Everything You Need to Know about CTD data

In August 2021, expert hydrographer, Leah McRaven (PO WHOI) from the US OSNAP (Overturning in the Subpolar North Atlantic Program) team, worked with the OOI team members aboard the R/V Neil Armstrong for the eighth turn of the Global Irminger Sea Array to support collection of an optimized hydrographic data product. A truly novel aspect of this collaboration was the near real-time sharing of OOI shipboard CTD data with the public. McRaven also shared her reports while the cruise is underway.  In doing so, she provided a detailed explanation of the process of ensuring that CTD profiles are accurate and useable for future research use.

We share her blogs below.  For archival purposes, they will also be available on the Community Tools and Datasets page.

BLOGPOST #4 (September 13, 2021)

Another OOI cruise is in the books! Now that things have wrapped up and I’ve had a chance to dig into the data a bit more thoroughly, how did we do? In my previous post I reported that the Irminger 8 CTD data looked to be very promising, but I like to include one more step before recommending data to be used for science: carefully considering salinity bottle data.

Salinity bottle data can be used in many ways to support a particular scientific objective or research question. The two that I’ve become most familiar with are 1) to support the analysis of additional bottle samples (e.g. dissolved oxygen) and 2) to provide an additional assessment and calibration of the CTD conductivity sensors. Both applications are necessary when researchers require salinity values more accurate than what CTD sensors are able to provide. However, even if this is not required, it can help ensure that users receive data that are reasonably within manufacturer specifications.

I find it easiest to consider the GO-SHIP approach to bottle data first. Using ship-based hydrography, GO-SHIP provides approximately decadal resolution of the changes in inventories of heat, freshwater, carbon, oxygen, nutrients, and transient tracers, covering the ocean basins with global measurements of the highest required accuracy to detect these changes. For a program like this, 36 salinity samples are taken every CTD station in order to provide an extremely accurate and precise calibration for the CTD sensors. Interestingly, the Irminger OOI array is bracketed by three GO-SHIP repeat transects. While GO-SHIP provides invaluable measurements, drawing a large number of samples can be expensive and time consuming. Additionally, measurements occur on a decadal timescale, so there is a lot of the picture we miss.

One of the research programs that aims to provide a higher temporal and special resolution picture of the North Atlantic is OSNAP. This program has several scientific objectives, but generally aims to quantify intra-seasonal to interannual variability of the Atlantic Meridional Overturning Circulation(AMOC) in the subpolar Atlantic. This includes a focus on heat and freshwater fluxes, pathways of currents throughout the region, and air-sea interaction, all of which require highly calibrated data products. In order to accomplish this, PIs from the program need to be able to consistently merge their shipboard and moored data products for cohesive and accurate quantification of parameters. Because much of the variability being studied is so large, researchers do not necessarily need salinity accuracies at the level of GO-SHIP, but they do need to use salinity bottle samples to ensure that CTD casts are at the very least within manufacturer specifications.

In the end, no one approach to hydrographic sampling is necessarily better than another. What is important is the delicate balance of resources while at sea that best support the scientific objectives. For both OSNAP and OOI, where the primary work at sea is focused on servicing moorings, the resources for a GO-SHIP approach to sample bottle collection is simply not feasible. However, one very key feature of the OOI CTD data is that they are collected annually, while ONSAP data are collected every two years, and GO-SHIP data are collected every ten years. Hence, OOI is able to fill in some of the temporal data gaps in the region and greatly bolster many of the international programs working in the region.

This year OOI collaborated with numerous PIs and representatives from research programs that operate in the Irminger Sea region to produce a more optimized CTD and bottle sampling strategy that better complements goals similar to GO-SHIP, as well as several additional objectives from international programs, such as OSNAP. The goal of this updated plan was to provide OOI data end users and collaborators with data that are more appropriate for CTD, mooring, glider, and float instrumentation calibration purposes. In particular, the update included increased sampling of the deep ocean. Such data are critical in the Irminger Sea region due to the uniquely large variability of temperature, salinity, and chemical properties throughout the shallow and intermediate depths of the water column. Deeper CTD and bottle data will allow all end users to more carefully reference their scientific findings to more stable water masses and allow for better intercomparison with other available datasets, such as the available GO-SHIP and OSNAP data from the region.

The majority of methods that I use when considering salinity bottle data have been adapted from GO-SHIP and NOAA/PMEL. In particular, many of the cruises I work with, including OOI, often have far fewer bottle samples than recommended by GO-SHIP or PMEL methods. This isn’t necessarily bad, since we don’t need to achieve the same goals as those programs, however, great care in adapting methods does need to be considered (and I encourage you to reach out if this is something you have an interest in). So, with the improved OOI sampling scheme, what are the potential benefits to CTD data quality?

