3D Model of Ta’an: Ancient Egyptian Sarcophagus

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Did you know that the only two ancient Egyptian mummies in Indiana are located in Richmond? One is in Wayne County Historical Museum, and the other is right here at Earlham College as a part of the Joseph Moore Museum. We are excited to introduce you to an exciting project we had been working on, in cooperation with the Computer Science Department and the Joseph Moore Museum.

Charlie taking photo of the Egyptian sarcoph
Charlie takes photographs of the sarcophagus. Ann-Eliza (not featured) is holding a white backdrop.

Despite the museum’s closure to the public since the pandemic, Joseph Moore Museum has been working to bring better and improved exhibitions to the public when it reopens. With an Indiana humanities grant, students in the Exhibit Design class redesigned the ancient Egypt exhibit. Over the winter break, the existing exhibit was demolished. For the first time in 10 years, the sarcophagus was taken out of the display case before the demolition and moved to a safe location.

As soon as the Spring semester started, Charlie, Craig, and Yujeong went down to the museum for a rare opportunity to digitize the sarcophagus. With the goal to build a 3-dimensional digital model of the sarcophagus, Charlie and Craig took overlapping photos of the sarcophagus from the top and its four sides, summing up to 180 photos. We then used the a 3D building software (ODM) to build a digital model of Ta’an’s sarcophagus.

Craig takes photographs of the sarcophagus from its side.

If you are already familiar, ODM, also known as OpenDroneMap, is an unusual tool of choice with its intended purpose of processing aerial imagery into maps and 3D models. In fact, ODM is a primary tool used by Icelandic Field Studies, an interdisciplinary research group that collaborates with archeologists in Iceland to build a widely applicable system out of open-source, open-hardware software. As one of its primary project recently funded by the National Geographic Society, the IFS group has been surveying several ancient Norse sites in Iceland to look for early settlement activity from subterranean features with tools like ODM.

A student take photographs in Iceland during a research trip for Icelandic Field Studies.

The digitized 3D model of the sarcophagus can be viewed on MeshLab, and it encompasses an incredible amount of details. Viewers can take a close look at the paintings, textures, and even cracks on the sarcophagus. Furthermore, even after the sarcophagus decomposes past its preservation plan, we now have an accurate visual data of the artifact that future scholars can use to study and honor.

We’re on track for summer

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Discussions are ongoing about the viability of summer travel given the pandemic. However, as Charlie has blogged recently, we are “acting as if”. As such, we are trying to maintain our original calendar.

Lo and behold, we have:

Imagine a “You are here” arrow by Spring 1

Here’s the full breakdown of that schedule and our progress:

Our plan for the fall was to find and test alternative UAV’s. This proved prudent, as the federal government banned DJI craft late last year. We are happy with both the Parrot and the Skydio craft, for different reasons which we’ll undoubtedly cover here on this blog in the future.

December and January, which were effectively a long winter break for a subset of us, were dedicated to testing the craft, capturing initial video, and possibly beginning development. This was a success as well. Additionally we have begun spinning up a more sophisticated web presence for the stories we’re telling – changes we will be prepared to publish soon.

We’ve now started the calendar for the spring, term 1 of 2. We are moving into scaling up our operation of the craft and developing software to automate that work. It’s a tough problem but one we can solve in the time we have.

We’re optimistic about our ability to meet the moment. If the world continues to make progress on COVID-19, we should be in shape to have a successful research trip.

Cross-posted to craigearley.com

The year in review

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For the first two months of 2020 we planned and worked as though we would be working in Iceland during June; once we realized that the Covid-19 pandemic would prevent that, and much else, we re-organized ourselves and our work in the new normal. This included accommodating people working remotely from a wide range of timezones and reprioritizing tasks based on a new timetable. Whenever possible we tried to make lemonade, for instance we were able to re-organize our data storage structures, something we could not have done without the long timeline available this past year. Here is a summary of the other ground we have covered, future posts will have more details about each of these bits.

Craft research – One of the challenges of doing system integration in this space is the fast pace at which the hardware is evolving. We refined our requirements and resurveyed the market, ultimately deciding to add the Parrott Anafi and the Skydio 2 to our kit. In addition to craft-mounted multi-spectral lens we are also working with a MapIR NIR equipped lightweight camera which we will use as payload on the Anafi.

