Chasing Coral now on Netflix

Please credit The Ocean Agency - XL Catlin Seaview Survey - Richard Vevers & Christophe Bailhache
Coral Bleaching and its Aftermath – a scene from Chasing Coral. Credit: The Ocean Agency – XL Catlin Seaview Survey – Richard Vevers & Christophe Bailhache

Several of the coral reef scientists featured in the film Chasing Coral are CRESCYNT participants, including our PI, Dr Ruth D Gates, and we congratulate and thank them all for their eloquence, passion, deep experience, scientific integrity, and significant intellectual contributions to this powerful film. Chasing Coral‘s producers are making it available free for public screenings, and its focus now is educating audiences and moving people to action.

It’s not too late for coral reefs…  indeed, for many other ecosystems that are facing challenges from climate change. It’s still possible to reduce the rate at which the climate is changing, and that’s within our power today.” – Dr Ove Hoegh-Guldberg
Chasing Coral now on Netflix

Resources for Coral Reef Education – by Judy Lemus

divers_lpittman_pixabay.jpgWe all recognize that communication and education about science concepts and the process of science is more important than ever.  Fortunately, coral reefs are charismatic ecosystems that inspire much curiosity, concern, and interest from many sectors of society.  While there is no shortage of stunning images and videos online, resources that combine these visuals with robust educational content can be more challenging to identify; they do exist and I’ve put together some of my favorites here. The list is not exhaustive, and we welcome your suggestions for great additions.

EDUCATIONAL WEBSITES. These resources provide educational information about coral reefs across multiple levels and concepts, often using multimedia.

Khaled bin Sultan Living Oceans Foundation Coral Reef Ecology Curriculum. The KSLOF has perhaps the most comprehensive website on coral reef ecology. The site is set up as a course with several units and resources with very nice graphics and high quality videos geared specifically for students and teachers. Lessons are aligned with the Next Generation Science Standards, Ocean Literacy Principles, and Common Core State Standards for K-12, but some of the material could easily be used in a college level course. A major downside to this site is that one must register to use it.

Smithsonian Ocean Portal. The Smithsonian’s website for coral and coral reefs is not as media-rich as the KSLOF, but does have a great deal of scientific information about corals.  Only a couple of lesson plans are offered, but the richness of the content lies in the embedded links to additional images and other stories. The science is backed up with oversight by Smithsonian coral reef biologist Nancy Knowlton.

MarineBio Coral Reefs. The MarineBio website is somewhat of a clearinghouse for other marine bio resources, but the educational content on coral reefs is good quality and quite extensive if you follow the links.  Like the Smithsonian site, there are links to both internal and external resources. The short videos featured throughout the site, generally from outside sources, are particularly engaging.


National Ocean Service

NOAA Coral Reef Conservation Program

USGS Coral Reef Project

Coral Reef Alliance

Teach Ocean Science


Great Barrier Reef Foundation

Coral Triangle Initiative

Endangered Reefs, Threatened People

Coral Health Atlas

VIDEOS ABOUT CORALS AND CORAL REEFS. There are loads of videos of corals and coral reefs on the web; these excellent examples incorporate educational content.

Catlin Seaview

Chasing Coral (available through Netflix)

Climate Change: Coral Reefs on the Edge

Exploring the Coral Reef: Learn about Oceans for Kids

Corals Under Confocal

Coral bleaching caused by heating water (time-lapse)

Life Noggin – What Happens if All the Coral Dies? (animation)

Coral Bleaching Animation – HHMI BioInteractive Video (animation)

Coral Bleaching on the Great Barrier Reef (animation)

SCIENCE NEWS SITES. These science news websites regularly post stories on coral reefs.



Thanks to Dr. Judy Lemus for this cream-of-the-crop list. Judy is a Faculty Specialist in Science Education at the Hawaii Institute of Marine Biology; fortunately for us, she is also the Education Node Leader for CRESCYNT. You can download Judy’s list in pdf format.

Resources for Coral Reef Education – by Judy Lemus

CoralNet: deploying deep learning in the shallow seas – by Oscar Beijbom


Having dedicated my PhD to automating the annotation of coral reef survey images, I have seen my fair share of surveys and talked to my fair share of coral ecologists. In these conversations, I always heard the same story: collecting survey images is quick, fun and exciting. Annotating them is, on the other hand, slow, boring, and excruciating.

When I started CoralNet ( back in 2012 the main goal was to make the manual annotation work less tedious by deploying automated annotators alongside human experts. These automated annotators were trained on previously annotated data using what was then the state-of-the-art in computer vision and machine learning. Experiments indicated that around 50% of the annotation work could be done automatically without sacrificing the quality of the ecological indicators (Beijbom et al. PLoS ONE 2015).