More strategically planned salinity bottle sample collection allows users to:

  • Decide if data from primary or secondary sensors are more physically consistent
  • Identify times when CTD contamination was not obvious
  • Assess manufacturer sensor calibrations
  • Potentially provide a post-cruise calibration

In the case of the Irminger 8 cruise, I see that all four uses of salinity bottle data are possible, which will make a lot of collaborators very happy! Starting with Figure 1, we can see a summary of CTD and bottle sample salinity differences as a function of pressure for both the primary and secondary sensors. As a rule of thumb, the average offset of these differences can be considered an estimate of sensor accuracy, and the spread, or standard deviation, can be considered an estimate of sensor precision. While the data have a fairly large spread to the eye, the standard deviations (indicated by the dashed lines) are placing the spread for each sensor within what we expect from the manufacturer precision. The striking result from this figure is that before using the bottle data to further calibrate the data, we see that the primary sensor had a higher accuracy than the secondary sensor. In going back to the Seabird Electronics calibration reports for the primary and secondary sensors (available via the OOI website), I noted that the calibrations for each sensor was a bit older than what we normally work with (last performed in May 2019). Additionally, the secondary sensor had a larger correction at its time of manufacturer calibration than the primary. This is corroborated by the differing sensor accuracies as determined by the bottle data. Lastly, while there are a few spurious differences shown, on average there doesn’t look to be any CTD and bottle differences due to factors other than expected calibration drifts.

Figure 1

In order to apply a calibration based on the bottle data to the CTD data, I first QC’d the bottle data and then followed methods described in the GO-SHIP manual. There are several sources of error that can contribute to incorrect salinity bottle values, ranging from poor sample collection technique to an accidental salt crystal dropping into a sample just before being run on a salinometer. This is why all methods of CTD calibration using bottle data stress the importance of using many bottle values in a statistical grouping. However, sometimes there are “fly-away” values that are so far gone they don’t contribute meaningful information to the statistics, and in those cases I simply disregard those values. As a reference, for the Irminger 8 cruise I threw out 9 of the ~125 salinity samples collected before proceeding with calibration methods. Note that within the methods described in the above documentation, systematics approaches are used to further control for outlier or “bad” bottle values.

Figure 2

Since the majority of CTD stations for OOI are performed close to one another (and consequently in similar water masses), I grouped all stations together to characterize sensor errors. The resulting fits produced primary and secondary sensor calibrations that allow for more meaningful comparison of data with other programs. Figure 2 shows how primary and secondary data compare before and after bottle calibrations have been applied. Post calibration, primary and secondary sensors now agree more closely in terms of their differences. Similarly, Figure 3 summarizes data before and after calibration in temperature-salinity space, providing visual context for the magnitude of bottle calibration. Many folks working with CTD data would say that this is a rather small adjustment!

Figure 3

Figure 4

However, Figure 4 shows a comparison of the bottle-calibrated OOI data with nearby OSNAP CTD profiles from 2020. The results here are extremely important as OSNAP currently has moorings deployed near the OOI array and the OOI CTD profiles provide a midway calibration point for the moored instrumentation that is currently deployed for two years. These midway calibration CTD casts are critical in providing information on moored sensor drift and biofouling in a region where there has been a slow freshening of deep water (colder than 2.5 ºC) throughout the duration of these programs. Quantifying the rate of freshening is one of the objectives that OSNAP focuses on, but it is nearly impossible without high-quality CTD data for comparison. Figure 4 demonstrates that the freshening trend has continued from 200 to 2021 and that the bottle-calibrated OOI CTD data will be critical for interpretation of moored data.

Finally, for those interested in the salinity-calibrated CTD dataset, please be in touch (lmcraven@whoi.edu). A more detailed summary of the calibration applied can be found in my CTD calibration report here.

BLOGPOST #3 (August 18, 2021)

Irminger 8 science operations are now fully underway, which means the stream of CTD data is coming in hot (actually the ocean temps are very cold)! So far, CTD stations 4 through 11 correspond to work performed near the Irminger OOI array location. I spent the weekend and past couple of days paying close attention to these initial stations. Here’s an update on how things look so far.

One of the concerns this year is that the R/V Neil Armstrong is using a new CTD unit and sensor suite (new to the ship, not purchased new). Any time a ship’s instrumentation setup changes, it’s a very good idea to keep a close eye on things as changes naturally mean there’s more room for human error. What better way to talk about this than to share my own mistakes in a public blog! When I first downloaded and processed the OOI Irmginer 8 (AR60) CTD data from near the Irminger OOI array location, I became very worried…

When I compared the Irminger 8 CTD data with three cruises from the same location last year, I was seeing very confusing and unphysical data in my plots. I was using Seabird CTD processing routines in the “SBE Data Processing” software (see https://www.seabird.com/software) that I had used for previous OOI Irminger cruises as a preliminary set of scripts, so I was confident that something strange with the CTD was going on. I immediately pinged folks on the ship to ask if there was anything that they could tell was strange on their side of things. Keep in mind, this OOI cruise focuses more on mooring work with only a handful of CTDs to support all additional hydrographic work, so any time there is a potential issue with the CTD data we want to address it as soon as possible. I started digging into things a bit more, and realized that I had made a mistake.

Within the SBE processing routines, there is a module called “Align CTD”. As stated in the software manual: “Align CTD aligns parameter data in time, relative to pressure. This ensures that calculations of salinity, dissolved oxygen concentration, and other parameters are made using measurements from the same parcel of water. Typically, Align CTD is used to align temperature, conductivity, and oxygen measurements relative to pressure.” When working in areas where temperature and salinity change rapidly with pressure (depth), this module can be very important (and I encourage you to read through its documentation). As you’ll see below, the OOI Irmginer Sea Array region can see some extremely impressive temperature and salinity gradients. This has to do with the introduction of very cold and very fresh waters from near the coast of Greenland, together with the complect oceanic circulation dynamics of the region. Based on data collected on the old CTD installed on the Armstrong, I had determined that advancing conductivity by 0.5 seconds produced a more physically meaningful trace of calculated salinity.