The Anafi with the MapIR camera payload. Image credit Charlie Peck.

ODM configurations – With time and computational resources we have been able to read and experiment with the ODM options that apply to our analysis workflow, and there are lots of them.

GIS integration – Our workflow now incorporates QGIS, this gives us the ability to use the powerful georeferencing plugin to accurately merge each of the data layers (sensor modes).

Storytelling – For many years we have been taking a fairly ad-hoc and often random approach to getting the word out about our work. We realized that we could now take the time to make a more organized run at storytelling, so a few of us have.

Planning for 2021 – We are now deep into the logistical and science planning for the 2021 field season, as I write this in mid-January we are working with the College and our colleagues in Iceland to plan our time there during June. One of our field sites, the Skalanes Nature Preserve, has experienced a number of mudslides this winter, destroying parts of Seydisfjordur and making travel along the fjord very difficult.

View to the North over the Eider colony at Skalanes. Image credit Charlie Peck.

And we’re off, again, hopefully…

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Today is the official re-start of our National Geographic Society supported near-Earth survey work in Iceland (Earlham’s press release). Like many other scientists we have been unable to travel to field sites since the onset of the pandemic, the National Geographic graciously gave us a one year deferral for our grant, and now we are beginning to plan towards working in Iceland this coming June. Our project is based on commonly available UAV technology, our group is designing and building inexpensive, open, software and hardware systems for domain scientists to easily measure a variety of Earth surface parameters. Our first two disciplines are archaeology and sustainability, both of which depend on a variety of sensing modes. A few details about the gear and workflows are below, and in subsequent posts we will describe them in more depth.

Our group is a collection of students, faculty, and professionals primarily based at Earlham College in Richmond, Indiana and at Skalanes, outside of Seydisfjordur, Iceland. Together we cover archaeology, biology, computer science, geography, storytelling, and sustainability. The faculty and professionals are: Emmett Smith, Craig Earley, Rannveig Thorhallsdottir, Olafur Petersun, and Charlie Peck (me). The students we are currently working with are: Dung (Kate) Nguyen, Tamara Blagojevic, Davit Kvartskhava, Pyone Win, and Yujeong Lee. Over the next year you will learn more about all of us as we write posts that describe the specific aspects of the project which we focus on. For the most part we fancy ourselves as generalists, but in reality each of us brings lots of domain knowledge and focus to our work where it is blended into solutions.

Our goal for this cycle is to make it easier and cheaper for archaeologists to locate subterranean points of interest within a known or suspected cultural activity area, and for environmental scientists to quickly survey large areas for e.g. invasive species measurement or erosion. Our approach combines three relatively recent advances in drone, sensor, and machine learning technologies. 

1) Consumer grade drones capable of doing basic field science tasks, at accessible costs. 
2) Significant growth in the types of sensors available, and at low cost. 
3) Powerful, relatively easy to deploy open source machine learning libraries, which can extract deep patterns from large, noisy, multidimensional data sets. 

These three trends can support an approach to subterranean feature detection that is faster, cheaper, and more accessible to a wider range of practitioners than existing methods. Rather than depending on a single very sensitive, often expensive and complicated sensor to detect subterranean features, e.g. satellite or aircraft based LiDAR; our Terrestrial Mapping Platform (TMP) makes it possible to do ground based surveys, in a combination of sensor modes, and then use machine learning algorithms to combine those data sets into a single analysis to detect subterranean anthropogenic features and characterize surface vegetation.

Lunch during a day of soil sampling and aerial surveying at Sólheimajökull, an outlet glacier of the Mýrdalsjökull icecap on the southern coast of Iceland, June 2019. Image credit Porter Libby.

Preliminary notes on the Parrot Anafi

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After three extremely short flights, these are my notes about the Parrot Anafi drone.

We’re experimenting with different UAV’s as part of the Iceland terrestrial surveying program (we’re being optimistic about travel in 2021…). These are some notes with my initial observations.