The Alpha version of CoralNet was thus created and started gaining popularity across the community. I think this was partly due to the promise of reduced annotation burden, but also because it offered a convenient online system for keeping track of and managing the annotation work. By the time we started working on the Beta release this summer, the Alpha site had over 300,000 images with over 5 million point annotations – all provided by the global coral community.

There was, however, a second purpose of creating CoralNet Alpha. Even back in 2012 the machine learning methods of the day were data-hungry. Basically, the more data you have, the better the algorithms will perform. Therefore, the second purpose of creating CoralNet was quite simply to let the data come to me rather than me chasing people down to get my hands on their data.

At the same time the CoralNet Alpha site was starting to buckle under increased usage. Long queues started to build up in the computer vision backend as power-users such as NOAA CREP and Catlin Seaview Survey uploaded tens of thousands of images to the site for analysis assistance. Time was ripe for an update.

As it turned out the timing was fortunate. A revolution has happened in the last few years, with the development of so-called deep convolutional neural networks. These immensely powerful, and large nets are capable of learning from vast databases to achieve vastly superior performance compared to methods from the previous generation.

During my postdoc at UC Berkeley last year, I researched ways to adapt this new technology to the coral reef image annotation task in the development of CoralNet Beta. Leaning on the vast database accumulated in CoralNet Alpha, I tuned a net with 14 hidden layers  and 150 million parameters to recognize over 1,000 types of coral substrates. The results, which are in preparation for publication, indicate that the annotation work can be automated to between 80% and 100% depending on the survey. Remarkably: in some situations, the classifier is more consistent with the human annotators than those annotators are with themselves. Indeed, we show that the combination of confident machine predictions with human annotations beat both the human and the machine alone!

Using funding from NOAA CREP and CRCP, I worked together with UCSD alumnus Stephen Chan to develop CoralNet Beta: a major update which includes migration of all hardware to Amazon Web Services, and a brand new, highly parallelizable, computer vision backend. Using the new computer vision backend the 350,000 images on the site were re-annotated in one week! Software updates include improved search, import, export and visualization tools.

With the new release in place we are happy to welcome new users to the site; the more data the merrier!


– Many thanks to Oscar Beijbom for this guest posting as well as significant technological contributions to the analysis and understanding of coral reefs. You can find Dr. Beijbom on GitHub, or see more of his projects and publications here. You can also find a series of video tutorials on using CoralNet (featuring the original Alpha interface) on CoralNet’s vimeo channel, and technical details about the new Beta version in the release notes.

CoralNet: deploying deep learning in the shallow seas – by Oscar Beijbom

CRESCYNT Toolbox – Powerful Temperature Visualizations

Temperature is a critical environmental parameter that has massive relevance in describing where coral reefs occur and growing direct and indirect threats to their existence.

Here are some powerful visualizations of global temperature data you may find useful or want to replicate for local temperature datasets.

First, spiralling global temperatures by Ed Hawkins (using MATLAB):

Click to animate.     Author: Ed Hawkins

The climate spirals page of Hawkins’ Climate Lab Book features global temperature change updates, as well as atmospheric CO2 and arctic sea ice volume animations. His small multiples assembly of global temperatures by decade is very useful, and could be used to describe environmental changes on a regional map scale as well.

Ed Hawkins also links to Robert Geiseke and Malte Meinshausen’s interactive tool and a set of video animations for offline use that build upon his work.

NASA’s temperature graphs and charts are varied and useful, and have pages for downloading different temperature products for specific date ranges, including global maps, surface temperature animations, and this 135-year time chart of zonal temperature anomalies:


See NASA’s Global Climate Change – Global Temperature site for rich multimedia resources and apps, including global temperature anomaly maps with year sliders and an embeddable 3-min video which graphs different potential factors with global temperature changes (surprise: the correlation is with anthropogenic CO2). High global temperatures and low Arctic sea ice cover both broke records in the first half of 2016.

NOAA has its own further derivations of very useful temperature representations, particularly for coral reef work, including global and regional sea surface temperature contour maps,  a suite of coral bleaching data products with predictive bleaching alerts derived from virtual stations, and their degree heating weeks maps, which some NOAA scientists prefer as their most accurate post-event indicator of peak bleaching intensity.


Thanks for inspiration to Andrew Freedman’s excellent article on Mashable featuring compelling temperature visualizations.

If there’s a temperature visualization you love – including simple – simple is good – please share it with us by leaving a comment. Thanks.

CRESCYNT Toolbox – Powerful Temperature Visualizations

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!

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.

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 an article on coral bleaching at Time online.

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