Using Eco-drone Sensors To Map Water Quality

The recent Lake Merritt Bioblitz organized by Nerds For Nature was a huge success from several angles. Besides the amazing biodiversity that was observed and documented there, and the scores of kids and families digging in the mud flats and otherwise discovering the nature around them, a few of us Nerds For Nature demonstrated a brand-new method to measure water quality.

Sean Headrick of Aerotestra is ready to put the lid on his “Hugo” quadcopter before the test run — photo by Ken McGary

Using a floating quadcopter made by local start-up Aerotestra, we proved that it is feasible for an autonomous flying robot to map various parameters at multiple GPS waypoints without human intervention. Lake Merritt is a particularly interesting location for this sort of environmental monitoring, as there are many different water flows into this tidal lagoon, which can dramatically affect the wildlife that can survive and even thrive here, as this research paper explains.

 

Arduino Micro board forms the heart of the DroneLogger — photo by Ken McGary

The story is summarized nicely in this article in Scientific American. Besides coming up with the idea and organizing the project overall, my technical contribution was a custom Arduino-based datalogger that can take readings from temperature, pH, salinity, and other sensing probes at regular intervals (once per second in this case) and record the data in CSV format on an xD memory card. You can see a lot more bioblitz photos in this Nerds For Nature Flickr set.

 

Eco-drone in flight between waypoints above Oakland’s Lake Merritt — photo by Ken McGary

The collected data shows probes in the water at start/end and four intermediate waypoints. You can also play with the dataset graphs yourself on the ManyLabs Data Hub. No formal calibration protocol was used but it’s in the ballpark and good enough for our proof of concept. Next up, accuracy!

 Logged data from temperature (top) and pH (bottom) probes from multiple waypoints — chart image by Ken McGary

Clearly the temperature sensor needed more time at each waypoint to equilibrate. Next time we’ll have a much better idea of how to optimize the testing sequence eliminate these errors. At any rate, we proved the concept wonderfully, thanks Sean! I only wish we had it all on video…

 

New Sensor Hardware from the N4N Air Quality Nerds

Reblogged from Nerds For Nature.

When the EPA wants to know what’s going on with air pollution, they install a sophisticated sampling and analysis station that can cost upwards of a million bucks. Or they roll out one of their their high-tech air-sleuthing vans, crammed with more specialized mobile electronics than your typical Bond film.

Which is all very impressive, but what if I have asthma or a heart condition and want to know about the pollution on my street? What if you live next to a factory and want to collect data for further investigation? What if we are students or scientists trying to comprehend how pollution propagates in our communities?

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Shaun’s Bluetooth-enabled mobile gas sensor board. — photo by Shaun Houlihan

 

 

Unfortunately, air quality sensors that are both relatively inexpensive AND accurate seem to be rare or non-existent. And not without reason: it’s a tricky task. Of course, new technology + inspiration = new opportunities. You may have heard about some of our electronics design and prototyping of less expensive, DIY-type air quality monitors to help address some of these needs.

To kick things off last year, Nature Nerd Shaun Houlihan developed an impressive PIC-based, Bluetooth-enabled, lithium-ion battery-powered toxic gas sensor board that can communicate with nearby smartphones and laptops. Nature Nerd Peter Sand is also testing a new air quality sensor board that uses a much cheaper (though much less accurate) metal oxide-based air quality sensor for use in his ManyLabs educational environment. You’ll be hearing more about this project soon.

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L to R —> DD Scientific CO sensor, Alphasense reference CO sensor/board, and the new e-chem sensor board on the bench (with scope probes attached) — photo by Ken McGary

What’s New?

And we now have a third brand-new air quality sensor prototype board to tinker with! Nature Nerd Ken McGary just got our new e-chem toxic gas sensor AFE (Analog Front End) board debugged on the bench and roughly calibrated with some Arduino test code, and we have some fun things to show you about our progress so far.

