research: Planktonic Foraminifera Atlas & Taxonomy
Example of a MatLab script that auto-detects the outline of planktonic foraminifera and scale bars within foraminifera plates. First the image is reduced to a binary black and white image, then 'gaps' are filled, and the edge is autodetected.
Image B. Metcalfe
Planktonic foraminifera are used routinely in Palaeoclimate reconstructions, either their abundance within ocean sediments or the geochemistry of their shells. With geochemsitry we are measuring smaller and smaller amounts, therefore placing specimens into the correct species is paramount for accurate reconstructions. As part of an NWO funded open round grant we have been photographing various species of planktonic foraminifera in more than one view (umbilical , spiral and side views) as a teaching aid. A side project of this has been to develop a MatLab routine that extracts morphological information from photographs.
Images were made using a Nikon Digital Research Microscope and associated features (including a prior stage that allows for micron-level stage adjustments allowing for extended depth of focus EDF images to be made). Specimens were photographed, using ethanol and 'balanced' in four orientations; umbilical; spiral and two side views in order to capture the morphological variability associated with changing orientation. For a number of species a 'paint chart' of either chromotypes (e.g., G. ruber commonly refferred to as G. ruber pink) or morphotypes have also been made (e.g., G. sacculifer and B. digitata). Where possible sediment trap, culture and plankton pump or tow material has been used in order to use the most pristine specimens, on occasion sedimentary fossil material has been used. The material is from the extensive collection of the VUA and NIOZ, equipment purchased (i.e., Digital Microscopes and desktop-SEMs) by Frank Peeters (VUA), Jan-Berend Stuut (NIOZ) and Wim Westeren (VUA) was used to make these images.
Several other images from this Atlas, can be found in the Atlas
See the new taxonomic resource: http://www.endlessforams.org/
Hsiang, A.Y., Brombacher, A., Costa Rillo, M., Mleneck-Vautravers, M.J., Conn, S., Lordsmith, S., Jentzen, A., Henehan, M.J., Metcalfe, B., Fenton, I., Wade, B.S., Fox, L., Meilland, J., Davis, C.V., Baranowski, U., Groeneveld, J., Edgar, K.M., Movellan, A., Aze, T., Dowsett, H.J., Miller, G., Rios, N., Hull, P.M., Endless Forams: >34,000 modern planktonic foraminiferal images for taxonomic training and automated species recognition using convolutional neural networks, Paleoceanography and Paleoclimatology, 34 DOI:
The taxonomic resource, endlessforams.org, produced by a project led by Hull and Hsiang.