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Fishman M, Matt A, Wang F, Gracheva E, Zhu J, Ouyang X, Komarov A, Wang Y, Liang H, Zhou C. A Drosophila heart optical coherence microscopy dataset for automatic video segmentation. Sci Data 2023; 10:886. [PMID: 38071220 PMCID: PMC10710430 DOI: 10.1038/s41597-023-02802-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
The heart of the fruit fly, Drosophila melanogaster, is a particularly suitable model for cardiac studies. Optical coherence microscopy (OCM) captures in vivo cross-sectional videos of the beating Drosophila heart for cardiac function quantification. To analyze those large-size multi-frame OCM recordings, human labelling has been employed, leading to low efficiency and poor reproducibility. Here, we introduce a robust and accurate automated Drosophila heart segmentation algorithm, called FlyNet 2.0+, which utilizes a long short-term memory (LSTM) convolutional neural network to leverage time series information in the videos, ensuring consistent, high-quality segmentation. We present a dataset of 213 Drosophila heart videos, equivalent to 604,000 cross-sectional images, containing all developmental stages and a wide range of beating patterns, including faster and slower than normal beating, arrhythmic beating, and periods of heart stop to capture these heart dynamics. Each video contains a corresponding ground truth mask. We expect this unique large dataset of the beating Drosophila heart in vivo will enable new deep learning approaches to efficiently characterize heart function to advance cardiac research.
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Affiliation(s)
- Matthew Fishman
- Washington University in St. Louis, Department of Computer Science and Engineering, St. Louis, MO, 63130, USA
| | - Abigail Matt
- Washington University in St. Louis, Department of Biomedical Engineering, St. Louis, MO, 63130, USA
| | - Fei Wang
- Washington University in St. Louis, Department of Biomedical Engineering, St. Louis, MO, 63130, USA
| | - Elena Gracheva
- Washington University in St. Louis, Department of Biomedical Engineering, St. Louis, MO, 63130, USA
| | - Jiantao Zhu
- Washington University in St. Louis, Department of Biomedical Engineering, St. Louis, MO, 63130, USA
| | - Xiangping Ouyang
- Washington University in St. Louis, Department of Computer Science and Engineering, St. Louis, MO, 63130, USA
| | - Andrey Komarov
- Washington University in St. Louis, Department of Biomedical Engineering, St. Louis, MO, 63130, USA
| | - Yuxuan Wang
- Washington University in St. Louis, Department of Biomedical Engineering, St. Louis, MO, 63130, USA
| | - Hongwu Liang
- Washington University in St. Louis, Department of Biomedical Engineering, St. Louis, MO, 63130, USA
| | - Chao Zhou
- Washington University in St. Louis, Department of Biomedical Engineering, St. Louis, MO, 63130, USA.
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Schoborg TA, Smith SL, Smith LN, Morris HD, Rusan NM. Micro-computed tomography as a platform for exploring Drosophila development. Development 2019; 146:dev.176685. [PMID: 31722883 DOI: 10.1242/dev.176685] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 11/07/2019] [Indexed: 12/20/2022]
Abstract
Understanding how events at the molecular and cellular scales contribute to tissue form and function is key to uncovering the mechanisms driving animal development, physiology and disease. Elucidating these mechanisms has been enhanced through the study of model organisms and the use of sophisticated genetic, biochemical and imaging tools. Here, we present an accessible method for non-invasive imaging of Drosophila melanogaster at high resolution using micro-computed tomography (µ-CT). We show how rapid processing of intact animals, at any developmental stage, provides precise quantitative assessment of tissue size and morphology, and permits analysis of inter-organ relationships. We then use µ-CT imaging to study growth defects in the Drosophila brain through the characterization of a bnormal spindle (asp) and WD repeat domain 62 (W dr62), orthologs of the two most commonly mutated genes in human microcephaly patients. Our work demonstrates the power of combining µ-CT with traditional genetic, cellular and developmental biology tools available in model organisms to address novel biological mechanisms that control animal development and disease.
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Affiliation(s)
- Todd A Schoborg
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samantha L Smith
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren N Smith
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - H Douglas Morris
- Mouse Imaging Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nasser M Rusan
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Automated drosophila heartbeat counting based on image segmentation technique on optical coherence tomography. Sci Rep 2019; 9:5557. [PMID: 30944361 PMCID: PMC6447591 DOI: 10.1038/s41598-019-41720-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/06/2019] [Indexed: 11/08/2022] Open
Abstract
Drosophila and human cardiac genes are very similar. Biological parametric studies on drosophila cardiac have improved our understanding of human cardiovascular disease. Drosophila cardiac consist of five circular chambers: a conical chamber (CC) and four ostia sections (O1-O4). Due to noise and grayscale discontinuity on optical coherence tomography (OCT) images, previous researches used manual counting or M-mode to analyze heartbeats, which are inefficient and time-consuming. An automated drosophila heartbeat counting algorithm based on the chamber segmentation is developed for OCT in this study. This algorithm has two parts: automated chamber segmentation and heartbeat counting. In addition, this study proposes a principal components analysis (PCA)-based supervised learning method for training the chamber contours to make chamber segmentation more accurate. The mean distances between the conical, second and third chambers attained by the proposed algorithm and the corresponding manually delineated boundaries defined by two experts were 1.26 ± 0.25, 1.47 ± 1.25 and 0.84 ± 0.60 (pixels), respectively. The area overlap similarities were 0.83 ± 0.09, 0.75 ± 0.11 and 0.74 ± 0.12 (pixels), respectively. The average calculated heart rates of two-week and six-week drosophila were about 4.77 beats/s and 4.73 beats/s, respectively, which was consistent with the results of manual counting.
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Tsai MT, Chang FY, Lee CK, Chi TT, Yang KM, Lin LY, Wu JT, Yang CC. Observations of cardiac beating behaviors of wild-type and mutant Drosophilae with optical coherence tomography. JOURNAL OF BIOPHOTONICS 2011; 4:610-618. [PMID: 21538996 DOI: 10.1002/jbio.201100009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 03/31/2011] [Accepted: 04/01/2011] [Indexed: 05/30/2023]
Abstract
Time-resolved optical coherence tomography (OCT) scanning images of wild-type and mutant fruit flies (Drosophila melanogaster), illustrating the heartbeat patterns for evaluating their cardiac functions, are demonstrated. Based on the heartbeat patterns, the beat rate and the relative phase between the first two heart segments can be evaluated. The OCT scanning results of mutant flies with impaired proteasome function in cardiac muscles show irregular heartbeat patterns and systematically decreased average beat rates, when compared with the regular patterns of ~4.97 beats/s in average beat rate of the wild-type. In both wild-type and proteasome mutant flies, the beatings at different locations in the same heart segment are essentially synchronized. However, between different heart segments, although the beating in the second segment shows a lag in phase behind that of the first segment in a wild-type, in a proteasome mutant, the beating in the second segment becomes significantly leading that of the first segment. Besides the comparison between the wild-type and proteasomal mutant flies, the influences of using different methods for immobilizing flies during OCT scanning on the heart functions are demonstrated.
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Affiliation(s)
- Meng-Tsan Tsai
- Department of Electrical Engineering, Chang Gung University, Kwei-Shan, Tao-Yuan, 33302 Taiwan.
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