Open Layers And Virtual Microscopy: Part 1

One of the topics of discussion at the recent Fine Gigapan Conference in November that Ron Schott and Callan Bentley was the 'dream' to layer images within a Gigapan interface that were taken under plain and polarized light. The current Gigapan interface doesn't allow for overlays or extensive annotation so I started working with Open Layers a few weeks ago for another project that requires extensive annotation. In the process, I found a simple way to address the dream for flipping back and forth between plain and polarized light.

This is just part 1 of the progression, but in the example below all I've done is call two different images into the Open Layers API and with two lines of code you can add the layer switcher feature. Right now, the images are not gigapixel images (that's part 2) but you get the idea how seamless the transition can be, once the images load. I'm still working out the details for part 3, which will illustrate how to annotate your images so that they can be used as teaching tools for students (e.g. - you can label different minerals and link out to ancillary information like phase diagrams). Unfortunately, still haven't figured out how to do this with a 'rotating' stage. I'll post part 2 as soon as I finishing uploading the tiles. Until then, enjoy! I also haven't figured out why Blogger won't let me copy the code directly into this page, so the image below opens up in a new page:

A Day With "Streetcar to Subduction"

View of Golden Gate Bridge from Fort Mason

It seems that Callan Bentley of Mountain Beltway and I had similar intentions while attending the fall AGU meeting in San Francisco last week. We both went on our own separate geologic excursions using Doris Sloan's "Geology of the San Francisco Bay Region" and Clyde Wahrhaftig's "A Streetcar to Subduction" guidebook. I've wanted to make use of this guide since hearing about in my graduate level igneous petrology course. Luckily it seems Callan and I decided to explore different sections of the city (with some overlap) and I think he had better luck with the weather!

View of Crissy Field Looking Towards Downtown San Francisco

I decided to walk down to Fort Mason, along the eastern coast via Crissy Field, under the Golden Gate Bridge on-ramp, through the Presidio (confusing!) and then down the Coastal Trail to Marshall and Baker Beach. The weather cooperate only in that it didn't rain on me while I was walking and I had about 40 minutes of sun right before sunset. I was a little underwhelmed by the Fort Mason sandstone exposures, they are relatively small and not as interesting as other localities in Wharfhaftig's book (I should have paid better attention to the descriptions). However, the walk along Crissy Field was quite scenic (even with the fog) and I even encountered a friendly Blue Heron!

The following slideshow contains photos associated with Trips #2 and #3 in A Streetcar to Subduction, which focus on Fort Mason on the eastern side of the city and the Coastal Cliff Trail along the the western edge. This tour visit sandstone within the Alcatraz Terrane, exposures of serpentinite, chert and both Marshall's and Baker Beach. My favorite 'finds' were an excellent exposure of ribbon chert and a serpentine boulder with a highly fractured surface likely caused by the differential weathering of chrysotile, both near Marshall's Beach. This is a simplified geologic map of the Coastal Trail area from Stoffer and Gordon (2001) that provides a nice overview of the geologic relations and geography within this area:

For more information on the images in the slideshow, click on full screen and then Show Info in the upper left hand corner. Enjoy!

Bookcrop #4: Illustrations of the geology of Yorkshire

This is an e-bookcrop as I don't have a desk copy of this fantastically illustrated book, however it is on my list I bring to bookstores and flea markets! You can get your own copy here if you wish.

This book was written in 1829 by the geologist John Phillips, who was raised by and traveled with Williams Smith - and incidentally married Smith's sister - thus the significance of the dedication to Smith in his Yorkshire text. My primary interest in this text lies in the fabulous sketches of both landscapes and fossils. Phillips provides a wonderfully colored (coloured) and sketched geologic map and I've included four example cross sections - my personal favorite is the last, which includes a stratigraphic column.


Finally, just two example plates of fossils he included in the text; I really enjoy the wonderful attention to detail and illustration:

I spend a lot of time looking through the e-collections on archive.org for old illustrations like this; maybe you'll find something you've been looking for too!?

Geology and the iPad Remixed

I think enough time has passed to update the progress made towards interacting with geology and GIS data within the iPad interface.


I had an amazing opportunity to sail on the JOIDES Resolution as part of the 2010 School of Rock (SOR) supported through the Consortium of Ocean Leadership. This was the best professional development experience I've had to date, which was entirely a function of the amazing people who also participated. The primary goal of Expedition 328 was to install an Advance Circulation Obviation Retrofit Kit (ACORK) observatory, which will eventually tie into the existing NEPTUNE network. This network is SO cool, they essentially have 5 sites punching into sediment and bedrock within the Juan de Fuca plate off the coast of Vancouver/Victoria. These observatories are cabled together and transmit real-time data back to shore - including seafloor webcams! If this sounds exciting, you too can join in the fun of exploring this data through the NEPTUNE iPad app. Enjoy!


