Archive by Author | kyleccav

Floating Forests Goes to Washington

wh_logo_sealLast week I had the opportunity to take part in a citizen science forum organized by the White House. It was inspiring to see how committed the White House is to harnessing the power of citizen science. A number of exciting announcements were made during the event. For one, the Federal Citizen Science and Crowdsourcing Toolkit was officially released. This toolkit, developed with the support and collaboration of over 25 federal agencies, provides step-by-step instructions, case studies, and other resources to help scientists use citizen science in their research. As you might imagine, Zooniverse projects are well represented in the successful case studies section! Then John Holdren, the Director of the Office of Science and Technology Policy, gave a talk where he announced the release of a memorandum promoting the use of citizen science by Federal Agencies. Towards the end of the forum Senator Chris Coons (D-DE) announced a new bill authorizing citizen science and crowdsourcing. This bill is co-sponsored by Senator Steve Daines (R-MT), making it bi-partisan! During his talk Senator Coons described how he and his family were citizen scientists themselves and have spent many evenings collecting data for a wide variety of different Zooniverse projects! So next time you are chatting with someone on Talk, know that he or she could very well be a senator or representative. Perhaps even President Obama has a Zooniverse account?

In between these exciting announcements there were panels on Community Science Leaders, Oceans and Coasts, Democratized Tools, Water and Agriculture, and Communities and Health. A number of really exciting citizen science projects were highlighted during these panels. These ranged from investigations of the impact of aggressive policing to surfboards that collect oceanographic data to the development of methods for utilizing indigenous traditional knowledge to our own Floating Forests! You can watch the entire forum here.

I had the honor to serve on the Oceans and Coasts panel with some HUGE names in the marine science world: Dr. Alex Dehgan, Dr. Sylvia Earle (aka Her Deepness), Dr. Daniel Pauly, and Dr. Janet Coffey. During the panel we talked about the importance of the ocean and how little we know about it. The oceans play a central role is supporting human life. Yet we’ve mapped less of the ocean floor at high resolution than the surface of Mars, Venus, and the Moon combined. We have limited information about the changes that coastal ecosystems like coral reefs, mangroves, and giant kelp have been experiencing in recent decades. Citizen science provides a powerful method for collecting data that will allow us to better understand and protect these critical ecosystems.

Let There Be Coast!

Note: This post is from Briana Harder, our newest Science Team member! We encountered Briana in Talk where she not only noted some issues, but then wrote code to reprocess images to fix them! Needless to say, we were impressed. What emerged was a wonderful dialogue between Briana, members of the science team, and the folk at Zooniverse. She’s made some large changes to our image processing pipeline and helped us all learn a lot about how to use Landsat for kelp in places *other* than California. As such, we asked Briana if she wanted to take her involvement to the next level, and join the Science Team. And we were delighted when she accepted! So, here are her comments on the awesome work she did and how our image processing has changed.

Hello, I’m Briana Harder, I’ve recently joined the science team to work on the processing pipeline that creates the images we classify. Some of you may know me from Talk as Quia. Back in November 2014, there was a blog post that ended with a shout out to anyone who wanted to collaborate on making the image selecting process better. I’m not a PhD in anything, but learning something new to solve a real life problem sounds like my idea of a fun weekend, and I have some experience with image processing. Turns out I’ve spent a wee bit more than a weekend on this, and I did make progress on the problem, so here I am to explain how my ‘fun project’ turns into improving the Floating Forests image pipeline!

The first thing to do upon finding an interesting problem is to find out if anyone else has solved it already. So I searched for research in the areas of image analysis and coastlines and satellite imagery. The majority of the papers were far too detail oriented to be very helpful, the problems in tracking the month to month changes of the coastline of a small island are wildly different from sorting coast from non-coast for FF! But I did find a fascinating paper on using Landsat data to build a highly accurate waterline database for all of Europe. They clearly solved the problem of finding ocean coastline, and then went a lot further!

The technique they used was to take a cloudless mosaic of the region–lots of preprocessing there!– and separate the image into three regions, water and land, selected with simple pixel value thresholds, and unassigned pixels. They then ran a region growing algorithm to add the unassigned pixels to either area.

This was good find for me, because they’re solving a very similar problem, and I know how to implement both those things! Unfortunately region growing is relatively slow and expensive, and it probably wouldn’t play nice with cloudy images. I did more digging over the next week, without finding anything else that was more promising. So I sat down, and wrote a little program.

Simplicity is important when you’re working with a lot of data; if the running time of the algorithm is longer than a person would take to do the same task, something has gone horribly wrong! I went through a couple iterations on how to find water, but in the end, this is what I ended up with.

Water is any pixel where the red value is between 1 and 25. Water’s very dark in all the bands, but it’s darkest in red, so that’s the best way to find it. If we’re clever about it, we only need to read the pixel values once, and perform some simple math operations, which means it should hardly take longer than opening up the image to view it.

– Count all the pixels that are water.
– Count all the pixels that are black, value 0. This ensures it’s not biased to throw out images that are on the edges of the Landsat scene.
– Calculate the percentage of non-black pixels that are water.
– If that percentage is above a certain threshold, we’re good to go, keep this image. I picked 5% as the threshold, based on a little trial and error.

And that’s it! It by no means gets rid of ALL the non-coast images, for example this does absolutely nothing for the abundance partially cloudy ocean images. It also gets tripped up by dark shadows on land, either from clouds or mountains, as shadows are just dark enough to fall within that threshold. Lakes are also selected, if they’re big enough.