While 0.5 seconds doesn’t seem large, it’s important to remember that most shipboard CTD packages are lowered at the SBE-recommended speed of 1 meter/second. Depending on how suddenly properties change as the CTD is lowered through the water, this magnitude of adjustment may seriously mess things up if it’s not the correct adjustment. In the case of the CTD system currently installed on the Armstrong, I’m finding that very little adjustment to conductivity is needed. There are many reasons as to why this value will change – from CTD to CTD, cruise to cruise, and even throughout a long cruise. The major factor is the speed at which water flows through the CTD plumbing and sensors and how far the pressure, temperature, and conductivity sensors are from each other in the plumbed line. Water flow is controlled by many things including CTD pump performance, contamination in the CTD plumbing, kinks in the CTD pluming lines, etc. (for more information, start here: https://www.go-ship.org/Manual/McTaggart_et_al_CTD.pdf and here: file:///Users/leah/Downloads/manual-Seassoft_DataProcessing_7.26.8-3.pdf). Note that the SBE data processing manual provides great tips on how to choose values for the Align CTD module.

Below is a figure that summarizes impact on my processed data before and after my mistake. This is a fun figure as it compares CTD data from four cruises that all completed CTDs near the OOI site: the 2020 OSNAP Cape Farewell cruise (AR45), the 2020 OOI Irminger 7 cruise (AR46), a 2020 cruise on R/V Pelagia from the Netherlands Institute for Sea Research, and stations 5-7 of the 2021 OOI Irminger 8 cruise (AR60). I’m plotting the data in what is called temperature-salinity space. This allows scientists to consider water properties while being mindful of ocean density, which as mentioned in the last post, should always increase with depth. I include contours indicating temperature and salinity values that correspond to lines of constant density (in this case I am using potential density referenced to the surface). For data to be physically consistent, we expect that the CTD traces never loop back across any of the density contours. These figures are also incredibly useful as the previous three cruises in the region give us some understanding of what to expect from repeated measurements near the Irminger OOI array.

The plot on the left shows the data processed with a conductivity advance of 0.5 sec. As you can see, the CTD traces appear much noisier than the other datasets, and contain many crossings of the density contours (i.e., density inversions). The plot on the right shows data that are smoother and less problematic in terms of density. You may also note that in the right plot, the AR60 traces are a bit shifted to the left in salinity (i.e. fresher or lower salinity values) when compared to the other datasets. This is because I am plotting bottle-calibrated CTD data from the other three cruises. Just as I type this, I’ve been given word that the shipboard hydrographer has begun analyzing salinity water sample data for Irminger 8. These bottle data are critical for applying a final adjustment to CTD salinity data and I’ll talk more about this in a future post.

For now, I’m happy to report that the data look physically consistent! For completeness, I include the core CTD parameter difference plots from stations 4 through 11 (CTDs completed near the array thus far). CTD difference plots are described in my previous post. All checks out from where I am sitting so far. Thanks to the CTD watch standers and shipboard technicians for working so hard and taking good care of the system while the cruise is underway!

BLOGPOST #2 (August 10, 2021)

For this post I’d like to introduce some of the tools that folks can use to identify CTD issues and sensor health while at sea. Most of what I’ll be discussing here is specific to the SBE911 system that is commonly used on UNOLS vessels; however, a lot of these topics are relevant to other types of profiling CTD systems.

There are several end case users of CTD data within science. These include people who perform CTDs along a track and complete what we call a hydrographic section (useful in studying ocean currents and water masses); those who perform CTDs at the same location year after year to look for changes; people who use CTDs to calibrate instrumentation on other platforms (moorings, gliders, AUVs, etc.); and those who use the CTD to collect seawater for laboratory analysis (collected samples can be used to further analyze physical, chemical, biological, and even geological properties!). For each of these CTD uses, a core set of CTD parameters are needed.

Core CTD parameters include pressure, temperature, and conductivity. Conductivity is used together with pressure and temperature measurements to derive salinity. These three variables are needed to give users the critical information of depth and density in which water samples are collected, and support the calculation of additional variables. For example, ocean pressure, temperature, and salinity together with a voltage from an oxygen sensor are needed to derive a value for dissolved oxygen. In addition to core CTD parameters, it is very common to add dissolved oxygen, fluorescence, turbidity, and photosynthetically active radiation (PAR) sensors to a shipboard CTD unit. Each of these additional measurements have errors that must be propagated from the core CTD measurements – creating a rather complex system to navigate when trying to understand the final accuracy of a given measurement.

For each CTD data application, varying degrees of accuracy are needed from the measured CTD parameters to accomplish the scientific objective at hand… And this is where a lot of folks get into trouble! For a first example, consider someone who would like to calibrate a nitrate sensor that is deployed for a year on a mooring using water samples collected from the CTD. For a second example, consider someone who is interested in the changing dissolved oxygen content of deep Atlantic Meridional Overturning Circulation waters. In both cases, the core CTD parameters are critical. In the first example, this person needs to know the pressure and ocean density at the exact location their water samples are collected during a CTD cast so they can correctly associate analyzed water sample values with the correct position of the sensor on the mooring. However, in the second example, this person may need to use both salinity and oxygen samples to improve the accuracy and precision of CTD measurements so that their final data product will be sensitive enough to resolve small, but potentially critical, changes in the ocean.The most important take away here (CTD soapbox moment!) is that even if end users are not specifically interested in studying physical oceanographic parameters, they still need tools to verify that 1) the core CTD measurements are of high enough quality for use in their application and 2) that there are no unnecessary errors from the core measurements that are impacting their ability to address their scientific objective.

