Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes
Summary: Characterization of zebrafish mutants is routinely time consuming as morphological phenotypes can be subtle or variable, thus hampering robust quantification. Here, we present a protocol to identify the overall phenotype by overlaying images of lymphatic vessels acquired from multiple zebra...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-03-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166725000383 |
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| _version_ | 1823861173871706112 |
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| author | Hannah Arnold Virginia Panara Amin Allalou Katarzyna Koltowska |
| author_facet | Hannah Arnold Virginia Panara Amin Allalou Katarzyna Koltowska |
| author_sort | Hannah Arnold |
| collection | DOAJ |
| description | Summary: Characterization of zebrafish mutants is routinely time consuming as morphological phenotypes can be subtle or variable, thus hampering robust quantification. Here, we present a protocol to identify the overall phenotype by overlaying images of lymphatic vessels acquired from multiple zebrafish embryos of a genetic background. We describe steps for preparing samples, obtaining confocal images, and their computational alignment. In addition, we supply sample images for testing.For complete details on the use and execution of this protocol, please refer to Arnold et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-46d3fb522908498eaa5c4592073b9a93 |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-46d3fb522908498eaa5c4592073b9a932025-02-10T04:34:56ZengElsevierSTAR Protocols2666-16672025-03-0161103632Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypesHannah Arnold0Virginia Panara1Amin Allalou2Katarzyna Koltowska3Immunology Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden; Corresponding authorImmunology Genetics and Pathology, Uppsala University, 751 85 Uppsala, SwedenDanioReadout, Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden; Department of Information Technology, Division of Visual Information and Interaction, SciLifeLab BioImage Informatics Facility, Uppsala University, Uppsala, SwedenImmunology Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden; DanioReadout, Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden; Beijer Gene and Neuro Laboratory, Uppsala University, Uppsala, Sweden; Corresponding authorSummary: Characterization of zebrafish mutants is routinely time consuming as morphological phenotypes can be subtle or variable, thus hampering robust quantification. Here, we present a protocol to identify the overall phenotype by overlaying images of lymphatic vessels acquired from multiple zebrafish embryos of a genetic background. We describe steps for preparing samples, obtaining confocal images, and their computational alignment. In addition, we supply sample images for testing.For complete details on the use and execution of this protocol, please refer to Arnold et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166725000383bioinformaticsdevelopmental biologymodel organisms |
| spellingShingle | Hannah Arnold Virginia Panara Amin Allalou Katarzyna Koltowska Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes STAR Protocols bioinformatics developmental biology model organisms |
| title | Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes |
| title_full | Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes |
| title_fullStr | Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes |
| title_full_unstemmed | Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes |
| title_short | Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes |
| title_sort | protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes |
| topic | bioinformatics developmental biology model organisms |
| url | http://www.sciencedirect.com/science/article/pii/S2666166725000383 |
| work_keys_str_mv | AT hannaharnold protocoltocomputationallyaverageconfocalimagesofzebrafishlymphaticvesselstoidentifyphenotypes AT virginiapanara protocoltocomputationallyaverageconfocalimagesofzebrafishlymphaticvesselstoidentifyphenotypes AT aminallalou protocoltocomputationallyaverageconfocalimagesofzebrafishlymphaticvesselstoidentifyphenotypes AT katarzynakoltowska protocoltocomputationallyaverageconfocalimagesofzebrafishlymphaticvesselstoidentifyphenotypes |