Not necessarily geology specific, but EMD PTE is a free and useful Periodic Table of Elements app. Hopefully we'll get to see the PTE for Earth Scientists ported over to a digital app soon? This app provides a general overview of each element, the history, discover, a photo of the element, and a summary of products used for analytical testing. A lot of information for free.

Image from here

I'm excited to see how the new Earth Observer app will run on the iPad - it is essentially a mobile version of GeoMapApp. So there's a lot of data behind this interface and I'm wondering how quickly it will be able to respond, however the site suggests there will be local caching available so that should speed things up. The website indicates it will be released on November 20th, so if you use GeoMapApp go check it out.

And just a few other fun and useful apps:

1. Jurassic - a virtual field trip interface of England's Jurassic Coast.
2. GeolCompass - a digital field compass that measures strike/dip and inclination.
3. Lambert - another digital compass, this one has a nicer interface and more options
4. Geologists Little Helper USA - useful for Oil Zone Analysis, Gas Zone Analysis, Leak Off Test, Formation Temperature and a Corrected D Exponent calculation
5. Virtual Microscope - a very cool little app that only has 4 samples right now but allows you to look at gabbro, schist, limestone, and a meteorite collected in Antarctica.

There are a lot of other apps out there that are related but aren't quite polished at this point in my opinion. I still haven't seen a 'game changer' in the world of geology yet. Will continue to update as new apps become available!

Three ROCKIN' Scenic Geology Roadways

This summer I had the great pleasure of driving the Needles Highway (South Dakota Highway 87), the Chief Joseph Scenic Byway and the Beartooth All American Road (US Highway 212) for the first time on a trip to Bozeman, MT. I had heard and read great things about these routes and they certainly delivered stunning vistas and fantastic geology (even thought it was raining and incredibly windy in some locations). I've driven across the country a dozen or so times and taken various routes, but I would have to agree that these three highways provide some of the best geology 'watching' in the country!

The Needles Highway was a bit congested since Sturgis was in full swing but luckily the views looking up weren't impeded by the traffic. However, the day was cut short by a hail-producing thunderstorm.

I also stopped at Dead Indian Hill Pass (see my Gigpan of this location here). This stretch of the road is full of switchbacks and quite steep (stay in low gear!):

This is one of my favorite vantage points on the Beartooth - it isn't as 'scenic' as some other photos I took, but I really like the sense of scale, isolation, serenity, and rugged nature of this landscape:

And these are a view other views driving the Beartooth, I think the partly cloudy drizzle really adds a nice effect to this landscape:

The paternoster lake system you can see in the photos from the Beartooth Highway are spectacular, I personally haven't seen such an easily accessible view of this stunning an alpine landscape. I've always enjoyed paternosters, as much for their morphology as the etymology of the word - it roughly translates from Latin as "Lords Prayer" and the fact that they look like a chain of rosary beads. None of the photos or Photosynths do the drives justice, if you like driving and you like geology, then put these on your list of must-do drives in the western United States!

Bookcrop #3: Geologic History of Yosemite Valley

Most of my bookcrops are unique, funny, sometimes bizarre or in this case a pioneering study in geology. I was given this book by a colleague with the Geological Survey of Canada when he was downsizing his collection. It is a canceled copy of Francois E. Matthes "Geologic History of the Yosemite Valley" published in 1930 as a USGS Professional Paper #160. You can view an online version here complete with all the plates and illustrations at the bottom of the page. Not all the plates are scanned full size but they are at least viewable.

Matthes's paper was the first comprehensive report of the geology and glacial history of the region and really championed the idea that Yosemite's landscape was a direct result of glacial activity. His descriptions and photographs were, and still are, compelling evidence to support this argument, which was first articulate by John Muir in "Studies in the Sierra." The historical link between Muir and Matthes is an interesting juxtopostion between a naturalist and an engineer - both with a love of mountains and glaciers. I think the most beautiful plate in the book is the "Map of Ancient Glaciers of the Yosemite Region."

Not only is the map beautifully drawn and colored but it offers a relatively good reconstruction of the extent of Wisconsin (or Tioga) glaciers. For a more recent account of the effects of glaciation in Yosemite you can read N. King Huber's "Geologic Story of Yosemite Valley" or Jeffrey Schaffer's "The Geomorphic Evolution of the Yosemite Valley and Sierra Nevada Landscapes."

One of my other favorite images is of the Dana Glacier taken by G.K. Gilbert - a pioneer in his own right. You can compare Gilbert's image (below left) with an earlier photograph taken my I.C. Russell (below right) in 1883 and get a sense of the amount of ice mass lost over the intervening decades. Similarly, if you compare it with a modern day image provided by Basagic (2004).

When you compare these two images with the one taken in 2004 by Basagic, the amount of ice volume lost since the late 1880s is dramatic! If you need further convincing that global ice volume is rapidly decreasing, visit Extreme Ice Survey for even more compelling images. Luckily you don't need to go out and by this book if you primarily want to look at the images - you can just explore the USGS online edition and really get a feel for the type of fieldwork and challenges Matthes must have faced writing this paper.