3D Mapping of Coral Reefs – How to Get Started – by John Burns

Rapid technological advancements are providing a suite of new tools that can help advance ecological and biological studies of coral reefs. I’ve studied coral health and disease for the last several years. One large gap in our research approach is the ability to connect changes in coral health to large-scale ecological processes. I knew that when corals died from disease it would alter the fundamental habitat of the system, which in turn would impact associated reef organisms. What I didn’t know was how to effectively document and quantify these changes. Sometimes we just need to alter our perspective to find the answers we are looking for. I starting reviewing methods used by terrestrial researchers to measure landscape changes associated with landslides and erosion. In doing so I came across structure-from-motion (SfM) photogrammetry, and it was immediately clear that this technique could improve our understanding of coral reef ecosystems. I spent the next few years developing methods to use this approach underwater, and have since used SfM to detect changes in reef structure associated with disturbances as well as improve our understanding of coral diseases.
 kiritimati_nature_figure

The first question I am usually asked is, “How easy is it to use this technique and what does it cost?” The best answer I can provide is the logistic constraints depend on your research question. If you are interested in accuracy and controlling the parameters of the 3D reconstruction process, then you should use proprietary software like Agisoft PhotoScan and Pix4D. These programs give you full control, yet require more understanding of photogrammetry and substantial computing power. Autodesk ReCap can process images remotely, which reduces the need for a powerful computer, but also reduces your control over the 3D reconstruction process. At the most simple level, you can download the Autodesk 123D catch app on your phone and create 3D reconstructions in minutes! There are also multiple open-source software options, but they tend to be less powerful and lack a graphical user interface. My advice is to start small. Get started with some simple and free open source tools such as Visual SfM or Bundler. Collect a few sets of images and get some experience with the processing steps to determine if the model outputs are applicable for your research approach.

The second question I receive is, “What is the best way to collect the images?” Unfortunately, the answer is not to use the ‘auto’ setting on your camera and just take a bunch of pictures. Image quality will directly affect the resolution of your model, and is also important for stitching and spatial accuracy. Spend time to understand the principles of underwater photography. A medium aperture (f-stop of 8 to 11) will let in enough light in ambient conditions while not causing blur and distortion associated with depth of field. Since images are taken while moving through a scene, a high enough shutter speed is required that will eliminate blur and dark images. Since conditions can be highly variable, one must adapt to changes in light and underwater visibility while in the field. Cameras with auto-ISO can be helpful for dealing with changing light conditions while surveying. I also recommend DSLR or mirrorless cameras with high-quality fixed lenses, as they will minimize distortion and optimize overall resolution and clarity. For large areas I won’t use strobes because I take images from large distances off the reef, and this will typically create shadows in the images. I take images of the reef from both planar and oblique angles to capture as much of the reef scene as possible in order to eliminate ‘black holes’ in the resulting model. There is no ‘perfect approach,’ but you will need 70-80% overlap for accurate reconstruction. I swim in circular or lawn-mower patterns depending on the scene, and swear by the mantra that more is better (you can always throw out images later if there is too much overlap). It is worth investing time in experimenting with methods to develop a technique that works best for your study are and experimental design. SfM is a very flexible and dynamic tool, so don’t be afraid to create your own methods.

The third question is then, “How do you ground-truth the model for spatial accuracy?” This is a critical step that often gets overlooked. In order to achieve mm-scale accuracy the software must be able to rectify the model to known x,y,z coordinates. I use mailbox reflectors connected by PVC pipe to create ground control points (GCPs) with known distances. The red color and white outline of the reflectors is easily distinguished and identified by the software and saves a lot of time for optimizing the coordinates of the model. Creating functional GCPs is exceptionally important is spatial accuracy is required for your work. I also use several scale bars throughout my reef plots to check accuracy and scaling. This step of the process is critical for accurately measuring 3D habitat characteristics.

Maybe I’ve taken you too far into technical details at this point, but hopefully this helps for anyone looking to venture into the world of SfM. There is no perfect approach, and we must be adaptable as software continues to improve and new tools are constantly being created. We also need to continue to develop new methods for quantifying structure from 3D models. I export my models into geospatial software to extract structural information, but this step of the process can be improved with methods capable of annotating the true 3D surface of the models. As new software becomes available for annotating 3D surfaces we are entering an exciting phase with endless possibilities for collating and visualizing multiple forms of data. Being open-minded and creative with these techniques may provide new insight into how these environments function, and how we can protect them in the face of global stressors.
– Mahalo to John Burns for this in-depth guest posting. You can see more of his work, simultaneously beautiful and useful, at the Coral Health Atlas. Click on the image below for more of John’s remarkable 3D coral reef mapping work:
johnburns_sketchfab
>>>Go to NSF EarthCube or the CRESCYNT website or the blog Masterpost.<<<
3D Mapping of Coral Reefs – How to Get Started – by John Burns

CRESCYNT Toolbox – Open Science Framework supports reproducible science

osf

The Open Science Framework, or OSF (osf.io) is a free and open source platform for supporting reproducible science. It’s designed more for documenting work than for streamlining work. It’s potentially a useful place to host a messy spread-out collaborative research project partly because of the add-ons it can connect with, (1) for storage: Amazon S3, Box, Dataverse, Dropbox, figshare, Google Drive, and GitHub, and (2) for references: Mendeley and Zotero. OSF also comes with a dashboard, a wiki, email notifications for your group, OSF file storage with built-in version control, data licensing background and assignment capability, ability to apply permission controls, and ability to make projects and components either private or public. Projects that one chooses to make public can be assigned DOIs (which can be transferred if you move your project elsewhere).

