Skyler’s Weekly Review – Week 5

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The Buzz: Orthomosaics, Bathymetry Gone Awry

Alsea Bay Orthomosaic

Orthomosaics: Most people are familiar with the term mosaic, but throw in a suffix like “ortho” and it might be a struggle trying to define it (unless you are a classic Latin/Greek root aficionado, then you might know ortho- as meaning straight, upright, or correct). A more widely-known technique called a panorama (or more appropriately, digital panorama) uses a similar process of digital image-stitching. An image-stitch matches two or more images, pixel-by-pixel, to create a single, nearly seamless image. Map makers also find stitched images useful, particularly stitched aerial images. As you probably know, panoramic images are stretched and distorted enough that most objects do not retain their original size and position in the frame. Map makers find this quality particularly annoying as they prefer accuracy and precision, so they devised ways to correct or rectify images (particularly aerial/satellite images) using known, geometrically corrected ground control points (GCPs) to reduce or eliminate distortion. When you rectify aerial images that are taken looking straight down with geometric corrections and then stitch them together, the result is an orthomosaic: a mosaic of georectified (fancy name for geometrically corrected) aerial images suitable for mapping. Consumer digital maps use orthomosaics almost exclusively when available, especially Google Earth’s “satellite” view. Unlike Google Earth, our imagery won’t come from airplanes; it will come from UAVs! Also unlike Google Earth, our mosaics will likely allow you to count rocks on the beach rather than grainy blobs resembling cars and mythological creatures.

Scale 1:200

Scale 1:150

Scale 1:125

As you can see (above), our preliminary UAV missions in Alsea Bay yielded plenty of promising images. The 1:125 scale image (right) shows clear features that are smaller than 30 cm in diameter. Upon closer inspection, we can also pick out shrimp burrows and clam shows. With improvements in our technique and dialing in on clearer and more focused images with our cameras, the data we collect will only get better.

Bathymetry: Unfortunately, our Bathymetry survey in Yaquina Bay was cancelled due to equipment problems. Hopefully SEACOR will have the opportunity to make another attempt once our equipment is repaired!

Next Week: Alsea Bay, Razor Clams in Astoria

Camping and Sampling

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Another week another adventure out here in Oregon! So not only did we have our mid-summer check in this Friday but we also had the chance to go camping in Willamette National Forest this weekend. It felt amazing to be back out in the woods just hiking around again. The last time I was able to go camping was in Laguna National Forest outside of San Diego; needless to say there was a tad more desert involved. To say the least, it’s the polar opposite of San Diego, or the rest of the Oregon coast for that matter. Old growth forest clings to the rolling hills as far as the eye can see and the far-off peaks of the Three Sisters and Mt. Washington were visible from the trails. It even reached the high 70s (gasp) and felt like real summer for a few days. It was simply spectacular and I would have been happy to skip work this entire week to stay and hike around some more. I’m sure the rest of this week’s blog posts will revolve around the weekend’s hikes so I’ll let them fill in the rest of the details about the natural side of things.

The pics are of Tamolich Pool, some streams below Klamath Falls, and all of us idiots posing in front of South Sister on our hike to Moraine Lake.

On a more ‘sciencey’ note Amy, TChris, and I went water sampling this week. We drove up to the Tillamook watershed and sampled the five main tributary rivers that drain into the bay. Although we were only taking nutrient, microbial, and parameter samples it was a solid 13hr day. Couldn’t have asked for better weather though and the day did of course involve a trip to the Tillamook Creamery so overall it was a great day!

The pics are of our very full car out on the field sampling trip and of an IDEXX tray that has been incubated to test for the presence of Enterococcus spp.

Week 4: Rule[r]s

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With Week 4 under our belts, we’re just about halfway finished with the program. I’m amazed at how fast time is passing (have I said that enough yet?). The mild, spring-like winter we had in the Midwest this year, combined with spending my actual spring in the Caribbean and my summer in a place where temperatures hover around the 50s and 60s, has disoriented me. I feel as though it is springtime now and that the humid Midwest summer is still to come, but instead I will be greeted with fall when I return home. Strange.

