CRESCYNT Toolbox – Stitched Images – 3D Reef Mapping and 360-Degree Imagery

Imagery REALLY feeds our monkey brains. Today: tools for 3D reef mapping. Bonus: some 360-degree images and video to use with virtual reality headsets.

Several exciting talks at the International Coral Reef Symposium featured 3D mapping of coral reefs using SfM, Structure from Motion techniques, to stitch together large numbers of overlapping images. The resulting 3D mapped images were used to help address a surprising range of research questions. The primary tools used to create these were Agisoft’s PhotoScan or the free and open source Bundler (github) by Noah Snavely.  Part of the challenge of this difficult work is organizing the workflows and data processing pipelines: it’s an example of a type of cyberinfrastructure need that eventually EarthCube architecture should be able to help stage. Look for a guest blog soon by John Burns to learn more!

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360 Film by Conservation International

BONUS: The process of creating spherical or 360-degree images or video is at root a similar challenge of stitching together images, though more of the work is done inside a camera or on someone else’s platform. There are some recent beautifully-made examples of spherical coral reef images and 360 videos, viewable through virtual reality (VR) headsets; these have great potential for education and outreach. Consider the XL Catlin Seaview Survey gallery of coral reef photo spheres and videos from around the world, (including bleaching and before-and-after images) and Conservation International’s 8-minute video, Valen’s Reef, both exhibited at the current IUCN World Conservation Congress in Honolulu.

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Catlin Seaview Survey – equipment

A new project, Google Expeditions, was launched this past week to facilitate synchronized use by multiple people of 360 videos and photo spheres as a design for class use. Google Streetview is being made more accessible as a venue for education and outreach, including creating and publishing one’s own photo spheres. Also find 360-videos of coral reefs on YouTube.

UPDATE: Visually powerful 360 bleaching images that Catlin Seaview debuted at ICRS, viewed by tablet or smartphone, are now accessible in this article on coral bleaching.

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

CRESCYNT Toolbox – Stitched Images – 3D Reef Mapping and 360-Degree Imagery

CRESCYNT Toolbox – Unifying a Search Through Species Databases

If the only tool you have is a hammer, everything looks like a nail.

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CRESCYNT wrenches

Our new Toolbox series for the coral reef community will highlight one tool each week relevant to data management, analysis, visualization, storage, retrieval, reuse, or collaboration. We’ll try to focus on the most comprehensive, useful, and relevant tools for coral reef work.