Aside from its primary role as a place to host research documentation and collaboration, OSF has also been used to teach classes in open science and reproducibility, and as a location to host conference products such as presentations and posters.

OSF is not a perfect platform for science – that elusive creature does not yet exist – but it’s a robust start with its ability to integrate other resources you may already be using, gets extra points for being free and open source, and could definitely be worth the learning curve of using with a next project. It continues to be improved over time, and how will we know what to ask of a platform if we don’t wrestle a bit with what’s already been built?

Learn more at the Open Science Framework FAQs and OSF Guides
or on YouTube (where everyone seems to learn new software these days):
+ Getting Started with the OSF (2 mins) (start here!) –
+ Most recent “OSF 101” intro webinar (1 hour) –
+ Deep dive into the OSF (1 hour) (thumbs up!) –
+ and more at OSF’s YouTube channel.

If you try it out, please let us know what you think!

Update: OSF now also connects with Bitbucket and ownCloud. See current Add-ons.

>>>Go to the blog Masterpost or the CRESCYNT website or NSF EarthCube.<<<

CRESCYNT Toolbox – Open Science Framework supports reproducible science

WELCOME to CRESCYNT – the Coral Reef Science and Cyberinfrastructure Network

The Coral Reef Science & Cyberinfrastructure Network (CRESCYNT) is a multi-tiered and multidisciplinary network of coral reef researchers, ocean scientists, cyberinfrastructure specialists, and computer scientists, and we invite you to join us. Scope of Sciences within EarthCube

As an EarthCube Research Coordination Network, our goals are to foster a dynamic, diverse, durable, and creative community; to collectively consider and develop standards and resources for open data, research documentation, and data interoperability while making best use of work already accomplished by others; and to offer input to those groups within EarthCube who will ultimately create the data architecture for all of EarthCube. Along the way CRESCYNT expects to collect and share community resources and tools, and to offer training opportunities in topics prioritized by our members through widely accessible formats such as webinars and their recordings. We will also work to nurture unforeseen collaborative opportunities that emerge from our integrated collective work.

Because the coral reef community has exceptionally diverse data structures and analysis requirements needed to forward integrative science, it is an exemplar for cyberinfrastructure-enabled advances to other geosciences communities. The CRESCYNT network is working to match the data sources, data structures, and analysis needs of the coral reef community with current advances in data science, visualization, and image processing from multiple disciplines to advance coral reef research and meet the increasing challenges of conservation. The network has begun to assemble to coordinate, plan, and prioritize cyberinfrastructure needs within the coral reef community.

Workflows within CReSCyNT: participants to nodes to collective project outputsThe structure of CRESCYNT is a network of networks, currently including 18 disciplinary nodes and 7 technological nodes, where each network node represents an area of coral reef science (disciplinary nodes: e.g., microbial diversity, symbiosis regulation, disease, physiology & fitness, reef ecology, fish & fisheries, conservation & management, biogeochemistry, oceanography, paleontology, geology) or an area of computer science or technical practice (technological nodes: e.g., visualization, geospatial analysis & mapping, image analysis, legacy & dark data, database management). These nodes may expand, coalesce, or divide to meet the needs and interests of the subdisciplinary communities, while maintaining connections to CRESCYNT through node coordinators and ongoing network activities. We invite you to become a member of CRESCYNT, join one or more nodes that would advance your own work, collaborate on shared resources and tools for the coral reef community, and ensure that the data architecture and cyberinfrastructure of EarthCube will meet the needs of the coral reef community, and that broader data interoperability within EarthCube will benefit both coral reefs and our ability to answer complex questions.

PLEASE VISIT OUR WEBSITE at http://crescynt.org to enroll in CRESCYNT, join a node, work on tasks, discuss data and research priorities, and help determine the future shape of cyberinfrastructure for supporting coral reef research and other geoscience work. This collaborative work is supported by the NSF EarthCube initiative.  Dr. Ruth D. Gates, Director of the Hawaii Institute of Marine Biology, University of Hawaii, is the Principal Investigator of the CRESCYNT project. The CRESCYNT blog is written by Dr. Ouida Meier, the project’s program manager (crescyntrcn@gmail.com).

This material is based upon work supported by the National Science Foundation under Grant Number 1440342. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

>>>Go to the blog Masterpost or the CRESCYNT website or NSF EarthCube.<<<

WELCOME to CRESCYNT – the Coral Reef Science and Cyberinfrastructure Network