//
you're reading...

ocean engineering

Acquisition and curation and management, oh my!

Schoening, T., Köser, K., & Greinert, J. (2018). An acquisition, curation and management workflow for sustainable, terabyte-scale marine image analysis. Scientific data, 5, 180181. DOI: 10.1038

When you take a picture with your phone, it gets stored in a database. Tech companies call this “cloud storage.” If you are an iPhone aficionado, those images end up in iCloud. If you are an Android user, they likely show up in Google Photos. All those images are stored with metadata identifying things like when and where the photo was taken. All this information can be used to archive, sort, and display your pictures in a meaningful way.

Figure 1 – A schematic of the decision making process the authors are advocating for. All of these items are often considered in isolation, but rarely from end to end. Adapted from Schoening et al., 2018.

In essence, the image data you are capturing gets shipped off and stored in a remote location. The whole process has been standardized and streamlined to the point that billions of smartphone users around the world can quickly store and access their information. The pipeline feels easy and simple to everyday users. Scientists are entering an era where they need a similar system for their data.

Modern oceanographers are producing loads of image data . From biologists to climatologists to physical oceanographers to geophysicists, everyone is taking pictures. And lots of them – it is not at all uncommon for scientists to return from sea with 10s to 100s of terabytes of data from a single cruise. But most of this data sits idle, never analyzed, never shared.

Data management is a distinctly unsexy topic. Everyone wants to get right from their adventures at sea to discussing their exciting new discoveries. But without rigorous techniques to store and maintain the vast amounts of data being collected, much of it will remain unanalyzed. Part of the reason so much oceanographic data is underutilized is that scientists often do not have a clear methodology for dealing with it. Recognizing these challenges, Timm Schoening and his colleagues at the Helmholtz-Center for Ocean Research and the Christian-Albrechts University in Kiel, Germany sought to provide a roadmap.

In their recent paper, the team laid out a set of best practices to ensure that data gets captured and stored as efficiently as possible. To illustrate their proposed work flow, the group layout the decision-making process for how they collected, stored, and distributed a terabyte-scale image set observing a simulated deep-sea mining site in the equatorial Pacific Ocean.

Figure 2 – Image data collected from the groups AUV in the Pacific. Notice the extra information in each panel. Adapted from Schoening et al., 2018.

Broadly speaking, the group considered three main questions as they designed their fieldwork: data acquisition, curation, and long-term management. Each stage involved a lot of nitty gritty detail and difficult decisions about what exactly the goals of the project were. At every step, Schoening emphasizes the need to think about the future – what is the data going to be used for in the short term? How about the long term? What sort of information should be held onto? Where will it live? How long does it need to live there?

To collect their data, Schoening and his group outfitted an Autonomous Underwater Vehicle (AUV) with a camera system to take pictures of the bottom. To facilitate future studies, each image was stored with a bunch of metadata including navigation information and environmental parameters ­– all puzzle pieces that might come in handy later. Over 21 dives, the system collected nearly 500,000 images for a total of about 30 terabytes of data. Once safely ashore, the data was cleaned and analyzed by hand before being stored in three separate locations. Finally, after some preliminary analysis, the group made the data publicly available on PANGEA, an Open Access earth sciences data repository maintained by consortium of German institutions.

A lot of the guidelines Schoening proposes are good common sense. But that does not make them easy to implement. There is an emphasis in oceanography on data collection and the community is just now beginning to deal with how to manage the huge influx of information. Coming up with long-term, widely accepted solutions to these simple but vexing questions is a challenge. Without answers, untold discoveries, about all manner of phenomena, will sit unobserved in dusty hard drives on forgotten bookshelves.

Discussion

No comments yet.