This is the first reason why I heavily encourage all CTD end users to become familiar not only with the accuracy of their particular measured parameter, but also the core CTD parameters. The second reason is that core CTD parameters are particularly useful in diagnosing early warning signs of CTD problems. Most shipboard systems install primary and secondary temperature and conductivity sensors on their CTDs, which provide an opportunity for in-situ sensor comparison. Additionally, calculated seawater density is particularly useful as it is one of the few properties we can make a strong assumption about – it should always increase with pressure. The density of seawater is determined by pressure, temperature, and salinity (conductivity), hence any time one or some of these recorded values is suspect, non-physical density “inversions” or “noise” may appear in the data record. 

Below are two figures that can be very helpful in diagnosing CTD problems. In these examples, I am using the Irminger 8 (AR60-01) deep test cast, which took place late Sunday evening, August 8th. Figure 1 shows difference plots of the two sensor pairs (temperature and conductivity). Each panel includes vertical dashed lines indicating expected manufacturer agreement ranges (see sensor specification sheets datasheet-04-Jun15.pdf and datasheet-03plus-May15.pdf). The values shown are, ±(2 x 0.001 ºC) and ±(2 x 0.003 mS/cm) for temperature and conductivity sensors, respectively (note that 0.003 mS/cm is close to 0.003 psu for reasonable temperature ranges). In general, sensor differences should fall within, or very close to, this range when calibrated by the manufacturer within the past year. The rule can be relaxed in the upper water column, however, differences between sensors deeper than approximately 500 m that consistently fall outside of this range indicate problematic sensor drift or contamination. Figure 2 shows the calculated seawater density profile using the primary sensors. Consistent density inversions larger than ~0.1 kg/m3 also indicate problematic sensor drift or contamination. When creating such figures, always look at the downcast and upcast (skipped here for the sake of brevity). The upcast will look a bit worse than the downcast (I encourage you to read about why), but those data are extremely important to anyone collecting water samples!

Figure 1 



Figure 2  


So, what can these plots tell us about the CTD system implemented on the Irminger 8 cruise so far? Figure 1 demonstrates an overall acceptable level of agreement between the sensor pairs. The particular sensors in use right now have calibrations older than one year, so this level of agreement is actually quite good. Figure 2 is also rather promising in showing a density profile that is continuously increasing. If you’re being picky (like me), you may notice that there are some small density inversions between roughly 200-500 m. After taking a closer look, I noted that the salinity profile indicates that there are some rather impressive salinity intrusions evident in the upper 500 meters (I encourage you to download data from cast 2 and verify!). This is normal for the Labrador Sea region where the cast took place (lots of melting ice nearby) and will naturally create a bit more “noise” in these plots. So, I’m not very concerned by this.

Now what do these plots look like when there’s a problem? There unfortunately isn’t one simple answer for this (I’ve been doing this for over ten years and am still learning subtle ways CTDs show problems!), but I’ll share two examples of when something was clearly wrong. The first example is from the Irminger 7 cruise (AR35-05). Figure 3 and Figure 4 show our two plots for stations 1-13 of the Irminger 7 cruise. Figure 3 shows a suspiciously large offset (well outside of the general threshold we expect in the conductivity differences) and incredibly noisy differences in both conductivity and temperature. Similarly, Figure 5 shows consistent and large density inversions for some of these casts. Several of the casts shown in Figures 4 and 5 were so bad that there are no usable profiles as far as scientific objectives are concerned. Luckily, however, there were a few casts in the set that could be corrected with water sample data (I’ll talk more about this later). Data loss is something that does happen while at sea, and the Irminger Sea in particular is an incredibly harsh environment to work in. However, if folks are diligent in creating these plots while at sea, the hope is that we can minimize time and data loss while striving for the highest quality data possible.

Figure 3   


Figure 4  

For my last example, I provide a quick reference guide for how core CTD parameter issues may look on a Seabird CTD Real-Time Data Acquisition Software (Seasave) screen. The reason for this is that a lot of people don’t have time to create fancy plots while at sea, so it’s helpful to know how to approach monitoring while watching the data come in. Follow the link here to download a one-page pdf that can be displayed next to your CTD acquisition computer.

BLOG POST #1 (August 2, 2021)

[caption id="attachment_21736" align="aligncenter" width="2560"] A CTD is performed near the coast of Greenland during one of the OSNAP 2020 cruises on R/V Armstrong. Photo: Isabela Le Bras©WHOI[/caption]

Hello folks and welcome to the Irminger 8 CTD blog! As the cruise progresses, tune in here for updates on Irminger 8 CTD data quality as well as tips on how best to approach using OOI CTD data. I plan to keep this information inclusive for folks with varying levels of experience with shipboard CTD data – from beginner to expert! If you have any questions about CTD data, feel free to send me an email (lmcraven@whoi.edu) and I’ll do my best to help. For this first post, I would like to summarize some important resources available to the community that will greatly help with CTD data acquisition and processing.

