Imaging

Experts

Anya Waite

• Alfred Wegener Institute for Polar and Marine Research
• anya.waite@awi.de

Heidi M. Sosik

• Woods Hole Oceanographic Institution
• hsosik@whoi.edu

Lionel Guidi

• Laboratoire Oceanographique Villefranche-sur-Mer
• lguidi@obs-vlfr.fr

Rainer Kiko

• GEOMAR
• rkiko@geomar.de

Michael Kloster

• Alfred Wegener Institute for Polar and Marine Research
• michael.kloster@awi.de

Barbara Niehoff

• Alfred Wegener Institute for Polar and Marine Research
• barbara.niehoff@awi.de

Lisa Campbell

• Texas A&M University
• lisacampbell@tamu.edu

Mike Brosnahan

• Woods Hole Oceanographic Institute

Articles (reviews and key papers)

Biard, T. et al. 2016. In situ imaging reveals the biomass of giant protists in the global ocean. Nature 532, doi:10.1038/nature17652

Guidi, L. E. A. 2016. Plankton networks driving carbon export in the oligotrophic ocean. Nature, 532, 465-471.

Hernández-León, S., and I. Montero. 2006. Zooplankton biomass estimated from digitized images in Antarctic waters: a calibration exercise. J. Geophys. Res. 111:C05S03 [doi:10.1029/2005JC002887].

Kiko, R., Biastoch, A., Brandt, P., Cravatte, S., Hauss, H., Hummels, R., Kriest, I., Marin, F., A. M. P. McDonnell, Oschlies, A., Picheral, M., Schwarzkopf, F. U., Thurnherr, A. M. & Stemmann, L. 2017. Biological and physical influences on marine snowfall at the equator. Nature Geoscience 10, 852-858

Lehette Pascal , Hernández-León Santiago , (2009), Zooplankton biomass estimation from digitized images: a comparison between subtropical and Antarctic organisms Limnol. Oceanogr. Methods, 7, doi:10.4319/lom.2009.7.304.

Picheral, M., Guidi, L., Stemmann, L., Karl, D. M., Iddaoud, G. & Gorsky, G. 2010. The Underwater Vision Profiler 5: An advanced instrument for high spatial resolution studies of particle size spectra and zooplankton. Limnology and Oceanography-Methods, 8, 462-473.

Robert K. Cowen, Adam T. Greer, Cedric M. Guigand, Jonathan A. Hare, David E. Richardson, Harvey Walsh Evaluation of the In Situ Ichthyoplankton Imaging System (ISIIS): comparison with the traditional (bongo net) sampler. Fishery Bulletin- National Oceanic and Atmospheric Administration, 01/2013; 111(1):1.

Sosik, H. M. & Olson, R. J. Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry. Limnol.Oceanogr. Methods 5, 204-216 (2007).

Waite, Anya M., Lars Stemmann, Lionel Guidi, Paulo H. R. Calil, Andrew Mc. Hogg, Ming Feng, Peter A. Thompson, M. Picheral, G. Gorsky. 2016. The wine glass effect shapes particle export to the deep ocean in mesoscale eddies. Geophysical Research Letters DOI:1002/2015GL066463

Protocols

Imaging FlowCytobot (IFCB)

• One-page overview (for NASA EXPORTS):

https://drive.google.com/open?id=1QI0BXXNw3uG4WGsoOziH4K-BLNZ0guk8Qwq-li5utYI

• IFCB at sea user guide: https://docs.google.com/document/d/14IfQBriV2AZs1akefM8JYirSAApnVFbDG2XQ74klIOI/

• IFCB data analysis: https://github.com/hsosik/ifcb-analysis/wiki

Report for Imaging

Report on the Marine Imaging Workshop 2017

Perspectives in Visual Imaging for Marine Biology and Ecology: From Acquisition to Understanding

SHERPA

Instrument and Analysis Summary