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OpenBloodFlow: A User-Friendly OpenCV-Based Software Package for Blood Flow Velocity and Blood Cell Count Measurement for Fish Embryos

SIMPLE SUMMARY: Artificial intelligence (AI) has been established to contribute in number of research areas such as medical imaging, diagnostic tools, ultrasound, cardiac scans, X-rays and blood flow analysis. OpenCV is a library having programming functions that provide ample of modules for digital...

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Autores principales: Farhan, Ali, Saputra, Ferry, Suryanto, Michael Edbert, Humayun, Fahad, Pajimna, Roi Martin B., Vasquez, Ross D., Roldan, Marri Jmelou M., Audira, Gilbert, Lai, Hong-Thih, Lai, Yu-Heng, Hsiao, Chung-Der
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9598615/
https://www.ncbi.nlm.nih.gov/pubmed/36290375
http://dx.doi.org/10.3390/biology11101471
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author Farhan, Ali
Saputra, Ferry
Suryanto, Michael Edbert
Humayun, Fahad
Pajimna, Roi Martin B.
Vasquez, Ross D.
Roldan, Marri Jmelou M.
Audira, Gilbert
Lai, Hong-Thih
Lai, Yu-Heng
Hsiao, Chung-Der
author_facet Farhan, Ali
Saputra, Ferry
Suryanto, Michael Edbert
Humayun, Fahad
Pajimna, Roi Martin B.
Vasquez, Ross D.
Roldan, Marri Jmelou M.
Audira, Gilbert
Lai, Hong-Thih
Lai, Yu-Heng
Hsiao, Chung-Der
author_sort Farhan, Ali
collection PubMed
description SIMPLE SUMMARY: Artificial intelligence (AI) has been established to contribute in number of research areas such as medical imaging, diagnostic tools, ultrasound, cardiac scans, X-rays and blood flow analysis. OpenCV is a library having programming functions that provide ample of modules for digital image processing and artificial intelligence. In this study, we introduced a software package as OpenBloodFlow that can measure blood flow velocity and blood cell count precisely by selecting the dorsal aorta of zebrafish. The program is based on python programing language, which is a high-level, general-purpose language to solve biological problems. We present a cost-effective and fully automatic tool to perform the analysis as compared to commercially available software(s) that are not freely available to access. The key features of the program include a user-friendly graphical user interface (GUI), blood flow velocity and blood cell count in the given video dataset. The results are automatically saved in a CSV file without using any external plugins or third-party software and the program does not require GPU average CPU can be used for the execution. ABSTRACT: The transparent appearance of fish embryos provides an excellent assessment feature for observing cardiovascular function in vivo. Previously, methods to conduct vascular function assessment were based on measuring blood-flow velocity using third-party software. In this study, we reported a simple software, free of costs and skills, called OpenBloodFlow, which can measure blood flow velocity and count blood cells in fish embryos for the first time. First, videos captured by high-speed CCD were processed for better image stabilization and contrast. Next, the optical flow of moving objects was extracted from the non-moving background in a frame-by-frame manner. Finally, blood flow velocity was calculated by the Gunner Farneback algorithm in Python. Data validation with zebrafish and medaka embryos in OpenBloodFlow was consistent with our previously published ImageJ-based method. We demonstrated consistent blood flow alterations by either OpenBloodFlow or ImageJ in the dorsal aorta of zebrafish embryos when exposed to either phenylhydrazine or ractopamine. In addition, we validated that OpenBloodFlow was able to conduct precise blood cell counting. In this study, we provide an easy and fully automatic programming for blood flow velocity calculation and blood cell counting that is useful for toxicology and pharmacology studies in fish.
