.ac.uk/display/157809746
https://www.sciencedirect.com/science/article/pii/S1046202316305072
https://upcommons.upc.edu/bitstream/2117/115439/1/1969-TED_-A-Tolerant-Edit-Distance-for-Segmentation-Evaluation.pdf
https://www.ncbi.nlm.nih.gov/pubmed/28108198
http://digital.csic.es/bitstream/10261/167081/1/TEDevalua.pdf
https://upcommons.upc.edu/handle/2117/115439

A Smart Region-Growing Algorithm for Single-Neuron Segmentation From Confocal and 2-Photon Datasets

Authors: Alejandro Luis Callara Chiara Magliaro Arti Ahluwalia et al.

Source: Frontiers in Neuroinformatics, Vol 14 (2020)

Subject Terms: neuron segmentation, confocal microscopy, 2 photon microscopy, expectation - maximization (EM) algorithm, mixture models, CLARITY, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fninf.2020.00009/full; https://doaj.org/toc/1662-5196

Access URL: https://doaj.org/article/d0f9449f05944e00a422968968872f52

AI Models for Neuron Segmentation: A Comparative Study

Authors: Wilcox, Stella Conklin, Ellie Schroeder, Nathan E.

Source: MICRO-CCS student projects

Subject Terms: neuron segmentation, artificial intelligence, ai, Life Sciences

File Description: application/pdf

Relation: https://spark.parkland.edu/micro_ccs_student/7; https://spark.parkland.edu/context/micro_ccs_student/article/1004/viewcontent/244939_291591___Stella_Wilcox___Jul_24__2024_346_PM___7FINALCOPY.pdf

Availability: https://spark.parkland.edu/micro_ccs_student/7
https://spark.parkland.edu/context/micro_ccs_student/article/1004/viewcontent/244939_291591___Stella_Wilcox___Jul_24__2024_346_PM___7FINALCOPY.pdf

Gotta Trace ‘em All: A Mini-Review on Tools and Procedures for Segmenting Single Neurons Toward Deciphering the Structural Connectome

Authors: Chiara Magliaro Alejandro L. Callara Nicola Vanello et al.

Source: Frontiers in Bioengineering and Biotechnology, Vol 7 (2019)

Subject Terms: structural connectome, segmentation algorithm, 3D neuron segmentation, single-cell segmentation, CLARITY, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fbioe.2019.00202/full; https://doaj.org/toc/2296-4185

Access URL: https://doaj.org/article/d3262720eb32492685f281b951fd1471

A Segmentation Scheme for Complex Neuronal Arbors and Application to Vibration Sensitive Neurons in the Honeybee Brain

Authors: Hidetoshi Ikeno Ajayrama Kumaraswamy Kazuki Kai et al.

Source: Frontiers in Neuroinformatics, Vol 12 (2018)

Subject Terms: complex neuron segmentation, reconstruction, image processing, insect brain, confocal laser scanning microscopic image, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fninf.2018.00061/full; https://doaj.org/toc/1662-5196

Access URL: https://doaj.org/article/0eee4f395e97488586aa01056f28b9ce

DataBrain: a web-accessible database for three-dimensional reconstructions and quantitative morphometrics of neurons

Authors: Magliaro, Chiara Callara, A. L. Arami, N. et al.

Source: IFMBE Proceedings ISBN: 9789811051210

Subject Terms: 0301 basic medicine, 03 medical and health sciences, 0302 clinical medicine, 3D morphometrics, 3D neuron segmentation, CLARITY, DATABRAIN, GFP, Bioengineering, Biomedical Engineering

Access URL: https://arpi.unipi.it/handle/11568/880891
https://link.springer.com/chapter/10.1007%2F978-981-10-5122-7_192
https://core.ac.uk/display/141688014

A segmentation scheme for complex neuronal arbors and application to vibration sensitive neurons in the honeybee brain

Authors: Ikeno, Hidetoshi Kumaraswamy, Ajayrama Kai, Kazuki et al.

