Fungi Digitisation Project
September 30, 2018
Through the support of the Office of Environment and Heritage, Heritage Near Me program, The NSW Plant Pathology & Mycology Herbarium have been imaging their collection (the largest of its kind in Australia), consisting of specimens and heritage items in order to make them available online to people worldwide for research and information.
As part of this grant I was provided with a scholarship to visit the herbarium and help to photograph some of the 2000+ fungi type specimens as high resolution images. It was a great opporunity to enjoy a visit to this wonderful facility to meet the scientists who are researching ways to reduce the introduction and impacts of disease and pests.
Photography Setup - The digitisation setup for photographing the fungi type specimens was straightforward using just a camera, stand, colour chart and lightbox. Items were placed on the stage ensuring key identification features could be readily photographed and the colour and size bars included. A remote shutter was used to fire, with a standard aperture of f11 and shutter speed of 1/60 used with the Canon EOS 6D.
Image Stacking - The photographic setup for digitising other specimens including insects and plant parts was more involved because the depth of field is so small, these images needed to be stacked so that all features were in focus. In order to capture these items correctly, we used the Canon and the amazing MP-E65mm f/2.8 1-5x Macro lens with an automatic rail to get all the images we required. Once these images were obtained, we processed them using a focus stacking software program to obtain a final result.
Whilst using the automated focus rail, I imagined how easy it would make my life out in the field photographing fungi, rather than hoping you've captured all the points you need! Alas though, limited budget means I do it the hard way for now :)
All in all a great 3 weeks photographing and learning more about our Australian fungi heritage.
Whilst visiting the herbarium it was a blast to be able to handle the fungi actually collected by visiting scientists I'd only read about in books. I was also honoured to be able to see the original colour illustrations of plant diseases and disorders painted by artist Margaret Senior, commissioned in the 1960s by the then Department of Agriculture and gorgeous illustrations of fungi by Kay Smith.
Established in 1802 by Robert Brown, the NSW Plant Pathology & Mycology Herbarium have preserved plants but they are all infected with some form of pathogen, like a fungus, bacteria or virus - good thing they are also a Biosecurity Containment Level 2 facility! They also have non-pathogenic fungi (like mushrooms and lichen) and are the only recognised mycology (fungi) collection in NSW.
Inside the mycology herbarium - An enjoyable afternoon was spent rehousing fungi specimens and talking nonsense with Dr Michael Priest - Associate Curator, Plant Pathology and Mycology Herbarium (DAR).
Dr Jordan Bailey kindly guided me through a DNA extraction