A 3D imaging and visualization workflow, using confocal microscopy and advanced image processing for brachyuran crab larvae. / Kamanli, Seyit; Kihara, Terue; Ball, Alex; Morritt, David; Clark, Paul.

In: Journal of Microscopy, Vol. 266, No. 3, 06.2017, p. 307-323.

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A 3D imaging and visualization workflow, using confocal microscopy and advanced image processing for brachyuran crab larvae. / Kamanli, Seyit; Kihara, Terue; Ball, Alex; Morritt, David; Clark, Paul.

In: Journal of Microscopy, Vol. 266, No. 3, 06.2017, p. 307-323.

Research output: Contribution to journalArticle

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Kamanli, Seyit ; Kihara, Terue ; Ball, Alex ; Morritt, David ; Clark, Paul. / A 3D imaging and visualization workflow, using confocal microscopy and advanced image processing for brachyuran crab larvae. In: Journal of Microscopy. 2017 ; Vol. 266, No. 3. pp. 307-323.

BibTeX

@article{22701d7e2af14dfabebc708a405783ca,
title = "A 3D imaging and visualization workflow, using confocal microscopy and advanced image processing for brachyuran crab larvae",
abstract = "Confocal laser scanning microscopy is an excellent tool for nondestructive imaging of arthropods and can provide detailed information on morphology including fine surface detail. A methodology is presented here for the visualization by confocal microscopy of arthropods, using brachyuran crab zoeal stages as examples and postprocessing techniques derived from micro-CT protocols to improve the final images. This protocol is divided into description of the preprocessing steps (cleaning, staining, digesting and mounting), confocal laser scanning microscopy and data visualization using open-source, freeware programs ImageJ and Drishti. The advantages of using ImageJ to standardize stack data and Drishti for surface rendering are discussed. The methodology has been comprehensively tested using data acquired from all four brands of confocal microscope (Leica, Nikon, Olympus and Zeiss).",
keywords = "Brachyuran crab larvae, confocal laser scanning microscopy, Drishti, ImageJ, visualization, 3D imaging.",
author = "Seyit Kamanli and Terue Kihara and Alex Ball and David Morritt and Paul Clark",
year = "2017",
month = jun,
doi = "10.1111/jmi.12540",
language = "English",
volume = "266",
pages = "307--323",
journal = "Journal of Microscopy",
number = "3",

}

RIS

TY - JOUR

T1 - A 3D imaging and visualization workflow, using confocal microscopy and advanced image processing for brachyuran crab larvae

AU - Kamanli, Seyit

AU - Kihara, Terue

AU - Ball, Alex

AU - Morritt, David

AU - Clark, Paul

PY - 2017/6

Y1 - 2017/6

N2 - Confocal laser scanning microscopy is an excellent tool for nondestructive imaging of arthropods and can provide detailed information on morphology including fine surface detail. A methodology is presented here for the visualization by confocal microscopy of arthropods, using brachyuran crab zoeal stages as examples and postprocessing techniques derived from micro-CT protocols to improve the final images. This protocol is divided into description of the preprocessing steps (cleaning, staining, digesting and mounting), confocal laser scanning microscopy and data visualization using open-source, freeware programs ImageJ and Drishti. The advantages of using ImageJ to standardize stack data and Drishti for surface rendering are discussed. The methodology has been comprehensively tested using data acquired from all four brands of confocal microscope (Leica, Nikon, Olympus and Zeiss).

AB - Confocal laser scanning microscopy is an excellent tool for nondestructive imaging of arthropods and can provide detailed information on morphology including fine surface detail. A methodology is presented here for the visualization by confocal microscopy of arthropods, using brachyuran crab zoeal stages as examples and postprocessing techniques derived from micro-CT protocols to improve the final images. This protocol is divided into description of the preprocessing steps (cleaning, staining, digesting and mounting), confocal laser scanning microscopy and data visualization using open-source, freeware programs ImageJ and Drishti. The advantages of using ImageJ to standardize stack data and Drishti for surface rendering are discussed. The methodology has been comprehensively tested using data acquired from all four brands of confocal microscope (Leica, Nikon, Olympus and Zeiss).

KW - Brachyuran crab larvae, confocal laser scanning microscopy, Drishti, ImageJ, visualization, 3D imaging.

U2 - 10.1111/jmi.12540

DO - 10.1111/jmi.12540

M3 - Article

VL - 266

SP - 307

EP - 323

JO - Journal of Microscopy

JF - Journal of Microscopy

IS - 3

ER -