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spelling pubmed-95986152022-10-27 OpenBloodFlow: A User-Friendly OpenCV-Based Software Package for Blood Flow Velocity and Blood Cell Count Measurement for Fish Embryos Farhan, Ali Saputra, Ferry Suryanto, Michael Edbert Humayun, Fahad Pajimna, Roi Martin B. Vasquez, Ross D. Roldan, Marri Jmelou M. Audira, Gilbert Lai, Hong-Thih Lai, Yu-Heng Hsiao, Chung-Der Biology (Basel) Article SIMPLE SUMMARY: Artificial intelligence (AI) has been established to contribute in number of research areas such as medical imaging, diagnostic tools, ultrasound, cardiac scans, X-rays and blood flow analysis. OpenCV is a library having programming functions that provide ample of modules for digital image processing and artificial intelligence. In this study, we introduced a software package as OpenBloodFlow that can measure blood flow velocity and blood cell count precisely by selecting the dorsal aorta of zebrafish. The program is based on python programing language, which is a high-level, general-purpose language to solve biological problems. We present a cost-effective and fully automatic tool to perform the analysis as compared to commercially available software(s) that are not freely available to access. The key features of the program include a user-friendly graphical user interface (GUI), blood flow velocity and blood cell count in the given video dataset. The results are automatically saved in a CSV file without using any external plugins or third-party software and the program does not require GPU average CPU can be used for the execution. ABSTRACT: The transparent appearance of fish embryos provides an excellent assessment feature for observing cardiovascular function in vivo. Previously, methods to conduct vascular function assessment were based on measuring blood-flow velocity using third-party software. In this study, we reported a simple software, free of costs and skills, called OpenBloodFlow, which can measure blood flow velocity and count blood cells in fish embryos for the first time. First, videos captured by high-speed CCD were processed for better image stabilization and contrast. Next, the optical flow of moving objects was extracted from the non-moving background in a frame-by-frame manner. Finally, blood flow velocity was calculated by the Gunner Farneback algorithm in Python. Data validation with zebrafish and medaka embryos in OpenBloodFlow was consistent with our previously published ImageJ-based method. We demonstrated consistent blood flow alterations by either OpenBloodFlow or ImageJ in the dorsal aorta of zebrafish embryos when exposed to either phenylhydrazine or ractopamine. In addition, we validated that OpenBloodFlow was able to conduct precise blood cell counting. In this study, we provide an easy and fully automatic programming for blood flow velocity calculation and blood cell counting that is useful for toxicology and pharmacology studies in fish. MDPI 2022-10-08 /pmc/articles/PMC9598615/ /pubmed/36290375 http://dx.doi.org/10.3390/biology11101471 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Farhan, Ali
Saputra, Ferry
Suryanto, Michael Edbert
Humayun, Fahad
Pajimna, Roi Martin B.
Vasquez, Ross D.
Roldan, Marri Jmelou M.
Audira, Gilbert
Lai, Hong-Thih
Lai, Yu-Heng
Hsiao, Chung-Der
OpenBloodFlow: A User-Friendly OpenCV-Based Software Package for Blood Flow Velocity and Blood Cell Count Measurement for Fish Embryos
title OpenBloodFlow: A User-Friendly OpenCV-Based Software Package for Blood Flow Velocity and Blood Cell Count Measurement for Fish Embryos
title_full OpenBloodFlow: A User-Friendly OpenCV-Based Software Package for Blood Flow Velocity and Blood Cell Count Measurement for Fish Embryos
title_fullStr OpenBloodFlow: A User-Friendly OpenCV-Based Software Package for Blood Flow Velocity and Blood Cell Count Measurement for Fish Embryos
title_full_unstemmed OpenBloodFlow: A User-Friendly OpenCV-Based Software Package for Blood Flow Velocity and Blood Cell Count Measurement for Fish Embryos
title_short OpenBloodFlow: A User-Friendly OpenCV-Based Software Package for Blood Flow Velocity and Blood Cell Count Measurement for Fish Embryos
title_sort openbloodflow: a user-friendly opencv-based software package for blood flow velocity and blood cell count measurement for fish embryos
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9598615/
https://www.ncbi.nlm.nih.gov/pubmed/36290375
http://dx.doi.org/10.3390/biology11101471
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