Post a Comment

Instagram

  • by oceanbites 4 weeks ago
    Not all outdoor science is fieldwork. Some of the best days in the lab can be setting up experiments, especially when you get to do it outdoors. It’s an exciting mix of problem solving, precision, preparation, and teamwork. Here is
  • by oceanbites 2 months ago
    Being on a research cruise is a unique experience with the open water, 12-hour working shifts, and close quarters, but there are some familiar practices too. Here Diana is filtering seawater to gather chlorophyll for analysis, the same process on
  • by oceanbites 3 months ago
    This week for  #WriterWednesday  on  #oceanbites  we are featuring Hannah Collins  @hannahh_irene  Hannah works with marine suspension feeding bivalves and microplastics, investigating whether ingesting microplastics causes changes to the gut microbial community or gut tissues. She hopes to keep working
  • by oceanbites 3 months ago
    Leveling up - did you know that crabs have a larval phase? These are both porcelain crabs, but the one on the right is the earlier stage. It’s massive spine makes it both difficult to eat and quite conspicuous in
  • by oceanbites 3 months ago
    This week for  #WriterWednesday  on  #Oceanbites  we are featuring Cierra Braga. Cierra works ultraviolet c (UVC) to discover how this light can be used to combat biofouling, or the growth of living things, on the hulls of ships. Here, you
  • by oceanbites 3 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Elena Gadoutsis  @haysailor  These photos feature her “favorite marine research so far: From surveying tropical coral reefs, photographing dolphins and whales, and growing my own algae to expose it to different
  • by oceanbites 4 months ago
    This week for  #WriterWednesday  on Oceanbites we are featuring Eliza Oldach. According to Ellie, “I study coastal communities, and try to understand the policies and decisions and interactions and adaptations that communities use to navigate an ever-changing world. Most of
  • by oceanbites 4 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Jiwoon Park with a little photographic help from Ryan Tabata at the University of Hawaii. When asked about her research, Jiwoon wrote “Just like we need vitamins and minerals to stay
  • by oceanbites 5 months ago
    This week for  #WriterWednesday  on  #Oceanbites  we are featuring  @riley_henning  According to Riley, ”I am interested in studying small things that make a big impact in the ocean. Right now for my master's research at the University of San Diego,
  • by oceanbites 5 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Gabby Stedman. Gabby is interested in interested in understanding how many species of small-bodied animals there are in the deep-sea and where they live so we can better protect them from
  • by oceanbites 5 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Shawn Wang! Shawn is “an oceanographer that studies ocean conditions of the past. I use everything from microfossils to complex computer models to understand how climate has changed in the past
  • by oceanbites 5 months ago
    Today we are highlighting some of our awesome new authors for  #WriterWednesday  Today we have Daniel Speer! He says, “I am driven to investigate the interface of biology, chemistry, and physics, asking questions about how organisms or biological systems respond
  • by oceanbites 6 months ago
    Here at Oceanbites we love long-term datasets. So much happens in the ocean that sometimes it can be hard to tell if a trend is a part of a natural cycle or actually an anomaly, but as we gather more
  • by oceanbites 6 months ago
    Have you ever seen a lobster molt? Because lobsters have exoskeletons, every time they grow they have to climb out of their old shell, leaving them soft and vulnerable for a few days until their new shell hardens. Young, small
  • by oceanbites 7 months ago
    A lot of zooplankton are translucent, making it much easier to hide from predators. This juvenile mantis shrimp was almost impossible to spot floating in the water, but under a dissecting scope it’s features really come into view. See the
  • by oceanbites 7 months ago
    This is a clump of Dead Man’s Fingers, scientific name Codium fragile. It’s native to the Pacific Ocean and is invasive where I found it on the east coast of the US. It’s a bit velvety, and the coolest thing
  • by oceanbites 8 months ago
    You’ve probably heard of jellyfish, but have you heard of salps? These gelatinous sea creatures band together to form long chains, but they can also fall apart and will wash up onshore like tiny gemstones that squish. Have you seen
  • by oceanbites 9 months ago
    Check out what’s happening on a cool summer research cruise! On the  #neslter  summer transect cruise, we deployed a tow sled called the In Situ Icthyoplankton Imaging System. This can take pictures of gelatinous zooplankton (like jellyfish) that would be
  • by oceanbites 9 months ago
    Did you know horseshoe crabs have more than just two eyes? In these juveniles you can see another set in the middle of the shell. Check out our website to learn about some awesome horseshoe crab research.  #oceanbites   #plankton   #horseshoecrabs 
  • by oceanbites 9 months ago
    Feeling a bit flattened by the week? So are these summer flounder larvae. Fun fact: flounder larvae start out with their eyes set like normal fish, but as they grow one of their eyes migrates to meet the other and
WP2Social Auto Publish Powered By : XYZScripts.com