The board was designed by Shaun, in collaboration with Ken and Peter — who successfully assembled the surface-mount parts onto the boards using his retro-tech “hot plate and a cheap skillet” technique. This new board is intended as a test and development platform for more refined and targeted sensor designs in the future, and as an educational tool for those trying to learn more about these sensors.

What’s An E-Chem Sensor?

This new breakout board provides the electrical interface between a microcontroller (like an Arduino board) and an electrochemical (e-chem) gas sensor cell. These sensors produce a tiny current in a diffusion medium by oxidizing or reducing the target gas. We are starting with carbon monoxide cells, but sensors are available for all sorts of species like carbon dioxide, nitrogen dioxide, ozone, and so on.

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Internal structure of an electrochemical gas sensor cell (courtesy SGX Sensortech)

 

 

These are the same devices used in countless safety monitors for mines, airports, industrial environments, hospitals, homes, and anywhere else there is a potential hazard from elevated toxic gas levels. However, their use in lower-concentration atmospheric sensing applications is more recent, so some subtle effects on their output signals are not yet well understood.

They are also not “gas analyzers”, as they can be cross-sensitive to other gas species, and have other quirks that preclude absolute measurement certainty. But properly used they are impressive sensors that can provide reasonable gas concentration accuracy (within a few percent), sensitivity (down to parts-per-billion levels with some sensors and circuits) and reliability (with a typical service life of several years).

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TI’s LMP91000 Analog Front End chip, the heart of the new sensor board, contains most of the analog circuitry for e-chem sensing — from TI datasheet.

 

What’s A Breakout Board?

After Shaun showed us his first working e-chem sensor board, we realized that there are other development platforms we’d like to experiment with the same gas sensors on as well — Arduino, RaspberryPi, and others. This wouldn’t be practical with his more specialized design, but Shaun’s gadget included one crucial teeny-tiny surface-mount interface chip that we still needed, the LMP91000 AFE from Texas Instruments.

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Top and bottom copper layers of the e-chem sensor prototyping board — CAD image by Shaun Houlihan

So we decided to develop this new “breakout board” that includes the tiny AFE chip and some other tiny supporting devices (like a TI ADS1115 16-bit Analog-to-Digital converter), along with a clever socket layout that will accommodate several different sensor pin placements. After we worked out the schematic and parts list, Shaun laid out a nice circuit board form factor that can either plug into a standard prototyping breadboard, or can be used as a “Grove-style” sensor at the end of a 4-wire power/ground/I2C serial cable.

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From analog (blue sensor signal out of the AFE chip at the top) to digital (serial clock and data signals on the I2C bus at the bottom), thanks to the ADS1115 A/D converter chip — digital scope capture by Ken McGary

Why Measure Carbon Monoxide?

Simply, to understand and potentially help diminish the complex stew of toxins and particulates that unfortunately find their way into our atmosphere and frequently our lungs. These pollutants come largely from vehicle exhaust pipes but also from industrial processes and power generation plants and even from the effluvia of our own consumer products being manufactured in other parts of the world.

Carbon monoxide is:

  • The most easily-found component of vehicle exhaust and industrial pollution, as typical atmospheric concentrations are in the ppm range rather than ppb. (EPA CO hazardous limits: 8 hours – 9 ppm, 1 hour – 35 ppm).
  • The least corrosive pollutant species and easiest/cheapest/safest to calibrate with using pre-mixed low-concentration gases (technically speaking, CO measurement is the “low-hanging fruit” of AQ sensing).
  • Colorless and odorless, yet deadly in moderately high concentrations, and potentially debilitating with chronic low-level exposure (see Zero to Million ppm CO concentration effects on the human body in this outdated but comprehensive chart).
  • Often a good proxy for other pollutants coming from the same sources (for example, NO2, SO2, fine particulates, and lots of other gunk spewed from diesel and gasoline engines).

How Are We Calibrating?

