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GlobalGigaPan: Integrating high-resolution imagery into DNA barcoding

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By M. Alex Smith

Since 2008, I’ve been one of a group of scientists beta-testing the GigaPan. This remarkable piece of equipment consists of three technological developments:

    – A robotic camera mount for capturing very high-resolution (gigapixel and up) panoramic images using a standard digital camera;
    – Custom software for constructing very high-resolution gigapixel panoramas; and
    – A new type of website for exploring, sharing and commenting on gigapixel panoramas and the detail users will discover within them.

Carnegie Mellon University researchers Illah Nourbakhsh and Randy Sargent developed the robot and the software, while working with NASA on the Mars Rover project.

Mars Bonneville Crater panorama

Each panorama is filled with a fantastic amount of information. Follow one of the links in the examples mentioned below. Zoom in, move around and explore.

A feature of the viewing software, called ‘snap-shoting’, allows viewers to highlight a section of the photo and then annotate or comment on it; very valuable for collaborations or outreach.

The initial snapshots are visible in the bottom left hand side of the panorama. If you select a snapshot, the comments the author has made appear to the right hand side, while the viewer is zoomed in to that section of the GigaPan.

GigaPans can also be integrated seamlessly into Google Earth. The view here is projected on a sphere so that you can explore in a more complete immersion of the image placed on the globe.

Here are three recent examples of how I have easily integrated the GigaPan into my collections, barcoding and ecological workflows.

Aboard the BIObus

In the spring and summer of 2008, 2009 and 2010, students and volunteers were trained in the use of the GigaPan as they accompanied the Biodiversity Institute of Ontario’s mobile collection vehicle, the BIObus, on collection expeditions across North America.

In 2009, this group travelled through six national parks in eastern Canada collecting invertebrates to add to a growing library of reference specimens and sequences in a library of DNA barcodes. At each collecting locality, GigaPans were taken to capture the environment, weather, habitat etc. of the collection site and of the act of collection itself.

Gros Morne National Park panorama

Some people took some convincing to place themselves in the GigaPan but they ended up enjoying the process.

Enjoying the process at Warren Lake

This was important because the point of the exercise is not just WHAT was collected and WHERE, but WHO, WHY and WHEN – and so our appearance in the shot is part of that narrative.

gigapan1

Miles Zhang, Alex Smith, Jill Smith and Renee Labbee in Cape Breton Highlands National Park, Nova Scotia, Canada – BIObus 2009.
(Photo by Jay Cossey)
Here’s the GigaPan
Here’s the same GigaPan embedded into Google Earth
but to see this you need the Free Google Earth Plug-in

Sampling ant community change in Costa Rica

When I am sampling ant communities on volcanos in northwestern Costa Rica, I often feel overwhelmed by the floristic diversity that surrounds me.

From low-elevation tropical dry forest, through wet mid-elevation rainforest to high-elevation cloud forest, I record my field notes with a concern in the back of my mind that my lack of botanical literacy may mean that I will miss an important piece of metadata that will help contextualize my collections and ecological tests.

To help mitigate this concern, I have begun carrying the GigaPan tripod and unit up to each sampling site. After I set up my traps and while I am actively collecting at that elevation, the GigaPan is snapping photographs.

The terabytes of spatially referenced gigapixel imagery is a far better descriptor of the habitat than my vocabulary. It is also much easier to share – whether as a scientific inquiry (Dear Dr. x – can you tell me what this plant is…) or as outreach.

Explore one of the collection sites from this winter on Volcan Orosi as a Google Earth file here .

 

gigapan2

GigaPan recording habitat from Volcan Orosi collection site, January 22, 2009. See the panorama here and embedded in Google Earth here (and you still need the Google Earth plug-in).

The Dairy Bush

The weekly GigaPan panoramas that I shot in the Dairy Bush, a patch of forest near the University of Guelph, between August 2009 and 2010 were an attempt to make this urban woodlot more accessible to the student and city population.

Urban forests are exposed to intense anthropogenic pressures of degradation, fragmentation, biological invasion and destruction – and there is evidence of such changes in the GigaPan series. The series also captured the phenology of the native flora and fauna of the forest.

The year-long Dairy Bush GigaPan has captured many examples of seasonal changes in both native and invasive understory plants and animals and examples of environmental damage> It is used in several ecology classes at the University of Guelph to complement field trips to the Dairy Bush.

gigapan3

Setting up the GigaPan in a local woodlot. The resulting panorama can be seen here and is projected in Google Earth here

 

Conclusions

There are many parallels between the GigaPan and DNA barcoding as complementary forces for democratizing information and bolstering bioliteracy. Both are publicly accessible, both will be annotated through time by a community of experts and non-experts alike and both exist as a synthetic connection from the digital to the natural world.

One key to our capacity to understand the changes caused by the increasing pressures of the urbanization and degradation of natural environments will be ongoing monitoring through time. If such monitoring is democratized and publically available as DNA barcodes and GigaPans, then a marginalized environment may become more valued by the human population.

Alex Smith is an assistant professor of molecular ecology at the University of Guelph, Department of Integrative Biology and the Biodiversity Institute of Ontario (BIO) where his research involves the discrimination of cryptic species and fragmented spaces using ants, parasitoids and amphibians. He is the Global co-Lead for Ants within iBOL Working Group 1.9 – Terrestrial Bio-Surveillance and is iBOL’s IDRC Project Coordinator for Costa Rica.

This article was published in the Barcode Bulletin, the quarterly newsletter of the International Barcode of Life Project.

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