The weather this past weekend was cool and damp, keeping us mostly indoors. I’ve been focusing on getting into a productive routine where I can accomplish small pieces of different things each day. My date with the GRE is looming, and I’m trying to make sure I crack open my study book for a bit every morning. Among that, working, going on a quick jog in the evenings, and making myself dinner (and one or two…or three episodes of The Good Wife), the day can get eaten up fast.

I’ve settled into a comfortable routine at ODFW that seems to be working well. I usually do research, data entry, or other computer-based tasks in the morning and interview crabbers in the afternoon. Lately, I’ve been getting about 8-9 interviews a day, which is more than I was getting when I started off, so that’s exciting.

I’ve been thinking a lot lately about the law. Rules. Maybe it’s just my mild addiction to a TV show about a law firm, but I think reading up on commercial and sport fishing regulations has gotten me thinking too. Especially about the difference between making a regulation versus simply encouraging people to do something. When it comes to the Dungeness crab fishery (and other fisheries as well), catch limits and restrictions keep the fishery thriving and sustainable. For example, even though ~90% of legal Dungeness crabs (male, larger than 5 ¾”) are taken from Oregon waters each year, enough crabs reproduce to sustain the population. With other things, such as the use of floating and sinking line, perhaps it is better to have fewer rules and more education. Perhaps rules and laws are always more effective. But now I’m tapping into a debate practically as old as America, so I’ll stay content with just musing for now. Regardless of rather an issue is better solved by regulations or encouragement, it is helpful when people have compassion for the earth – it makes them want to follow rules and recommendations. This seems like a factor that is hard to account for in deciding which course of action to take.

Differences among fishery regulations have also caught my attention during my research. In the Puget Sound sport fishery, for example, the minimum legal Dungeness crab size is 6 ¼” and the daily limit is 5 males (instead of 12, as in Oregon). Sorry for delving into numbers, but the amount of research and monitoring that is necessary to make regulations like this is a point of curiosity for me. Something – fishing effort, crab population dynamics, something – caused rules in these two fisheries to be made a bit differently. Rather this is indicative of extensive research, differences of opinion, or small bits of arbitrariness in the system, there is an interesting story behind these rules. I am fascinated by how much human effort, will, and opinion is behind laws and rules, things that seem so absolute and cold.

In fear of bombarding you with pictures of sunsets, I’ve included a lone photo of me measuring an ocean-caught crab. We have our mid-summer check-in (with a PowerPoint presentation and some workshops) and camping trip this week, so more on that soon.

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“Claire, I can’t see your face.” — Justin

As always, thanks for checking in.

An Unexpected Catch

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Over the past few weeks of fish seining I have observed a wide variety of fish species ranging from salmon and flounder to gunnels and pipefish. Most fish we catch are juvenile and under 1 ft in length. Of all of the species I expected to encounter during my work this summer, a sturgeon was not even on my radar. It was to my surprise last week when we found one in the bag of our net. I was intrigued by this amazing creature and couldn’t help but read up on these fish in my free time.

Oregon is home to two different species of sturgeon: the green sturgeon and the white sturgeon. While white sturgeons’ populations are healthy enough for commercial and recreational fishing, the green sturgeon are a protected species.

Green sturgeon are seldom collected with seine nets in South Slough. In fact, the last green sturgeon collected by SSNERR was during a similar monitoring program in 1986. Coming across one of these dinosaur like fish was quite the treat. Their bodies have changed little over the last 200 million years and are lined with rows of bony plates. The green sturgeon’s are especially pointed and sharp. These fish also have barbels on the underside of their snout that they use to navigate along riverbeds and find their prey.

Unfortunately, certain characteristics of sturgeon put them at risk of extinction. First off, females full of eggs have historically been over-harvested to provide markets with caviar. The average lifespan of a sturgeon is 50-60 and sexual maturity is not reached until around age 15. This heightens the risk of a population collapse do to over-fishing. If all of this wasn’t enough, most of these fish are anadromous, meaning they feed in coastal waters and spawn in freshwater. As rivers are dammed, anadromous fish lose critical spawning habitat and populations most often decline.