We are using a high-quality CO-B4 e-chem sensor from Alphasense [$115] for our calibration reference. It uses a recently-developed fourth “auxiliary” terminal to offset temperature and other sensor cell error signals. It is several times more sensitive than typical 3-terminal cells. This model is also much easier to calibrate in the system, as each unit is individually characterized at the factory and bar coded with the results — providing very good accuracy right out of the box.

We also purchased a matching Alphasense Individual Sensor Board (ISB)[$150] that provides amplified and filtered output signals, which are then directly measured by the same 16-bit A/D converter that is watching the AFE output from the sensor under test. Full-scale output for this ISB is 13ppm of carbon monoxide — impressive!

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Dualing sensors in the cal chamber – Alphasense reference sensor using ISB Board (blue) and DD Scientific test sensor using new breakout board and preliminary calibration software — graph by Ken McGary
The other sensor you see in the graph is a less sensitive but much cheaper unit by DD Scientific [$38].There are several vendors of these types of devices, and a major goal is to characterize as many of them as we can get our hands on so that we can make the right cost/performance decisions for particular sensor applications. We are inspired by the efforts of Tim Dye and his associates at Sonoma Tech and beyond as well as the AirCasting researchers, and hope to soon be extending our understanding of these sensors in similar directions.

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The Alphasense CO-B4 Individual Sensor Board (ISB), with an concentration accuracy of better than +/-1% and noise floor of around 10 parts per billion, is our carbon monoxide standard reference sensor, and costs about $300 including fees and postage from the UK. — photo by Ken McGary 

We’re also continuing our development of simple yet “pretty good” calibration rigs for e-chem and metal oxide sensors. We are starting with carbon monoxide and then we’ll tackle trickier species like nitrogen dioxide. We are using premixed cal gases, homemade test chambers, custom Arduino-based valve-metering equipment, and eBay-acquired flowmeters and gas regulators (more details on our new cal methods soon).

This straightforward and relatively inexpensive DIY approach will help us do our initial cal studies with some confidence without breaking the bank on fancy and expensive analytic instruments.This apparatus might also be used for “Cal Parties” and other community-based efforts to better calibrate and evaluate some of the cheaper sensor units that are out there, and could also be replicated for other groups to use in their own sensor projects.

So How Good Are These Sensors, Really?

To give you an idea of what these sensitive environmental sniffers can do, here’s some non-crucial yet sort of interesting preliminary data just from these sensors sitting on the bench. Sensor temperature (a few degrees higher than room ambient) and CO concentration was recorded every minute, starting around midnight.

The temperature data was mostly quiet until the timer on the house thermostat kicked in the burners for the central heat early on a chilly morning. Then the temp data starts to cycle as the furnace maintains temperature in the house. After a several-hour pause in the thermostat programming, afternoon heat kicks in again.

The CO data is pretty boring except for a couple of things: a) the large spike in the middle of the day corresponds to several doors opening up in the house, including the big garage door, so this shows the transient response of the sensor. The second item to notice is the modulation of the CO signal by the house heater in those tiny stair steps on the decay slope. These suggest a usable resolution on the Alphasense sensor of well under 100ppb (The spec sheet claims resolution of <10ppb!).

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Sensor temperature signal (blue at top) shows mainly HVAC system cycling according to programmable thermostat. Alphasense CO sensor signal (bottom in red) shows large spike from outside (“fresh”) air incursion, then slow decay, with some modulation of CO levels by HVAC system — graph by Ken McGary

How Might We Use These Sensors?

We’re not going to be replacing the EPA vans anytime soon. But we think there are opportunities to develop moderately-priced yet “pretty good” DIY-oriented, well-tested and documented, and open-sourced:

  • Air monitoring stations for schools, towns, and community groups
  • Personal air quality monitors, dataloggers, and mappers for home, school, and work, various field investigations
  • Community-based calibration stations
  • Re-programmable smart sensor/datalogger boards and modules that can be economically adapted to new and novel uses.