The more complicated part comes after algorithms are made and tested: building them into the existing image processing pipeline. I wrote my algorithm in Python, making use of a few key libraries to do all the image processing; the pipeline is in Ruby, and uses a tool call ImageMagick for its image processing. I’m good at programming Python, I’d never touched Ruby until working on this project! And ImageMagick does seem quite ‘magical’ to someone who hasn’t used it before.

After reducing the problem of non-coast images, there’s the problem of the dark and red images that are especially common in the Tasmania dataset. The red part has been solved, but the darkness is still there for a lot of images. I have more work to do! But for now, we can say goodbye to a big chunk of the non-coast images in the next data set. No more bright blue snow-capped mountains, or solid fluffy cloud tops, or endless squares of farmland.

I’ll see you on Talk!

Tasmania Images Back!

You may have noticed that for the past few months Floating Forests has only been serving up California images. The Tasmania images that we were analyzing last year have been offline due to some image quality issues. However, thanks to a lot of hard work by the Zooniverse team and power user/image processing magician Briana Harder we are happy to announce that the Tasmania images are back! Not only are the image quality issues fixed, Briana has helped us implement an algorithm to filter out cloudy images and images that don’t contain any coastline (see upcoming post for more details). As a result, hopefully you will be spending less time skipping bad images and more time outlining those beautiful kelp forests!

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Less of this…

 

and more of this!

and more of this!

We have also improved the way in which we obtain images from USGS/NASA. This will make it easier for us to introduce data from other regions, so expect to see some images from Baja California, Chile, South Africa, and other temperate coastlines soon.

In the meantime, have fun with these Tasmania images. We’ve already started to document some major declines in kelp abundance in Tasmania over the past few decades thanks to your classifications. We are eager to obtain a better picture of these changes, but we need your help!

Where are we getting these images?

All of the images we are currently using in Floating Forests come from the Landsat satellite program. The Landsat program is an incredible series of satellites managed jointly by NASA and USGS that has been collecting imagery of the earth almost continuously since the early 1970s! This first Landsat satellite was launched in 1972 and the most recent, Landsat 8, was launched in February 2013. For Floating Forests we are using data from Landsat 4, 5, 7 and 8. We aren’t using data from earlier Landsat missions because the coarser resolution of these earlier satellites makes identifying kelp even more difficult than it already is. We also are not using data from Landsat 6 because this sensor crashed into the Indian Ocean soon after it was launched.

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Timeline of the Landsat program

My favorite Landsat sensor has to be Landsat 5.  This satellite was launched in 1984 and had an expected life span of 3 years. But it kept chugging along for an incredible 29 years and was only recently decommissioned in June 2013, giving it the Guinness World Record for the “longest operating earth observation satellite”. The long-term nature of the Landsat program is what makes it special. This data allows us to peek back in time to see how the earth has responded to climate change, human land-use change, disturbances like forest fires, mudslides, earthquakes, volcanic activity, and many other processes. Landsat has been used to monitor crop and forest harvests, map geologic features, monitor coral reef health, explore for oil and gas, measure changes in glacial coverage, track oil spills, aid regional planning, and for many, many other applications including, of course, tracking changes in giant kelp forests!

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Landsat false-color infrared image of Long Island, Bahamas. Image from NASA.

Yellowstone

These images from July 22 and October 2, 1988 document the dramatic forest fires that occurred in and adjacent to Yellowstone National Park. Image from NASA

Best of all, since 2008 Landsat imagery has been available to the public at no cost. This has dramatically increased the ability of scientists to conduct the kind of long-term study that we are doing here at Floating Forests. It also has unleashed a flood of data: millions of scenes have already been collected and hundreds of new scenes are acquired each day by the Landsat satellites currently in orbit (Landsat 7 & 8). The challenge now is in developing ways to make sense of all of this data. Citizen science projects like Floating Forests are one exciting approach for tackling this problem, new automated processing algorithms are another.

 

Are you interested in performing your own analysis on Landsat imagery? Or would you like to make some art from these beautiful images? If so, it’s easy to download the data. Simply go to GLOVIS or EarthExplorer to get started. You can also watch a live feed of Landsat acquisition here.

Keybindings!

Looking for a quicker way to move through the non-kelp images? You can now type ‘n’ on your keyboard instead of clicking the “NEXT IMAGE” button. You can also use ‘c’ to toggle the cloud button. Happy hunting!

Endangered Kelp Forests in Tasmania

Not seeing much kelp in the Tasmania images taken in recent years? This may be due to the fact that this region has seen dramatic declines in Giant Kelp (Macrocystis) over the past few decades. This decline has been linked to warming sea temperatures off the east coast of Tasmania. The loss of this critical habitat has been so dramatic that the Australian government has listed the forests as endangered. This is the first time that an entire ecological community has been given this kind of protection.

One major goal of this Zooniverse project is to better document these declines. While SCUBA diving is a great way to see and study kelp forests, divers can’t get everywhere and so there are many places where we don’t know how much kelp has been lost. With your help we can observe the entire coastline of Tasmania! And we will get many views of this coastline each year going back to 1984! So don’t get discouraged if you aren’t seeing kelp in the more recent years. These zeroes are incredibly important data for us. If we start seeing kelp in those same places when we look at images from the 1980s and 1990s then we can measure how much kelp has been lost.

Read more about the Tasmanian kelp declines here and here.

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A nutrient starved kelp frond. Photo courtesy of the SBC LTER