We hope you’ll take time to try each one out, and then tell us what you think.

~~~~~~~~~~~~~~~~~~

This week:  Biodiversity information aggregated at GBIF (http://gbif.org ).

The Global Biodiversity Information Facility (GBIF) pulls together species and taxonomic entries from over 800 authoritative data publishers and constantly updates them. GBIF intake includes favorite coral reef species databases (WoRMS, iDigBio, ITIS, Paleobiology,…). Bonus: GBIF makes it easier to search NCBI to find ‘omics data on corals, symbionts, and holobionts.

Search by taxon, common name, dataset, or country; apply filters, and link directly to providers’ websites. Explore species now at http://gbif.org/species .

Yours for a more robust toolbox.

gbif

 

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

CRESCYNT Toolbox – Unifying a Search Through Species Databases

CRESCYNT at ICRS 2016

CRESCYNT IS AT #ICRS2016 – International Coral Reef Symposium in Honolulu, Hawaii!

EVENTS:

WORKSHOP – Cyber Tools and Resources for Coral Reef Research and Analysis
Sun. June 19 8:30am-4:00pm, Hawaii Convention Center rm 314
(breakfast, lunch provided – register here)
ask about materials / future webinars if you miss
sponsored by EarthCube CRESCYNT – some seats still open!

CRESCYNT Node Coordinators Meeting
Mon June 20 6:00-8:30pm, Hawaii Convention Center 307 A/B

OPEN MEETING – CRESCYNT Participants with Node Coordinators
Wed June 22, 11:30am-12:45pm, Hawaii Convention Center 307A/B
(bring your ICRS lunch – we’ll have ice cream)
OPEN TO ALL – come if you’re interested!

DISCUSSION & SYNTHESIS SESSION: Emerging Technologies for Reef Science and Conservation
Fri June 24, 9:30am-3:45pm, Hawaii Convention Center 312icrs2016-footer
(Discussion 11-11:30am. CRESCYNT at 2pm)

UPDATE: Find all the meeting abstracts in this 414-page pdf book

 

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

CRESCYNT at ICRS 2016

Successful Forum at Ocean Sciences Meeting, New Orleans – iSamples, CRESCYNT, & SeaView

The topic was:  Physical Samples in the Ocean Sciences. It was great to co-host with these terrific EarthCube groups – thanks to iSamples for providing lunch!  Details:

This event was jointly hosted by the EarthCube groups:
iSamples Research Coordination Network,
CRESCYNT Coral Reef Science & Cyberinfrastructure Network, and the
SeaView Integrative Activity.

OSM attendees were invited, and we had a great discussion over lunch; we were also pleased to be joined by EarthCube’s Marine Annually-Resolved Proxy Archives group.

The discussion provided opportunities for researchers to learn about these collaborative groups, how they support digital and physical sample management, options for sample citation in publications, links to related content such as field expeditions, datasets, and ORCIDs for investigators, and to tell us about YOUR challenges with your sample collections, their curation, documentation, and preservation, and how you want to access and visualize data related to samples. The forum was also an opportunity to check out existing tools that can help you manage your samples. Participants of all levels and from all disciplines were encouraged to attend – and did. You can register your physical samples with SESAR to obtain IGSNs for unique sample identification.

On a related note – just prior to the Ocean Sciences Meeting, CRESCYNT was able to attend a workshop offered by SeaView, and we admire the work  they’re doing to get data facilities, toolmakers, and domain scientists in the same room and on the same page in order to integrate disparate datasets. It’s an ambitious and groundbreaking practical project, and it was impressive to see people begin to address and solve some of the inevitable challenges of metadata interoperability.

Crescynt-at-EarthCube-booth-OSM2016We also had a great time hanging out at the EarthCube table periodically  and talking with so many creative people who came by: scientists, tech people, underwater filmmakers(!), students ambitious for innovation…  The conversations were a reminder that EarthCube is all about people and open sharing and integration of ideas.

 

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

Successful Forum at Ocean Sciences Meeting, New Orleans – iSamples, CRESCYNT, & SeaView

CRESCYNT at Ocean Sciences Meeting 2016 – and nearly 100 coral reef presentations!

The 2016 Ocean Sciences Meeting is coming up in New Orleans 21-26 February 2016, and we hope to see you there! There are 97 oral and poster session presentations scheduled with CORAL in the title (plus a lunchtime presentation from CRESCYNT, making 98), and we hope to talk with coral reef researchers about YOUR needs and priorities for data, analysis, and cyberinfrastructure.

1 – Joint lunchtime discussion held with iSamples, CRESCYNT, and SeaView on Monday, Feb. 22, 12:30-2:00pm. Lunch will be provided! Register at http://bit.ly/1QFHLd1.

2 – CRESCYNT coral reef RCN will be at the EarthCube exhibitor booth 507 periodically, including Tuesday, Feb. 23, 9:30am – 2:00pm and on other days by appointment. Come by at that time or any time to fill out a CRESCYNT priority survey and learn more about EarthCube.

3 – Please email us at crescyntrcn@gmail.com to set something up. We’d love to talk with you while at OSM (or any other time).

The chart below shows when the coral-related oral papers and poster sessions will take place. Hope to see you there!

Coral Presentations at OSM 2016
Coral Presentations at OSM 2016

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

CRESCYNT at Ocean Sciences Meeting 2016 – and nearly 100 coral reef presentations!

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