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The AirCasting project is an inspiring first step towards DIY air quality monitoring — image from aircasting.org 

One inspiration is the AirCasting project. It was developed as a platform for developing future mobile sensor projects and provides some interesting innovations and very nice (and recently upgraded) smartphone-based software.

Another interesting example is the EveryAware SensorBox project from Belgium, Italy, and the UK. The SensorBox design includes several electrochemical and metal oxide sensors along with an Arduino-based microcontroller core, forming a portable multisensor array or “e-nose” that reacts to traffic-related pollution. There are even efforts to use these to optimize traffic light patterns in real time, thus actually reducing pollution levels rather than just monitoring them.


So What’s Next?

Besides our sensor characterization and calibration efforts, we are also looking at options for commercializing some of these circuits so that other nature nerds can more easily tinker with these useful devices. And we’re looking for funding opportunities and research partnerships, as well, to help us design specialized apparatus and to further refine and document our DIY calibration methods. And we are eager to speak with any community, citizen action, or research group that can help us understand the real-world requirements for such devices to achieve actionable results.

We have the prototyping hardware, and a growing team with the skills and commitment to take the next steps, so let’s see what we can accomplish next! Maybe we can even come up with the AQ-monitoring equivalent to bioblitzing…

Join the N4N AQ Google Group or contact one of the team members to get involved.

Ken McGary for the N4N AQ Team

[Special thanks to Tony Trocian of SGX Sensortech for some of the information used in this blog post.]

Mare Island/USGS NatureNerdFest Report

[Reblogged from Nerds For Nature]

Here’s the complete report on last December’s fantastic NatureNerdFest field event with the US Geological Survey. You can see even more photos on the N4N Flickr stream.

Thanks to Isa and Susan and William and the other WERC researchers who gave us such a warm welcome, and a special thanks to Dan Rademacher for helping pull the carpool effort together under quickly-changing circumstances. And thanks as well to our drivers, you all saved the day for us carless Nerds!

 

USGS Overview

Wildlife biologists Isa Woo and Dr. Susan De La Cruz gave us a fascinating overview of their work, which generally focuses on the impact of climate change on coastal estuaries and the crucial habitat they provide for many struggling and/or protected species. Several detailed slides showed us helpful cross-sections of the types of areas that they monitor, but perhaps the most striking part of the presentation was a video of the tide coming in at China Camp State Park in the not-too-distant future, if current projections for sea level rise hold true.

The USGS info page for this video explains further:

This time-lapse video shows the dramatic natural tidal cycles of a salt marsh in San Francisco Bay — daily rhythms to which animals take refuge in high ground, and the marsh receives sediment and nutrients from the estuary. But what will happen to these marsh ecosystems under sea level rise scenarios? Will we see shifts in vegetation and animal species, or lose some marsh ecosystems altogether? Learn more at the San Francisco Bay Sea Level Rise Project website.

This video really captures the urgency of the work that the Western Ecological Research Center and other climate change researchers are facing, and why we are so enthused to be talking with them about possible collaborations. For much more information on their mission and ongoing projects, check out their website.

Flight For Nature – Drones and eco-research

Several drone experts had to back out for the day due to various schedule conflicts, so the UAV activity was not quite as organized as we had hoped. But several other DIY flight enthusiasts jumped in to provide us with some definite thrills.

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Quadcopter getting a good look at Mare Island — photo by Ed Brownson

 

Reiner’s quadcopter with GoPro camera attached was the star of the show. He showed the gawking crowd some impressive low-level maneuvers, a nice vertical lift with some fun spins and twirls, and generally gave us eco-drone newbies an idea of the possibilities. Brain-gears were almost audibly grinding through exciting new things to do with autonomous flying platforms.