This is based on the base case: taking the craft out, taking off, flying for at most a few minutes, and touching back down. As such, don’t take a single word of this as gospel – it’s just preliminary opinions for the historical record. 🙂

Short version of the review: holy portability! One thing I don’t like about the DJI Phantoms is that they are so heavy (both the craft and the RC-tablet unit). If it’s a pain here on-campus, where trips are short, I imagine it’s a pain in the field. The Anafi is ludicrously lightweight and doesn’t feel like a chore to carry around.

Video quality on the built-in camera is fantastic (4K etc.).

It’s not a perfectly seamless integration with our existing workflows. Within our group, for example, we usually use tablets, which are handy for their big screens. The Anafi seems built around the assumption of a phone. That’s true all the way down to the RC unit being designed to accommodate a phone but not a tablet. That’s different, but if we can only get this app for phones I am not necessarily sad about it.

There are many X factors I haven’t yet been thorough enough to review. For example: battery life, stability in breezes (heavy winds make most UAV’s hard to use), and the software/developer ecosystem.

These have been my extremely preliminary notes about the Parrot Anafi. It’s not even close to a comprehensive evaluation of everything we care about. Still, those usability factors are important if this is going to scale and be useful for others. So for now, I’m impressed.

This is a cross-post from Craig Earley’s personal website.

See you next time Iceland

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This is our last full day in Reykjavik and in Iceland. In the morning we visited the Hellisheiði Power Plant for the ON Geothermal Exhibition, which gives us a detailed introduction including the history of Iceland using geothermal energy and the significance of geothermal energy to Iceland.

To use geothermal energy, there must exist a geothermal area, which is created by groundwater flowing through hot layers of rock generated by volcanic activities. The geothermal areas are They are categorized based on the temperature of the water in the bedrock into high- or low-temperature areas. The locations of the high- and low-temperature areas is a result of the age and temperature of the bedrock, where production in high-temperature areas focuses on using steam to produce electricity. Eight power plants in total produce 30% of Iceland’s 100% renewable electricity. Whereas within low-temperature areas geothermal hot water can be used for space heating. Approximately 90% of people living in Iceland use geothermal energy for that purpose.

a simplified flow chart of the geothermal plant

 

The outdoor view of part of the plant (pipe, cooling tower, steam exhaust)

 

 

The graph for a high-pressure turbine

 

the turbine connecting condenser and electricity generator

 

How they deal with the geothermal gas remaining in water such as carbon dioxide and hydrogen sulphide is also impressive. After the method of pumping the water back into the basaltic bedrock to let the gas turned into minerals by chemical combination is introduced, the percentage gets even lower.

We had a free afternoon again after we came back from the geothermal plant. Some of us went to the public pool (heated up by geothermal of course) to release the tiredness accumulated for three weeks. I personally walked around the main street downtown looking for souvenirs.

 

After dinner together, we all reflected on the whole trip. It is a pleasure to hear what people learned about Iceland from all aspects, how we grow by doing science and living together with each other and to think about what I achieved, accomplished and can do better.

 

I hope everyone can get some kind of sleep and ready to catch up the 8.30 am flight tomorrow. 🙂

We’re Freeeeeee!!!

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Finally, freedom!

We were back in Reykjavik and each of us got the whole day free to do whatever the heck we wanted in the capital. I decided to stay in for lunch, made myself an omelette and some ramen, and then headed to the public pool called Laugardalslaug. Unfortunately, phones and cameras were prohibited in the pool area so capturing pictures was not possible. However, I ended up enjoying the place and the vibe quite a bit as I went around dipping in the hot tub and steambath, completing a couple of laps and then going down a slide (a definite spot of fun for the young ones). There was also a small hot tub in a corner that had geothermal seawater, extracted from a borehole near the coast and heated further. It also had a few interesting salts (6 different ones, cannot recall all of them) – you would be able to feel the difference in texture if you went for a dip in it.

Later, I decided to have dinner at this food court that was within a 10-minute walk from the hostel and I did not regret that decision at all since I got to enjoy some absolutely delicious salmon. It was also the summer solstice, so a lot of people were hanging out in downtown and around the city. I decided to go for a walk, hoping to catch a view of the midnight sun and I was served just right!