CTDs have been around for a while, which on the surface makes them a bit less interesting than many of the new exciting technologies used at sea. The fact remains that the CTD produces some of the most accurate and reliable measurements of our ocean’s physical, chemical, and biological parameters. Aside from being very useful on their own, CTD data serve as a standard by which researchers can compare and validate sensor performance from other platforms: gliders, floats, moorings, etc. Sensor comparison is particularly important for instruments that are deployed in the ocean for a long time (as is the case for OOI assets) as it is normal for sensors to drift due to environmental exposure and biological activity. As it turns out, CTD data provide a backbone for all OOI objectives.

However, just because CTDs have been performed for decades, we can’t always assume that that collection of quality data is straightforward. For example, one of the unique challenges of collecting CTD data near the OOI Irminger site and Greenland region is that there is an elevated level of biological activity throughout the year. While biological activity is exciting for many researchers, it can clog instrument plumbing, build up on sensors, and just be plain annoying to watch out for. CTDs utilized in the Irminger Sea are also subject to extreme conditions such as cold windchills and rough sea state (Cape Farewell is actually the windiest place on the ocean’s surface!), leading to the potential for accelerated sensor drift and the need to send sensors back to manufacturers for more regular servicing and calibration. As one can imagine, there are a lot of potential sources of error when simply considering the environment that OOI Irminger CTD data are collected in.

To help combat some of these potential sources of error, I’ll be picking apart CTD and bottle data cast by cast to look for evidence of CTD problems during the Irminger 8 cruise. But before we can talk about unique sources of CTD data errors, it’s helpful to remember errors that can become systematic throughout the entire data arc: from instrument care, to acquisition, to data processing, and to final data application. Improving our awareness of these issues will allow all CTD data users the opportunity for more meaningful data interpretation. So before I move forward, I thought it would be important to share some of my favorite resources available on community-recommended CTD practices. I encourage folks to comb through these resources and find what might be most appropriate for your respective research objectives.

Recommended CTD resources are provided here.





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CGSN Infrastructure and Operations Webinar

In case you missed it, here’s another chance to join the leaders of the Coastal and Global Scale Node (CGSN) team to hear them describe the infrastructure making up the CGSN arrays, the current status of deployment, and how researchers and educators can get involved with the OOI.


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Endurance 15 Happening in Sept

On September 8th, a science team of ten and three students from Oregon State University will depart the dock at Newport, Oregon, aboard the R/V Thomas Thompson for the 15th turn of the Coastal Endurance Array.  The team will recover and deploy seven moorings. Four of the moorings are located on the Washington Shelf, with the remaining three on the Oregon Shelf. It’s a busy expedition. The team also will be recovering four and deploying three Coastal Surface Profilers and recovering three gliders that are low on power. When not turning the arrays, they will be taking CTD (connectivity, temperature, and depth) casts to verify and calibrate instrumentation. Because of the quantity of the equipment to be recovered and deployed, the cruise will consist of three legs.

“As we head to sea for the fifteenth time to turn this array, it’s remarkable to consider that the Endurance Array has been generating data for researchers, teachers, and others interested in the ocean, every day, 24/7 for the past seven years, said Jonathan Fram, who is the chief scientist for Endurance 15.  “Our data has helped identify everything from warm blobs to low-oxygen events, to even the impact of forest fire smoke miles from shore.”

[media-caption path=”https://oceanobservatories.org/wp-content/uploads/2021/09/Screen-Shot-2021-09-03-at-3.17.24-PM.png” link=”#”]Members of the Coastal Endurance Array 15 team prepare moorings for moving to pier for loading onto the R/V Thomas Thompson. Credit: Jon Fram, OSU.[/media-caption]

To help advance science, the Endurance 15 team also will be sampling for researchers with instruments on the Endurance Array moorings.  The team will collect fouling communities growing on panels attached to its deployed buoys for researcher Linsey Haram of the Smithsonian Institution. They will also collect settling organisms on devices attached to two multi-function nodes for Oklahoma State researcher Ashley Burkett.

The team also will be testing potential instrument replacements and new sampling strategies for coastal moorings. Additionally, they will be assessing technical improvements to the moorings and instrumentation that range from a new solar panel frame design to prevent sea lions from unplugging the panels to improvements to cameras deployed on the moorings with off-the-shelf replacement parts to ensure longevity and resilience.

Check back here often during September as the Endurance Array 15 team shares reports and photographs of their expedition.

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RCA Cruise Turns Toward Recovery Operation

The Regional Cabled Array team successfully completed its annual operations and maintenance cruise and was supposed to be back in port September 2. The R/V Thompson and ROV Jason, however, were called on to assist the E/V Nautilus recover its two ROVs Hercules and Argus.  Don’t miss the remarkable opportunity to watch this operation live http://nautiluslive.org/

The two ROVs were successfully recovered.  After a 26-hour diversion, the Thompson headed back to port for the official end of the RCA expedition.

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Video of OOI Data Users Town Hall

On 24 August, OOI Data Lead Jeff Glatstein, Axiom Data Science Designer Brian Stone, and Axiom Data Science Coder Luke Campbell gave a preview of upcoming additions to Data Explorer that will help users access glider data. The presenters sought input from OOI’s user community to improve the platform to ensure it meets data users’ needs when it goes live in September 2021. You can see the demonstration of the upcoming Data Explorer changes in the video below and hear suggestions from OOI’s data users community.




