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For: Parekh R, Armañanzas R, Ascoli GA. The importance of metadata to assess information content in digital reconstructions of neuronal morphology. Cell Tissue Res 2015;360:121-7. [PMID: 25653123 DOI: 10.1007/s00441-014-2103-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 12/21/2014] [Indexed: 12/23/2022]
Number Cited by Other Article(s)
1
Tecuatl C, Ljungquist B, Ascoli GA. Accelerating the continuous community sharing of digital neuromorphology data. FASEB Bioadv 2024;6:207-221. [PMID: 38974113 PMCID: PMC11226999 DOI: 10.1096/fba.2024-00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 07/09/2024]  Open
2
Leite J, Nhoatto F, Jacob A, Santana R, Lobato F. Computational Tools for Neuronal Morphometric Analysis: A Systematic Search and Review. Neuroinformatics 2024;22:353-377. [PMID: 38922389 DOI: 10.1007/s12021-024-09674-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2024] [Indexed: 06/27/2024]
3
Tecuatl C, Ljungquist B, Ascoli GA. Accelerating the continuous community sharing of digital neuromorphology data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585306. [PMID: 38562736 PMCID: PMC10983892 DOI: 10.1101/2024.03.15.585306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
4
Mehta K, Ljungquist B, Ogden J, Nanda S, Ascoli RG, Ng L, Ascoli GA. Online conversion of reconstructed neural morphologies into standardized SWC format. Nat Commun 2023;14:7429. [PMID: 37973857 PMCID: PMC10654402 DOI: 10.1038/s41467-023-42931-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]  Open
5
Bijari K, Zoubi Y, Ascoli GA. Assisted neuroscience knowledge extraction via machine learning applied to neural reconstruction metadata on NeuroMorpho.Org. Brain Inform 2022;9:26. [PMID: 36344713 PMCID: PMC9640520 DOI: 10.1186/s40708-022-00174-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/06/2022] [Indexed: 11/09/2022]  Open
6
Ljungquist B, Akram MA, Ascoli GA. Large scale similarity search across digital reconstructions of neural morphology. Neurosci Res 2022;181:39-45. [PMID: 35580795 PMCID: PMC9960175 DOI: 10.1016/j.neures.2022.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/12/2022] [Accepted: 05/12/2022] [Indexed: 01/18/2023]
7
Efficient metadata mining of web-accessible neural morphologies. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022;168:94-102. [PMID: 34022302 PMCID: PMC8602463 DOI: 10.1016/j.pbiomolbio.2021.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/09/2021] [Accepted: 05/12/2021] [Indexed: 01/03/2023]
8
Sullivan AE, Tappan SJ, Angstman PJ, Rodriguez A, Thomas GC, Hoppes DM, Abdul-Karim MA, Heal ML, Glaser JR. A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling. Neuroinformatics 2022;20:221-240. [PMID: 34601704 PMCID: PMC8975944 DOI: 10.1007/s12021-021-09530-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2021] [Indexed: 01/09/2023]
9
Reed JD, Blackwell KT. Prediction of Neural Diameter From Morphology to Enable Accurate Simulation. Front Neuroinform 2021;15:666695. [PMID: 34149388 PMCID: PMC8209307 DOI: 10.3389/fninf.2021.666695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/10/2021] [Indexed: 11/29/2022]  Open
10
Anderson KR, Harris JA, Ng L, Prins P, Memar S, Ljungquist B, Fürth D, Williams RW, Ascoli GA, Dumitriu D. Highlights from the Era of Open Source Web-Based Tools. J Neurosci 2021;41:927-936. [PMID: 33472826 PMCID: PMC7880282 DOI: 10.1523/jneurosci.1657-20.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/22/2020] [Accepted: 11/29/2020] [Indexed: 12/20/2022]  Open
11
Comprehensive Estimates of Potential Synaptic Connections in Local Circuits of the Rodent Hippocampal Formation by Axonal-Dendritic Overlap. J Neurosci 2020;41:1665-1683. [PMID: 33361464 DOI: 10.1523/jneurosci.1193-20.2020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 10/19/2020] [Accepted: 12/13/2020] [Indexed: 12/12/2022]  Open
