John B. LOWE's picture

Fine photographs of fungus

Collaboration among researchers in the curation of digital resources is becoming the norm these days.  However, even if your intention is to make your digital assets available to the research community and to link them appropriately, it can still be challenging to make that happen.

Here's a short and satisfying story of one such collaboration in the field of natural history -- serendipitous to be sure, but likely to become more and more common.

Andrew Doran, Assistant Director for Collections and Curator of Cultivated Plants at the University and Jepson Herbaria ("UC/JEPS"), sent us a short note with a link recently.

Another nice example of a specimen that went out on loan and came back with multiple images which we were given permission to upload into CollectionSpace.

You can follow the link to the UC/JEPS Public Search Portal yourself here but I have reproduced the page below. 

Screenshot, UC/JEPS Public Search Portal

(The UC/JEPS Public Search Portal provides access to the publicly available data extracted nightly from the UC/JEPS CollectionSpace collection management system (you’ll need credentials to login). UC/JEPS and five other campus museums manage their collections in CollectionSpace, supported at UC Berkeley by Research IT.)

Brent Mishler, Professor in Integrative Biology and Director of the UC/JEPS Herbaria commented:

Nice! People making dissections from borrowed specimens is typical for cryptogams (fungi, lichens, bryophytes, algae), and it would be good to get the images back with the specimens.

Please allow me to unpack Andrew's and Brent's remarks a bit -- it really is quite a good tale.

First, the specimen. As you can see when you visit the link to the UC/JEPS Public Search Portal page given above, it is UC2056151, an example of the species Phlebia faviformis W. B. Cooke, and as you can see from the Full record display in the public search portal it is a fungus collected in 1956 by the very prolific and well-known botanist E. Yale Dawson "on bridge timbers" in the state of Goias in Brazil. This particular specimen is an isotype, that is "any duplicate specimen (part of single gathering made by collector at one time) of the holotype."

Of course, you already know your holotypes from your isotypes, right? If not you can study up on your botanical nomenclature here.

The original digital record of this specimen, before the loan, included two photographs, each including a scale, showing it to be a rather uninteresting-looking chunk of brown stuff a few centimeters across vaguely resembling a fish.  Here's one of them.

UC2056151, an example of the species Phlebia faviformis W. B. Cooke

exterior photograph of UC2056151, Phlebia faviformis W. B. Cooke

Next, the loan. The UC/JEPS Herbaria, like many herbaria, has a program to lend specimens out for research purposes. (Parenthetically, UC/JEPS also has an "e-loan" program, where researchers can ask herbarium staff to research specimen data and gather together and present a set of digital specimens; this saves on mailing costs and the risks attendant with shipping specimens around, and is sufficient for many research needs.)

In this case the researcher did a dissection (a few microscopically thin slices) and took several brilliant color photomicrographs (not to be confused with microphotographs), which he returned to UC/JEPS with the specimen. Andrew added these to the record in CollectionSpace, the collection management system used by UC/JEPS, and these are the pretty purply images you see in the Full record display. I've included one of them below; the metadata for this image reveals it to be a "cross-section, magnified 10X, width reduced to 6 inches, 1280 x 1024 pixels", 1.7MB in size.

Photomicrograph of UC2056151, an example of the species Phlebia faviformis W. B. Cooke, \"cross-section, magnified 10X, width reduced to 6 inches, 1280 x 1024 pixels

photomicrograph of UC2056151, Phlebia faviformis W. B. Cooke

You can see the original high-resolution image online.

I don't know about you, but I think it is pretty special to be able to have, at one's fingertips, color photomicrographs of a sixty-year-old fungus from Brazil. This is just one example of the (literally) millions of priceless specimens in the UC/JEPS Herbaria, which document biodiversity from around the world and over the centuries.