As my understanding of Oregon’s coastal fish species grows, so does my appreciation for the work South Slough conducts to protect these species. I am excited to come into the lab each day, because I know the data we collect will be used to manage and conserve estuarine ecosystems. I’m grateful to be a part of such work and I look forward to future unexpected catches.

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Week 4

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It’s Week 4 so we are almost to the halfway point of the program. This is crazy. There are still so many things I want to see and do while I am still in Oregon but we are running out of time! This past week has been, yep you guessed it, all about soil processing. We have over 200 samples that we are currently processing through the PSA machine and there are more to come! We are doing a last minute site next Monday to get 5 more cores (which could be about 50 more samples) so the entire soil process will re-start with those samples next week. I’m definitely getting myself some Tillamook ice cream. Since we have a better feel of how to get these samples done, hopefully they will be processed quickly. Then we can play with the data!

This is the PSA machine I've been working with. The water in the jugs feeds into the machine so the soil samples can be circulated easily.

This is the PSA machine I’ve been working with. The water in the jugs feeds into the machine so the soil samples can be circulated easily. There is a computer monitor to the left of the PSA machine (I couldn’t fit it into the shot) where you can control how it operates.

There are a lot of opportunities to stay active while in Newport. I hate running. So I try to get as involved in sports as possible. My mentor Jody, and a couple of other interns play ultimate frisbee every Monday and Thursday with some really awesome members of the community. There is also a pick-up soccer game that happens every Wednesday at noon outside of Hatfield. Even though Newport tends to be a bit cold for me, it is the absolute perfect weather for running around (unless it’s super windy, then throwing the frisbee can be difficult).

This past weekend, a couple of the interns at the EPA went to Jody’s house to make pasta! I’d never done anything like it before but it was actually a lot of fun. It took about 3 hours to make enough pasta for 5 people and it was pretty tedious work flattening the dough over and over again, but wow was it good. I put a picture below of all of the pasta we made. We had to hang it on a drying rack so the pieces wouldn’t fall apart or stick to each other.

PASTA!

We have our mid-summer check in this coming Friday where we have to give a small presentation about the work we have been doing so far and then we go camping! I’ll have more details about that next week.

Skyler’s Weekly Review – Week 4

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The Buzz: Trask River Dam Removal & Netarts Bay UAV Flights

Finding a Takeoff/Landing Site at a Trask River Dam

Trask River Dam Removal: 18 Miles East of Tillamook lies a small fork of the Trask River and the remnants of a very small dam. One day prior to the removal of the dam wall, I had the opportunity to tag along with Erik Suring (Project Lead for Salmonid Life-Cycle Monitoring, Western Oregon Fish Research and Monitoring Program and ODFW UAV pilot) as well as SEACOR’s resident UAV expert, Liz Perotti, to capture pre-removal aerial photography with UAVs. The dam was originally built in the 1970’s to support the operations of a hatchery/rearing pond co-located with the dam. Following recent studies on dams, fish ladders, culverts, and other barriers’ impact on fish passage (particularly anadromous fish or those that travel from salt to fresh water to spawn such as salmon and steelhead), dams across the country have been targeted for removal by State governments. Ideally, we will be able to return to aerially observe the “after” effects of the dam removal such as the movement of 40 years of built up sediment. Check back soon for a view of the final product!

