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

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

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

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

Research output: Contribution to journalArticlepeer-review

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Kamanli, Seyit ; Kihara, Terue ; Ball, Alex ; Clark, Paul. / A 3D imaging and visualisation 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{38f84eb8fbd2405e88abc84bfbb12cef,
title = "A 3D imaging and visualisation workflow, using confocal microscopy and advanced image processing for brachyuran crab larvae",
abstract = "Confocal laser scanning microscopy is an excellent tool for non-destructive imaging of arthropods and can provide detailed information on morphology including fine surface detail. A methodology is presented here for the visualisation by confocal microscopy of arthropods, using brachyuran crab zoeal stages as examples and post-processing techniques derived from micro-CT protocols to improve the final images. This protocol is divided into description of the pre-processing steps (cleaning, staining, digesting and mounting), confocal laser scanning microscopy and data visualisation using open-source, freeware programmes ImageJ and Drishti. The advantages of using ImageJ to standardise 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). ",
author = "Seyit Kamanli and Terue Kihara and Alex Ball 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 visualisation workflow, using confocal microscopy and advanced image processing for brachyuran crab larvae

AU - Kamanli, Seyit

AU - Kihara, Terue

AU - Ball, Alex

AU - Clark, Paul

PY - 2017/6

Y1 - 2017/6

N2 - Confocal laser scanning microscopy is an excellent tool for non-destructive imaging of arthropods and can provide detailed information on morphology including fine surface detail. A methodology is presented here for the visualisation by confocal microscopy of arthropods, using brachyuran crab zoeal stages as examples and post-processing techniques derived from micro-CT protocols to improve the final images. This protocol is divided into description of the pre-processing steps (cleaning, staining, digesting and mounting), confocal laser scanning microscopy and data visualisation using open-source, freeware programmes ImageJ and Drishti. The advantages of using ImageJ to standardise 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 non-destructive imaging of arthropods and can provide detailed information on morphology including fine surface detail. A methodology is presented here for the visualisation by confocal microscopy of arthropods, using brachyuran crab zoeal stages as examples and post-processing techniques derived from micro-CT protocols to improve the final images. This protocol is divided into description of the pre-processing steps (cleaning, staining, digesting and mounting), confocal laser scanning microscopy and data visualisation using open-source, freeware programmes ImageJ and Drishti. The advantages of using ImageJ to standardise 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).

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 -