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Kathleen Gonzalez: Student Ambassador for VISIONS’21 Expedition

The first time Katie Gonzalez went to sea was as a student participant on the 2017 Ocean Observatories Initiative (OOI) annual operations and maintenance Regional Cabled Array (RCA) VISIONS’17 cruise. From that experience, she knew that whatever she did in the future needed to involve the oceans.

Katie recently graduated as a first-generation college student from the University of Washington (UW) with her bachelor’s degree in biological oceanography. But despite her young age, she has amassed a vast amount of sea-going experience. This year marks her fifth time joining the RCA VISIONS cruises, and the third time she has participated in all legs of the expedition.

Last year, when UW limited the number of people who could go on the cruise due to COVID restrictions, Katie was one of only two student participants aboard. As restrictions eased this year, she was excited to welcome back her peers as their student ambassador, using her extensive knowledge and experience to mentor the first-time students on how to use the equipment and interact with the scientists and crew aboard the ship. “Compared to the other students, I’ve had so much more prior experience, and that’s definitely been helpful,” she says. “I’m excited to have some new responsibilities.”

This year, she is also a key member of the science party, mentoring the 19 undergraduate VISIONS’21 students on the intense logging operations and acquisition of 4K and digital still imagery in the  remotely operated vehicle Jason control van.

[media-caption path="https://oceanobservatories.org/wp-content/uploads/2021/08/Eve_Katie_Newport_20180701_153908_L2_startSmall.jpg" link="#"]Katie Gonzalez (left) poses with Eve Hudson (right) on the VISIONS ’18 cruise. Katie is currently acting as student ambassador on the VISIONS ’21 cruise. Credit: University of Washington, V18.[/media-caption]

Katie first became interested in oceanography when she was attending high school in Clallam Bay, Washington. During one very memorable science class, Dr. Deb Kelley, an oceanography professor at UW and PI/Director for the RCA, came to show her class how to make environmental sensors, which they deployed in the school’s garden.

This experience inspired Katie to pursue a college degree in oceanography, and she decided to apply to UW to work with Professor Kelley. Since decisions for UW’s Seattle campus had already closed, she decided to attend the UW at Bothell and transferred to the Seattle campus the following year. In the meantime, she still wanted to work with Professor Kelley, so she commuted 45 minutes on public transportation to the main campus to work on OOI RCA projects in Professor Kelley’s lab.

Katie’s extensive experience working with OOI and doing research at sea motivated her to write her senior thesis using RCA data.

“I knew that whatever I was doing for my thesis, I wanted to use data from the RCA,” she recounts. As a biological oceanography student, she was most interested in biological happenings in the ocean to which she felt a personal bond. That’s when she heard about the RCA hydrophone data. The RCA hydrophones are used to listen for seismic events along the Juan de Fuca Ridge and Cascadia Margin, but they are also constantly bombarded with marine mammal calls, including whale vocalizations. “That was the connection I was looking for,” explains Katie. She decided to investigate fin whale calls at two different sites along the RCA by analyzing the timing and frequency of their calls. She chose to look at vocalizations from the Slope Base (~125 km from the Oregon coast) and the Axial Base (~475 km from the Oregon coast) sites because whales tend to congregate in areas of high bathymetric relief.

Fin whales are considered a vulnerable species because they have been heavily impacted by human activity.

“Looking into what the whales are doing, where they’re going, and how they’re interacting with their environment will be helpful in guiding the protection of these species,” says Katie.

Working with Dr. William Wilcock, a UW Oceanography professor and a seismologist who has been studying whale calls in the Northeast Pacific for several years, she fed five years of RCA hydrophone data into an algorithm that helped filter out data that matched the frequencies of fin whale calls. She then visualized the data as a spectrogram, which allowed her to make comparisons for frequency correlations.

“That was the moment when everything—the oceanography, the data science, and my human emotion for biological creatures—came together,” she recalls.

The preliminary results of this research showed that the whales appeared at the Slope Base site closer to the continental shelf two to three months earlier in their calling season, before moving out to the far off shore blue water environment of Axial Base. Both sites had their largest volume of calls in January.

Katie has several hypotheses about the seasonal patterns she observed. “They could be following their prey, or coastal upwelling could be providing them with more food closer to the shelf during those months. As for why both sites have peaks in January, that’s a question for further research.”

Her thesis detailing her research and its conclusions was published in the UW FieldNotes Journal.

Now that she has graduated, Katie hopes to continue with her research on whales. For now, she is happy to carry on working in the Kelley lab and helping out on the RCA VISIONS ’21 cruise. She will be writing two guest blog posts about her experience on the VISIONS ’21 cruise. Live updates for the VISIONS ’21 cruise can be found here.

[media-caption path="https://oceanobservatories.org/wp-content/uploads/2021/08/CTD_Katie_MIkeV-scaled.jpg" link="#"]Katie Gonzalez (right) and Mike Vardaro (left) work with the CTD rosette on the VISIONS ’18 cruise. Katie is a key member of the science party on the VISIONS ’21 cruise. Credit: University of Washington, V18.[/media-caption] Read More

Students Participate Virtually in Irminger Sea 8

Twelve students from Paige Teves’ fourth-grade class virtually boarded the R/V Neil Armstrong via Zoom in early August to learn what it’s like to be at sea transporting lots of ocean observing equipment in and out of the water for a month. The connection was made through John Lund, an engineer at Woods Hole Oceanographic Institution and chief scientist for the eighth turn of the OOI’s Global Irminger Sea Array. John’s daughter, Annika, is a student in Ms. Teve’s class in the Summer Adventures in Learning (SAIL) program, a summer education program in Marion, MA for students in pre-kindergarten through 8th grade.