Dam Removal In Progress

Makeshift Plywood Landing Pad

Netarts Bay UAV Flights: It is easy to imagine flying UAVs being quite simple: you can automate their flight paths, algorithms keeps them stable in the air, and just about anyone can afford one these days. Now throw in a camera you have to stabilize and calibrate, prepare a specific mission to capture aerial photographs, work in a narrow low-tide window, anticipate daily weather, troubleshoot technical problems, ensure there are no people under your flight path, file a Notification to Airmen with the FAA, plan your landing/takeoff area, and… well, it gets complicated quickly to say the least. Camera settings need to be set: focus, ISO, shutter speed, aperture. Time of day has a massive impact on the quality of photos and unfortunately, opportune weather and good lighting rarely align with low tides. While our UAV is rated to fly in up to 40 mph winds and maintaining smooth video, flying in gusts while taking stills is much more difficult. During the UAV flights, we have several other concurrent tasks needing completion to ensure our UAV aerial imagery can be used for measuring: our GPS RTK ground-truth survey of the GCPs which are evenly distributed over our project area (~1km2) and the evaluation of randomly distributed quadrats for eelgrass, macroalgae, and clam shows. Each of these tasks have their own set of challenges. With each flight we conduct, I realize that the need for near-perfect conditions becomes more of a necessity than a hopeful wish. We shall see how our efforts panned out soon. In the meantime, I have plenty of computer processing tasks to be completed.

Autopilot Takeoffs, Manual Landings…

Next Week: Orthomosaics, Bathymetry RTK Surveys

Fried Fish and Fish Fraud

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In 2012, an ocean conservation group, Oceana, conducted one of the largest seafood fraud investigations in the world to date. They collected over 1,200 samples from 674 retail outlets in 21 states to determine how honestly seafood was labelled. The results were staggering. Of 1,212 seafood samples, DNA testing found 33% were mislabeled, according to U.S. Food and Drug Administration guidelines.

“Oceana found one in three seafood samples mislabeled nationwide.”

Mislabelling can occur in several ways. Wild fish can be swapped for farmed, which can lead to consumers paying almost twice as much. Species can also be swapped. Oceana researchers found that 84% of white tuna sampled was substituted with escolar, a species known as the “Ex-lax fish” because it can be known to cause digestive problems (yikes).

And although the U.S. imports up to 90% of its seafood, an audit by the Government Accountability Office found that the FDA inspects less than 2% of its imported seafood. Mislabelled fish can result in inflated prices and health risk to consumers and a general misinformation about the health of fish populations and the ocean.

Many are calling for more transparency in the supply chain, increased seafood inspections and improved documentation and verification to allow for traceability. There are several things consumers can do to prevent seafood fraud:

  1. Ask questions– What kind of fish is it? Is it wild or farm raised? Where, when and how was it caught?
  2. Check prices– If the price seems too good to be true, it’s likely the species is different than what is on the label.
  3. Buy the whole fish– It makes it more difficult to swap species.

Buying local and off the docks is a great opportunity to ensure that consumers are truly getting what they pay for. Consumers can ask questions directly to the fisherman who caught the fish, see the whole fish filleted, and leave knowing they got an honest product.

This Friday, July 15th will be the first Shop at the Dock event, which I’m really excited for! I was lucky enough to cook lingcod this week, and I have to say, knowing it was fresh and local made it taste all the better.

lingcod

Pan-fried lingcod with herb and parmesan crust and caramelized fennel and onions!

I’ll leave you with a nice ocean tune. Thanks as always for reading and I hope you have a fantastic week!

A Bandon Way of Life

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Bandon is the awesome little town that I’m calling home for the summer. Population of around 3,000, it’s situated right where the Coquille River runs into the ocean. Since I’ve spent a few weeks exploring now, and here are a few of my favorite things that I’ve found:

Lighthouses and Wildlife

There are 11 lighthouses are the Oregon Coast, reminiscent of Oregon’s rich and long history as a haven for sailors and fishermen alike. The youngest of these lighthouses is the Coquille River lighthouse, constructed in 1891. It’s located in Bandon by the north jetty of the Coquille River, in Bullard’s Beach State Park. The lighthouse is open to the public, and there I learned about the hard life of a lighthouse keeper. I tried to imagine the days before electricity, when the lives of sailors depended on one man walking miles in a storm to remain awake and alone throughout the night to shine a light out to sea, and guide sailors to safe harbor.

