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Jiang L, Xu D, Xu Q, Chatziioannou A, Iwamoto KS, Hui S, Sheng K. Exploring Automated Contouring Across Institutional Boundaries: A Deep Learning Approach with Mouse Micro-CT Datasets. ARXIV 2024:arXiv:2405.18676v1. [PMID: 38855547 PMCID: PMC11160888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Image-guided mouse irradiation is essential to understand interventions involving radiation prior to human studies. Our objective is to employ Swin UNEt Transformers (Swin UNETR) to segment native micro-CT and contrast-enhanced micro-CT scans and benchmark the results against 3D no-new-Net (nnU-Net). Swin UNETR reformulates mouse organ segmentation as a sequence-to-sequence prediction task, using a hierarchical Swin Transformer encoder to extract features at 5 resolution levels, and connects to a Fully Convolutional Neural Network (FCNN)-based decoder via skip connections. The models were trained and evaluated on open datasets, with data separation based on individual mice. Further evaluation on an external mouse dataset acquired on a different micro-CT with lower kVp and higher imaging noise was also employed to assess model robustness and generalizability. Results indicate that Swin UNETR consistently outperforms nnU-Net and AIMOS in terms of average dice similarity coefficient (DSC) and Hausdorff distance (HD95p), except in two mice of intestine contouring. This superior performance is especially evident in the external dataset, confirming the model's robustness to variations in imaging conditions, including noise and quality, thereby positioning Swin UNETR as a highly generalizable and efficient tool for automated contouring in pre-clinical workflows.
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Affiliation(s)
- Lu Jiang
- Department of Radiation Oncology, University of California San Francisco
| | - Di Xu
- Department of Radiation Oncology, University of California San Francisco
| | - Qifan Xu
- Department of Radiation Oncology, University of California San Francisco
| | - Arion Chatziioannou
- Department of Molecular and Medical Pharmacology, University of California Los Angeles
| | | | - Susanta Hui
- Department of Radiation Oncology, City of Hope
| | - Ke Sheng
- Department of Radiation Oncology, University of California San Francisco
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Parobková V, Kompaníková P, Lázňovský J, Kavková M, Hampl M, Buchtová M, Zikmund T, Kaiser J, Bryja V. Ch OP-CT: quantitative morphometrical analysis of the Hindbrain Choroid Plexus by X-ray micro-computed tomography. Fluids Barriers CNS 2024; 21:9. [PMID: 38268040 DOI: 10.1186/s12987-023-00502-8] [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: 08/30/2023] [Accepted: 12/11/2023] [Indexed: 01/26/2024] Open
Abstract
The Hindbrain Choroid Plexus is a complex, cerebrospinal fluid-secreting tissue that projects into the 4th vertebrate brain ventricle. Despite its irreplaceability in the development and homeostasis of the entire central nervous system, the research of Hindbrain Choroid Plexus and other Choroid Plexuses has been neglected by neuroscientists for decades. One of the obstacles is the lack of tools that describe the complex shape of the Hindbrain Choroid Plexus in the context of brain ventricles. Here we introduce an effective tool, termed ChOP-CT, for the noninvasive, X-ray micro-computed tomography-based, three-dimensional visualization and subsequent quantitative spatial morphological analysis of developing mouse Hindbrain Choroid Plexus. ChOP-CT can reliably quantify Hindbrain Choroid Plexus volume, surface area, length, outgrowth angle, the proportion of the ventricular space occupied, asymmetries and general shape alterations in mouse embryos from embryonic day 13.5 onwards. We provide evidence that ChOP-CT is suitable for the unbiased evaluation and detection of the Hindbrain Choroid Plexus alterations within various mutant embryos. We believe, that thanks to its versatility, quantitative nature and the possibility of automation, ChOP-CT will facilitate the analysis of the Hindbrain Choroid Plexus in the mouse models. This will ultimately accelerate the screening of the candidate genes and mechanisms involved in the onset of various Hindbrain Choroid Plexus-related diseases.
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Affiliation(s)
- Viktória Parobková
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Petra Kompaníková
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Jakub Lázňovský
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Michaela Kavková
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Marek Hampl
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 602 00, Brno, Czech Republic
| | - Marcela Buchtová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 602 00, Brno, Czech Republic
| | - Tomáš Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic.
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.
- Department of Cytokinetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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First person – Sara Rolfe. Biol Open 2023. [DOI: 10.1242/bio.059840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
ABSTRACT
First Person is a series of interviews with the first authors of a selection of papers published in Biology Open, helping researchers promote themselves alongside their papers. Sara Rolfe is first author on ‘ Deep learning enabled multi-organ segmentation of mouse embryos’, published in BiO. Sara is a Research Scientist in the lab of Murat Maga at Seattle Children's Research Institute, investigating quantifying morphology from 3D images, automated phenotyping, and open image science.
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