The Irminger Sea Array 8 team took turns holding up the “Zoom phone” to share their experiences with the students and the implications of their work in helping better understand the ocean and its role in the changing climate. The Irminger sea Array 8 team took the opportunity to showcase the different roles and genders involved in the work onboard the ship to demonstrate to the students the many possibilities in STEM careers.

Chief Scientist John Lund initiated the visit by explaining what the project was about (gathering real-time ocean data in one of the most important and difficult to sample regions in the Atlantic Ocean ), where they were (in the Atlantic off the Southeast coast of Greenland) and what they were doing (recovering and deploying ocean observing equipment).


[caption id="attachment_21913" align="aligncenter" width="487"] Chief Scientist John Lund showed off the CTD rosette, which is used to measure the temperature, conductivity, and density of seawater.  He had the bonus of seeing his daughter via the Zoom call, who was a participant in the SAIL program. Credit: ©WHOI, Andrew Reed.[/caption]


Engineer and Instrumentation Lead Jennifer Batryn explained her role working with the instruments.  She took them on a virtual tour of one of the surface moorings, pointing out the different instruments and explaining what the measure.


[caption id="attachment_21914" align="aligncenter" width="610"] Engineers Jennifer Batryn (in back) and Stephanie Petillo (on phone) took turns talking about the equipment they are responsible for aboard the R/V Neil Armstrong. Credit: ©WHOI, Andrew Reed.[/caption]


Senior Oceanographic Engineer, Software Architect & Manager, Oceanographic Roboticist and Technologist Stephanie Petillo explained her role as software lead and how the data are collected and relayed back to shore for the engineers and scientists, both to operate the array and to study the data.


[caption id="attachment_21912" align="aligncenter" width="566"] Engineer Dan Bogorff showed the 4th grade SAIL program students the floats that comprise part of OOI’s subsurface moorings. Credit: ©WHOI, Andrew Reed.[/caption]


Engineer and Subsurface Mooring Lead Dan Bogorff presented the Subsurface Moorings, explained their different requirements from surface moorings.  Like Batryn, he explained to the students the different instrument on these below-the-surface moorings and what kind of data they collect and report back.

The students peppered each of the presenters with great questions, demonstrating their curiosity and engagement.

Teacher Paige Teves summed up the experience, saying: “What an awesome experience we had today! It was so cool for everyone, including myself, to see everything we have learned in our summer session about climate change come together by listening to scientists and engineers share what they do.”

Added Chief Scientist Lund, “We are glad the kids enjoyed the experience and hope some of them will be inspired to pursue the fields of science and engineering.”

The SAIL program is sponsored by the Old Rochester Regional School District and Superintendency Union #55.  The school district includes the towns of Marion, Marion, Mattapoisett, and Rochester in Plymouth County, Massachusetts.






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OOI Data Users Town Hall: Special Gliders Session Aug 24

OOI is seeking input from its data users.  All are welcome to attend and contribute to an OOI Data Users Town Hall: Special Glider Session.  The Town Hall will take place on August 24 AT 3 PM Eastern.  Simply click here to register.  We look forward to hearing your ideas.

Since Data Explorer’s inaugural launch in October 2020, OOI has been working with users of Data Explorer to learn what features worked for them, which could be improved, and what could be added to optimize users’ experiences. A version update (1.2) to the Data Explorer is now under development for release in early September. Among the new features include enhancements to the display and user interaction with underwater gliders.

During an upcoming Data Users Town Hall, August 24 at 3 pm Eastern, the new beta features will be demonstrated with the goal of soliciting feedback and suggestions from glider experts to ensure the tool meets users’ needs.

Here is a brief summary of the features that will be reviewed:
1) visualizations of glider previews alongside static instrument previews
2) searchable map interface for visualizing and downloading glider and discrete cruise data
3) mapping interface for finding and visualizing glider and discrete sample profiles that are within range of the selected instrument

Please register, mark your calendar, and see you soon.


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OOI Data Center Transferred to OSU

It’s official. As of Friday 30 July 2021, OOI data are now being stored and served on their new Cyberinfrastructure housed at the OOl Data Center at Oregon State University (OSU).  The transfer of data from Rutgers, the State University of New Jersey, has been in the works since last October, when OSU was awarded the contract for the center.

“The transfer of 105 billion rows of data was nearly seamless, which attests to the collaboration between the OOI technical and data teams, said Jeffrey Glatstein, OOI Data Delivery Lead and Senior Manager of Cyberinfrastructure.  “It literally took a village and we are grateful to the marine implementing organizations at the University of Washington, Woods Hole Oceanographic Institution, and Oregon State University for their part in making this transfer happen while data continue to be collected 24/7.”

OSU Project Manager Craig Risien added, “July 30, 2021 was the culmination of about ten months of working with our Dell EMC partners, the OOI Marine Implementing Organizations, and the OOI Cyberinfrastructure team to deliver a state-of-the-art and highly extensible data center to meet OOI’s present and future data handling needs. We are very pleased with how the data center migration project has proceeded, thus far.”