12
Sielemann K, Hafner A, Pucker B. The reuse of public datasets in the life sciences: potential risks and rewards. PeerJ 2020;8:e9954. [PMID: 33024631 PMCID: PMC7518187 DOI: 10.7717/peerj.9954] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]  Open
13
Nguyen VT, Uchida R, Warling A, Sloan LJ, Saviano MS, Wicinski B, Hård T, Bertelsen MF, Stimpson CD, Bitterman K, Schall M, Hof PR, Sherwood CC, Manger PR, Spocter MA, Jacobs B. Comparative neocortical neuromorphology in felids: African lion, African leopard, and cheetah. J Comp Neurol 2020;528:1392-1422. [DOI: 10.1002/cne.24823] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 02/03/2023]
14
Bijari K, Akram MA, Ascoli GA. An open-source framework for neuroscience metadata management applied to digital reconstructions of neuronal morphology. Brain Inform 2020;7:2. [PMID: 32219575 PMCID: PMC7098402 DOI: 10.1186/s40708-020-00103-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/14/2020] [Indexed: 12/21/2022]  Open
15
Armañanzas R. Revealing post-transcriptional microRNA-mRNA regulations in Alzheimer's disease through ensemble graphs. BMC Genomics 2018;19:668. [PMID: 30255799 PMCID: PMC6157163 DOI: 10.1186/s12864-018-5025-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]  Open
16
Mining Big Neuron Morphological Data. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2018;2018:8234734. [PMID: 30034462 PMCID: PMC6035829 DOI: 10.1155/2018/8234734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 05/09/2018] [Accepted: 05/24/2018] [Indexed: 11/26/2022]
17
López-Cabrera JD, Lorenzo-Ginori JV. Feature selection for the classification of traced neurons. J Neurosci Methods 2018;303:41-54. [DOI: 10.1016/j.jneumeth.2018.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 03/19/2018] [Accepted: 04/04/2018] [Indexed: 10/17/2022]
18
Akram MA, Nanda S, Maraver P, Armañanzas R, Ascoli GA. An open repository for single-cell reconstructions of the brain forest. Sci Data 2018;5:180006. [PMID: 29485626 PMCID: PMC5827689 DOI: 10.1038/sdata.2018.6] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/08/2018] [Indexed: 02/06/2023]  Open
19
An evolutionary developmental approach for generation of 3D neuronal morphologies using gene regulatory networks. Neurocomputing 2018. [DOI: 10.1016/j.neucom.2017.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
20
Polavaram S, Ascoli GA. An ontology-based search engine for digital reconstructions of neuronal morphology. Brain Inform 2017;4:123-134. [PMID: 28337675 PMCID: PMC5413594 DOI: 10.1007/s40708-017-0062-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/13/2017] [Indexed: 11/27/2022]  Open
21
Ascoli GA, Maraver P, Nanda S, Polavaram S, Armañanzas R. Win-win data sharing in neuroscience. Nat Methods 2017;14:112-116. [PMID: 28139675 PMCID: PMC5503136 DOI: 10.1038/nmeth.4152] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
22
Peng H, Meijering E, Ascoli GA. From DIADEM to BigNeuron. Neuroinformatics 2016;13:259-60. [PMID: 25920534 DOI: 10.1007/s12021-015-9270-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
23
Ascoli GA. Sharing Neuron Data: Carrots, Sticks, and Digital Records. PLoS Biol 2015;13:e1002275. [PMID: 26447712 PMCID: PMC4598120 DOI: 10.1371/journal.pbio.1002275] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
24
Gillette TA, Ascoli GA. Topological characterization of neuronal arbor morphology via sequence representation: I--motif analysis. BMC Bioinformatics 2015;16:216. [PMID: 26156313 PMCID: PMC4496917 DOI: 10.1186/s12859-015-0604-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/30/2015] [Indexed: 01/03/2023]  Open
25
von Bartheld CS, Wouters FS. Quantitative techniques for imaging cells and tissues. Cell Tissue Res 2015;360:1-4. [PMID: 25773453 PMCID: PMC4380763 DOI: 10.1007/s00441-015-2149-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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