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Walking down the north jetty by the lighthouse, I looked up to see a very curious Harbor Seal staring straight at me, about 100 yards away. He was really loving the wave action that day – he made loops out to sea, down back to the beach, and back across to the rocks where I was sitting. I watched him for a while, thinking how cool it was that this was his home and how much I wanted to make sure that I did something to conserve these waters to make sure that he, and all other marine organisms, could enjoy their waves.

Sea Stacks

Bandon is also famous for its sea stacks, which are like giant columns of rock right off the coast. They’re formed by constant wind and wave erosion against the headlands for millions of years. Here in Bandon, there are sea stacks at varying sea-levels, some on the sand itself, and some jutting straight up from the ocean. With the changing tides, every trip to the stacks is a brand-new experience. Below are a few photos of the same rocks, but at different tide levels:

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In Bandon, Face Rock, which is just to the right of the pictured photos, is one of the famous sea stacks. I’m hoping to catch this beauty at sunrise or sunset before I leave.

Coos Bay, Independence Day and the Music Scene

It’s hard to talk about Bandon without mentioning the larger town of Coos Bay that lies about 20 mile north. North Bend and Charleston are right next door, making for a pretty big coastal town (many people that work in Bandon commute from Coos Bay, and most people in Bandon drive up to Coos Bay pretty often for groceries, restaurants, movies, etc.) Aside from having a Safeway, and the awesome 7 Devils Brewery (named after 7 Devils Sea Stacks, just north of Bandon; I tried the delicious Quebecan dish Poutine there, French fries with cheese curds and gravy),

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they also have the Mill Casino on the bay, where they had an incredible fireworks display on the 3rd of July. I think just about the whole town came down to see the show, and so it was incredible to see people hanging out, playing Corn Hole (very popular here), or throwing a football. Neighborhoods all around the Bay set off a few fireworks too, making for a spectacular light show.

The actual 4th was, amazingly, even more incredible than the fireworks at the Mill. Bandon had an all-day music festival set up downtown by the dock. There were over 6 bands that ranged from “Irish Reggae Folk” to “Gypsy Jazz”.  We enjoyed walking around the cute artsy stores downtown, Ice Cream from Face Rock Creamery, and when it began to get dark, they even had a fire dancing show. It was probably some of the coolest fireworks I’ve ever seen, as the sunset turned into the firework display over the ocean.

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While Bandon seems like a little blip on the map, this tiny town has a lot to offer. I’ve been meeting super nice people every day, and I definitely know that I’m going to miss exploring the town and seeing the magnificent wildlife and sea stacks.

Week 4 – Seeing Stars

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Last week, I spent two of my mornings hunched over tide pools looking for sea stars. We were out conducting sea star surveys as part of a research effort documenting the effects of sea star wasting disease, an epidemic that has affected populations of these iconic animals up and down the West Coast.

Not your typical day at the office.

To be honest, I wasn’t enthused at the thought of groggily getting up at 5 AM. But I quickly warmed up to the idea – especially after measuring tapes and clipboards were handed out and we were turned loose to hunt down sea stars.

I think the main reason I became so immersed in my work that morning was because it resembled a lot of what I did throughout my childhood: roaming independently outside and exploring whatever nature offered to us. I didn’t grasp it at the time, but I was reaching back to my roots – roots buried and forgotten a long time ago as I grew up and moved on to other endeavors.

It seems that stress bombards us from all sides these days. I’ve definitely been feeling it this week – from working 21 total hours those two days of sea star surveys, to getting writer’s block on a difficult topic for my very first post on the ODFW Marine Reserves website, to preparing a presentation for the midsummer check-in at the end of this week.

So as we near the halfway point of the program, I suppose now is a more than apropos time to raise the importance of not getting lost within the rat race that’s convinced many of us to chase societal success. We miss a lot of the little things – things that tend to keep us sane – when we don’t stop to appreciate what’s around us. I’ll keep the rest of the text in this post short and sweet by sharing some of my own little things from this week:

A foggy morning greeted us at Otter Rock Marine Reserve, one of the sites of our sea star surveys.

