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

Seyit Kamanli, Terue Kihara, Alex Ball, David Morritt, Paul Clark

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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).
Original languageEnglish
Pages (from-to)307-323
Number of pages18
JournalJournal of Microscopy
Issue number3
Early online date7 Mar 2017
Publication statusPublished - Jun 2017


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

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