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Hoffmann C, Cho E, Zalesky A, Di Biase MA. From pixels to connections: exploring in vitro neuron reconstruction software for network graph generation. Commun Biol 2024; 7:571. [PMID: 38750282 PMCID: PMC11096190 DOI: 10.1038/s42003-024-06264-9] [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] [Received: 11/10/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
Digital reconstruction has been instrumental in deciphering how in vitro neuron architecture shapes information flow. Emerging approaches reconstruct neural systems as networks with the aim of understanding their organization through graph theory. Computational tools dedicated to this objective build models of nodes and edges based on key cellular features such as somata, axons, and dendrites. Fully automatic implementations of these tools are readily available, but they may also be purpose-built from specialized algorithms in the form of multi-step pipelines. Here we review software tools informing the construction of network models, spanning from noise reduction and segmentation to full network reconstruction. The scope and core specifications of each tool are explicitly defined to assist bench scientists in selecting the most suitable option for their microscopy dataset. Existing tools provide a foundation for complete network reconstruction, however more progress is needed in establishing morphological bases for directed/weighted connectivity and in software validation.
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Affiliation(s)
- Cassandra Hoffmann
- Systems Neuroscience Lab, Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, Australia.
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Parkville, Australia
| | - Andrew Zalesky
- Systems Neuroscience Lab, Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, Australia
- Department of Biomedical Engineering, The University of Melbourne, Parkville, Australia
| | - Maria A Di Biase
- Systems Neuroscience Lab, Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, Australia
- Stem Cell Disease Modelling Lab, Department of Anatomy and Physiology, The University of Melbourne, Parkville, Australia
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
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Li CW, Hsu AL, Huang CWC, Yang SH, Lin CY, Shieh CC, Chan WP. Reliability of Synthetic Brain MRI for Assessment of Ischemic Stroke with Phantom Validation of a Relaxation Time Determination Method. J Clin Med 2020; 9:jcm9061857. [PMID: 32545907 PMCID: PMC7356822 DOI: 10.3390/jcm9061857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/30/2022] Open
Abstract
The reliability of relaxation time measures in synthetic magnetic resonance images (MRIs) of homemade phantoms were validated, and the diagnostic suitability of synthetic imaging was compared to that of conventional MRIs for detecting ischemic lesions. Phantoms filled with aqueous cupric-sulfate (CuSO4) were designed to mimic spin-lattice (T1) and spin-spin (T2) relaxation properties and were used to compare their accuracies and stabilities between synthetic and conventional scans of various brain tissues. To validate the accuracy of synthetic imaging in ischemic stroke diagnoses, the synthetic and clinical scans of 18 patients with ischemic stroke were compared, and the quantitative contrast-to-noise ratios (CNRs) were measured, using the Friedman test to determine significance in differences. Results using the phantoms showed no significant differences in the interday and intersession synthetic quantitative T1 and T2 values. However, between synthetic and referenced T1 and T2 values, differences were larger for longer relaxation times, showing that image intensities in synthetic scans are relatively inaccurate in the cerebrospinal fluid (CSF). Similarly, CNRs in CSF regions of stroke patients were significantly different on synthetic T2-weighted and T2-fluid-attenuated inversion recovery images. In contrast, differences in stroke lesions were insignificant between the two. Therefore, interday and intersession synthetic T1 and T2 values are highly reliable, and discrepancies in synthetic T1 and T2 relaxation times and image contrasts in CSF regions do not affect stroke lesion diagnoses. Additionally, quantitative relaxation times from synthetic images allow better estimations of ischemic stroke onset time, consequently increasing confidence in synthetic MRIs as diagnostic tools for ischemic stroke.
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Affiliation(s)
- Chia-Wei Li
- Department of Radiology, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan; (C.-W.L.); (A.-L.H.); (C.-W.C.H.); (S.-H.Y.)
| | - Ai-Ling Hsu
- Department of Radiology, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan; (C.-W.L.); (A.-L.H.); (C.-W.C.H.); (S.-H.Y.)
| | - Chi-Wen C. Huang
- Department of Radiology, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan; (C.-W.L.); (A.-L.H.); (C.-W.C.H.); (S.-H.Y.)
- Department of Radiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Shih-Hung Yang
- Department of Radiology, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan; (C.-W.L.); (A.-L.H.); (C.-W.C.H.); (S.-H.Y.)
- Department of Radiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | | | | | - Wing P. Chan
- Department of Radiology, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan; (C.-W.L.); (A.-L.H.); (C.-W.C.H.); (S.-H.Y.)
- Department of Radiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Medical Innovation Development Center, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
- Correspondence: ; Tel.: +886-2-2930-7930 (ext. 1300); Fax: +886-2-2931-6809
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