View from inside the Devil’s Punchbowl at Otter Rock. The hollowed-out structure is dry and explorable at low tide, but come high tide the basin fills up with water.

A winding channel cutting through the tide pools.

A very well hidden, and very much alive, red rock crab.

Pisaster ochraceus, commonly known as the ochre star, can actually come in a variety of colors, but the major color morphs are orange, purple, and brown.

A not-so-healthy sea star. Those affected by the wasting disease experience external lesions, decaying limbs, and overall body deterioration.

A dense school of juvenile rockfish welcomed us as soon as we reached the tide pools at Cascade Head Marine Reserve on the second morning of our sea star surveys. This was an unexpected discovery – juvenile rockfish typically recruit nearshore by the time they reach the size of the ones in this pool, but to see so many all in one place was surprising.

A flamboyantly blue nudibranch, found in the same pool as the rockfish. The colors are much more electrifying when seen in person.

Not positive, but I’m guessing this is another nudibranch, although much bigger than the first.

The most interesting find of the afternoon – an octopus! It took several minutes of gentle coaxing to tease him out of the hole he was hiding in.

Saying goodbye to Cascade Head for the day.

I find that one of the more intriguing things about nature is that you can leave with a sense of fulfillment just from silently wandering about and observing. When I look down into a tide pool, I’m usually searching for fish and other little creatures hiding amongst the rocks and algae. But more so than that, I realize now that I’m peering deeper into a window of my childhood days, when the only things with an iota of consequence at the end of the day were our dirty clothes and grass-stained knees.

So slow down, take a deep breath, and go find your own tide pool, wherever it may be.

In Full Swing

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Somehow, we’re already halfway through the summer. After weeks of preparation and design, this was my first week in the field conducting surveys. Aside from this being a short workweek following the July 4th holiday, the days sure seemed to fly by much quicker than usual. Of course it helps when your office is the Oregon coast and your job is talking to new people. Additionally, I spotted 8 whales off the coast while sampling… my favorite marine animal!

Enjoying the view while conducting surveys at Otter Rock.

This first round of surveys proved successful, without too many visitors reluctant to participate. Surprisingly, the rain and wind doesn’t stop visitors from exploring Oregon’s many coastal attractions. Along the central coast, I met visitors from Germany, Italy, Brazil and Canada. In the coming weeks I will have a change of scenery as we begin sampling on the North and South coast, which I have yet to explore for myself.

Rainy day sampling in Yachats.

Living on the central coast has given me an advantage when answering questions that visitors have while they are filling out their ocean awareness survey. As we expand our sampling range, I will be seeing new places for the first time, along with some of the coastal visitors. If all goes according to plan, I will have traveled the Oregon coast from North to South six times in total by the end of this summer. That’s a lot to pack into the few remaining weeks, but that’s not all I have on my agenda when it comes to exploring Oregon.

Planning a fishing trip “on the fly.”

As time flies by, I’m taking every chance I can to slow down and take it all in. This weekend, I went exploring “on the fly.” Despite some stormy weather that inhibited my prior weekend plans, Sunday shaped up to be fairly nice and I grabbed my fly-fishing rod and took a dirt road into the Siuslaw wilderness to unwind. Well, it wasn’t quite that easy. Fly- fishing generally takes a little more effort and planning, but once you find your spot, it can be one of the most meditative ways to refresh your mind in nature. Of course I’m biased, but there is compelling evidence to support that fly-fishing is truly a natural stress reliever.

Resident cutthroat trout I caught (and released) in the Oregon wilderness.

As my previous blog alluded to, there is good reason to spend our free time out in nature, rather than indoors and in front of a screen. The only trouble I’ve found with spending time in the outdoors is that the more you seek new places and adventures, the more you find you’re missing out on. Oregon is loaded with more opportunities than ten weeks can fulfill, but it’s a matter of making the best of every opportunity as it comes.

 

Survey Count: 145

Whale Count: 8