Source: Front Neuroinform
Frontiers in Neuroinformatics, Vol 12 (2018)

Subject Terms: 0301 basic medicine, 03 medical and health sciences, reconstruction, 0302 clinical medicine, confocal laser scanning microscopic image, 1. No poverty, insect brain, Neurosciences. Biological psychiatry. Neuropsychiatry, complex neuron segmentation, image processing, RC321-571, Neuroscience

Access URL: https://www.frontiersin.org/articles/10.3389/fninf.2018.00061/pdf
https://pubmed.ncbi.nlm.nih.gov/30319384
https://doaj.org/article/0eee4f395e97488586aa01056f28b9ce
https://www.biorxiv.org/content/biorxiv/early/2018/05/16/323758.full.pdf
https://www.biorxiv.org/content/10.1101/323758v1
https://www.biorxiv.org/content/early/2018/05/16/323758
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168625
https://dblp.uni-trier.de/db/journals/fini/fini12.html#IkenoKKWA18
https://epub.ub.uni-muenchen.de/59412/
https://europepmc.org/article/MED/30319384
https://doi.org/10.3389/fninf.2018.00061
https://www.frontiersin.org/articles/10.3389/fninf.2018.00061/full
https://epub.ub.uni-muenchen.de/59412/

Smart Region-Growing: a novel algorithm for the segmentation of 3D clarified confocal image stacks

Authors: Alejandro Luis Callara Chiara Magliaro Arti Ahluwalia et al.

Source: Front Neuroinform
Frontiers in Neuroinformatics, Vol 14 (2020)

Subject Terms: 0301 basic medicine, neuron segmentation, 0303 health sciences, 2 photon microscopy, CLARITY, confocal microscopy, expectation - maximization (EM) algorithm, mixture models, Biomedical Engineering, Neuroscience (miscellaneous), Neurosciences. Biological psychiatry. Neuropsychiatry, Computer Science Applications, 03 medical and health sciences, RC321-571, Neuroscience

File Description: application/pdf

Access URL: https://www.frontiersin.org/articles/10.3389/fninf.2020.00009/pdf
https://pubmed.ncbi.nlm.nih.gov/32256332
https://doaj.org/article/d0f9449f05944e00a422968968872f52
https://www.biorxiv.org/content/biorxiv/early/2019/06/04/287029.full.pdf
https://www.biorxiv.org/content/10.1101/287029v2
https://www.biorxiv.org/content/10.1101/287029v1
https://www.biorxiv.org/content/early/2018/03/22/287029
https://www.biorxiv.org/content/biorxiv/early/2018/03/22/287029.full.pdf
https://europepmc.org/abstract/PPR/PPR17141
https://www.frontiersin.org/article/10.3389/fninf.2020.00009/full
https://doi.org/10.3389/fninf.2020.00009
https://pubmed.ncbi.nlm.nih.gov/32256332/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7090132
https://www.frontiersin.org/articles/10.3389/fninf.2020.00009/full

MICrONS: Machine Intelligence from Cortical Networks

Authors: MICrONS Consortium

Subject Terms: Connectomics, Electron Microscopy, Neural Circuit Reconstruction, Neuron Segmentation, Mouse Visual Cortex

Relation: https://zenodo.org/records/5760218; oai:zenodo.org:5760218; https://doi.org/10.5281/zenodo.5760218

Availability: https://doi.org/10.5281/zenodo.5760218
https://zenodo.org/records/5760218

FlyWire: Online community for whole-brain connectomics

Authors: Dorkenwald, Sven McKellar, Claire Macrina, Thomas et al.

Subject Terms: Connectomics, Electron Microscopy, Neural Circuit Reconstruction, Neuron Segmentation, Fly Whole-Brain, Drosophila melanogaster

Relation: https://zenodo.org/records/5748891; oai:zenodo.org:5748891; https://doi.org/10.5281/zenodo.5748891

Availability: https://doi.org/10.5281/zenodo.5748891
https://zenodo.org/records/5748891

Developing Practical Tools and Algorithms for Biomedical Image Compression and Analysis

Authors: Duan, Bin Yan, Yan

Contributors: Duan, Bin Yan, Yan

Source: Illinois Institute of Technology ; CS / Computer Science

Subject Terms: Computer science, Biomedical Image Processing, Biomedical Image Toolkit, Image Compression, Image Registration, Neuron Segmentation, Neuron Tracing

File Description: application/pdf

Relation: islandora:1025473; http://repository.iit.edu/islandora/object/islandora%3A1025473/datastream/TN/view/Developing%20Practical%20Tools%20and%20Algorithms%20for%20Biomedical%20Image%20Compression%20and%20Analysis.jpg

Availability: http://repository.iit.edu/islandora/object/islandora%3A1025473/datastream/TN/view/Developing%20Practical%20Tools%20and%20Algorithms%20for%20Biomedical%20Image%20Compression%20and%20Analysis.jpg