[caption id="attachment_21888" align="aligncenter" width="519"] The primary repository of OOI raw data is the Dell EMC Isilon cluster, a scale out network-attached storage platform for storing high-volume, unstructured data. Photo: Craig Risien, OSU.[/caption]


OSU’s Data Center was designed to handle telemetered, recovered, and streaming data for OOI’s five arrays that include more than 800 instruments.  Telemetered data are delivered to the Data Center from moorings and gliders using remote access such as satellites.  Recovered data are complete datasets that are retrieved and uploaded once an ocean observing platform is recovered from the field.  Streaming data are delivered in real time directly from instruments deployed on the cabled array.

“The OSU Data Center includes modern storage solutions, Palo Alto next-generation firewalls that ensure system security, and a hyperconverged ‘virtual machine’ infrastructure that makes the OOI software and system easier to manage and more responsive to internal and external data delivery demands, “ explained OSU Principal Investigator Anthony Koppers. “With this equipment now operational at OSU, we are well positioned to seamlessly serve the more than 1 PB of critically important data collected by the OOI to the wide-ranging communities doing marine research and education with ample space to grow well into the future.”

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Testing of New Glider Models Underway

Last fall, the Coastal Endurance team conducted an initial test run of a Slocum G3 glider to determine its capabilities and operational differences to the G2 glider, currently used by the Endurance and Coastal & Global Scale Nodes (CGSN) teams.  The test was prompted by glider vendor Teledyne’s announcement that it would no longer support the G2 glider past 2023.

Both the Endurance and CGSN teams have since expanded testing. The Endurance team recently completed a two-month deployment of a G3 glider, with plans to deploy another later this summer. The CGSN team, which operates the Pioneer and two global arrays, is testing three G3 gliders. One is being tested for use as a coastal glider at the Pioneer Array and the other two are being configured for the Irminger Sea and Station Papa global sites.

“Recent testing at the Pioneer Array was really valuable for us,” said Peter Brickley, CGSN Observatory Operations Lead. “We got a chance to see that our missions were workable, we found and made the changes that were needed, and we were also able to get a better estimate of how much energy these things were going to use.”

[media-caption path="https://oceanobservatories.org/wp-content/uploads/2021/07/IMG_3107-2-1-scaled.jpg" link="#"]Diana Wickman of the CGSN team at Woods Hole Oceanographic Institution is responsible for keeping the CGSN gliders operational.  Here she has stripped the exterior of the glider to ensure that all internal parts are functional.  Once refurbished, the gliders are tested in a water tank before being deployed at sea. Credit: Jade Lin ©WHOI.[/media-caption]The G3 gliders use more power than the G2 gliders, so the logistics of when and where they are deployed will require some adjustments. When powered by primary lithium batteries, for example, the G2 gliders can be deployed for about 90 days. The initial tests of the G3 gliders showed they could last in the water for around 75 days using primary lithium batteries. For trial runs using rechargeable batteries, the time in the water for the G3 gliders was reduced to about 30 days.

OOI is working with the vendor to evaluate operational alternatives to extend the operating window of the G3 gliders.

Improvements may require tweaking

“The rechargeable batteries are a really cool feature, but because they are about half of the energy density of the usual batteries, we’re going to have to adjust sampling schemes and plans for time in the water when we use the rechargeable batteries,” said Stuart Pearce, who works with the Endurance gliders. For now, the Endurance team intends to test the rechargeable batteries in the near shore gliders in the spring and summer when they can reliably get out to sea to recover and deploy the gliders.

G3 gliders also come equipped with larger volume buoyancy pumps than the G2 models in response to users’ feedback. “The gliders rise and fall in the water column by changing their volume and therefore density,” explained Pearce. “The new gliders have 800-1000 cubic centimeters of fluid volume to rise and dive with, compared to the 500 cubic centimeters of volume in the G2 gliders. This means that the G3 gliders can climb and dive in a greater buoyancy range.” One option being explored is whether power consumption can be reduced by adjusting the volume of the reservoir fluid needed to make the glider rise and fall.

The new G3 gliders incorporate some changes that address feedback from OOI and other users who have operated G2 gliders. “If you put anything in the ocean and use it as much as we do, you will find things that unexpectedly fail,” said Peter Brickley, CGSN Observatory Operations Lead. “We’ve been operating gliders since 2013, so we have lots of experience. In the early days, for example, we had a lot of problems with the digifin, the steering rudder that’s on the back of the vehicle. We worked closely with Teledyne to document and study this issue and they ultimately made needed improvements.” Other issues have been similarly addressed over the years.

Integrating the new G3 gliders into its Global Arrays may offer greater reliability as older G2 models are phased out. Diana Wickman, Senior Engineering Assistant II at Woods Hole Oceanographic Institution who keeps the CGSN gliders operational, explained “We need the equipment to work really well, and it needs to work for the entire year. At Pioneer, if we have problems, we can replace vehicles that are struggling with vehicles that we can refurbish in-house, but we simply can’t do that at the global sites.”

For now, the teams will continue with testing to make sure the new gliders will work for OOI’s purpose of long-term ocean monitoring.

OOI shares its glider data with the Integrated Ocean Observing System (IOOS) Glider Data Assembly Center and the OceanGliders project, which is a part of the Global Ocean Observing System (GOOS). Both serve as repositories for researchers interested in using glider data.


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