Spotted on a main street, looked very intriguing

View of Hallgrimskirkja, the largest Lutheran church (probably the tallest building in Reykjavik), under the midnight sun

Program finds itself one hour ahead of schedule, one leader feints from shock…

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Today was our last day at Skalanes, which is always a bit sad. After spending a wonderful week here doing science, hiking, cooking, and eating together with a group of students from Scotland we are packing-up to head back West for a couple of days in Reykjavik before the program ends on 23 June. Did I mention Fyrir the amazing dog? And Oli and Rannveig the wonderful hosts? We also work with Oli and Rannveig on a couple of science projects related to ecology and archaeology.

Early this morning was a scrum of packing, eating, making lunches, cleaning-up, and saying goodbye. Our travel plan was a trucks to take the gear to the first river, people hiking there, and then a bus to Seyðisfjörðurand and over the Fjarðarheiði mountain pass to the airport in Egilsstaðir. At approximately 10:00 GMT the group found itself completely packed and ready to go, at which point they realized they did not need to leave until 11:00. One of the leaders, who shall remain anonymous, had never been ready ahead of schedule before and feinted from the shock. Hilarity ensued and we Euchre and Carcassonne until it was time to leave.

The trip was uneventful other than the bus trip from RKV airport to the hostel, construction at the hospital has changed the bus route so rather than knowing where to disembark (12 people with baggage and 10 cases of science gear and samples) we were a bit lost. Fortunately a very helpful local explained where we could get off that would be close to our lodgings.

And here are a couple of pictures from Skalanes, which is a place that pictures can hardly do justice to.


Fyrir, local security.

 


View to the North from the house.

Last day in Skalanes

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Today was the last full day here at Skalanes, a bittersweet kind of day. It started out with a presentation from Òli, who is currently working on his dissertation on the subject of the sustainability of Skalanes. The work here at Skalanes has taken several years, Òli bought the property for tourism and conservation but it has transformed into a multidisciplinary project. They have planted trees in hopes to offer a habitat for further avian species and to offset carbon. They have included students in the efforts to converse, not just to take data but to use that data in order to pursue more sustainable living and offer a more holistic habitat for the wildlife. This place continues to pursue better ways of living sustainably, including pursuing measures now for future events (like global warming).

After the presentation, we split up. Drone people did some flying. Soil and bio people packed up our bio boxes, which was quick and painless. After removing some tubes and gloves that we are keeping here, it was surprising to see how much space there was in the boxes compared to the packing job coming here.

Then we all did our own things, it was a relaxing afternoon. Around 2-3 Sydney recruited me for another batch of banana bread. We had 19 bananas, resulting in two large regular pans, one gluten frene tinto pan, and another small pan (cuz   I accidentally made the intended GF bread with real flower first). In the end, the bread ended up being delicious as dessert. Joyce madre Curry, which was so very good.

After dinner we all gathered together for group photos, a couple with the Glasgow crew and a couple with the gorgeous “Takk Fyrir” sign that Sydney drew to thank Òli and Rannveig. This was followed by our nightly group meeting (rest of trip logistics), then a trip to see the puffins by several of us. We were able to get quite close, they adorable creatures.


All in all it was a good last day. Excited to go back to Reykjavik, but going to miss this little piece of heaven.

 

Relaxing Day for Everyone at Skalanes

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Hey everyone! My name is Jordan Christian and I am a rising senior with a major in Computer Science and a minor in Global Management. My work here in Iceland has been primarily concerned with networking and configuration for our virtual machine as well as drone flying.

Some science work was completed here at Skalanes yesterday but for the most, it was a pretty relaxing day for all of us here in Iceland. The biology peeps were able to successfully complete some NPK work in the morning and by afternoon were able to relax for the rest of the day. Rain once again deterred the drone group from getting as much flying done as they would have liked, however they were able to capture some VLI imagery over a few spots. Em, Charlie, and Faith went into town to do some independent work on the 16s project and once again could experience the convivial atmosphere any Icelandic town can offer.

Hopefully tomorrow brings us some better weather so we can continue our science work in what will be our last full day at Skalanes!

 

Peace!

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