Ragi Burhum (GIS/Geo programmer/entrepreneur and organizer of GeoMeetup) summarizes the discussion around the “drone table” and throws out some ideas for the next gathering:

This meeting was about exploration. Initially, people were interested in what we could do with drones. The concerns about resolution, precision and such went away after we explained that these little guys can take whatever you are willing to lose in a crash!

I think it would be interesting to set some fun, useful, and doable goals for the next event. This will definitely gather interest from a larger pool of drone enthusiasts.

  • Take ortho-photos of a particular area.
  • Overlay drone photos on a map.
  • Do manual reconnaissance of a stationary target.
  • Do automatic reconnaissance/image acquisition of a stationary target at a particular latitude/longitude.
  • Do manual/automatic reconnaissance of a moving object tagged with a GPS and wireless/radio connectivity.
We’ve also heard from other biologists and eco-researchers just in the past few days about using hyper-spectral imaging from low-flying drone platforms to image underwater vegetation in a local lake — and also from researchers studying the regrowth of habitat in a Bay Area natural area recently ravaged by a fierce forest fire, they are hoping to use drones to gather high-quality vegetation coverage data over large swaths of land.
We’re just getting started here, folks, so strap on your Nerd hats, spin up your Nerd propellers, and buzz on over to the Flight For Nature Google discussion group!
Crowdsourcing Nature — Bioblitzing and DNA Barcoding (and Spiders)
 
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Damon shows Dan how to use an iPhone-mounted microscope to take a picture of an unidentified little hopper — photo by Ken-ichi Ueda
We took about a one-hour out-and-back hike on an old roadbed trail and found plenty of birds, some interesting plants, and even some curious bits of a skull that several Nerds pieced together into an official iNat observation. This “microblitz” was big fun, not for racking up huge numbers (64 observations at latest count) but for the chance to introduce new Nature Nerds to the practice, and to explore new technologies like a smartphone-mounted microscope. The Mare Island microblitz page features several cute little critters taken with this device and other close-up techniques, so go take a look!
imageUnidentified lichen at 50x — photo by Damien Tighe
Ken-ichi Ueda, developer of iNaturalist and inveterate species-hound, spent much of the day looking for spiders in mundane places like inside building roof vents and under moldy old mattresses. And what do you know (to no one’s surprise) he uncovered some real beauties.
imageFlatmesh Weaver found on Mare Island — photo by Ken-ichi Ueda
So what’s the focus on creepy-crawlies all about? Ken-ichi and a few other Nature Nerds are developing a standard protocol to help citizen scientists add DNA barcoding to their biodiversity-exploring repertoire. Ken-ichi explains what he and his fellow bug-hunters were up to:
Kaldari, Damon, and I successfully collected a bunch of spiders and we will be sending parts of them to Quintara Biosciences in Albany later this week for sequencing. In January we hope to do the same work ourselves at the Cal Academy to see how hard it is and what the cost difference is.

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Join us on the N4N Bioblitzing Google Group to explore these ideas further.
Networking Nature — Remote yet connected environmental and ecological sensors
For those of you who saw the NerdBuoy demo at Mare Island, thanks for all of your encouragement and feedback! And for those of you who didn’t, read on…
So what’s a NerdBuoy? Well, it might or might not float, but we’ve borrowed the idea of a “buoy” being a general source of crucial information from a remote, possibly environmentally hostile location. We could have called it a “probe” or a “beacon” or a “Remote Telemetry Unit (RTU)” but general consensus among the designers has denied the acronym trend for something more inspirational.
imageNerdBuoy poses in front of the infamous Building 505 (previously a Navy communications complex where some of the first signals from the Pearl Harbor attack were received) — photo by Ed Brownson

 

The NerdBuoy, then, is primarily a technology exploration platform for open-source citizen science types like us Nature Nerds to take our sensors out in the field and provide enough information to design more targeted systems that solve real problems in ecological research. It was inspired by USGS requirements to monitor water depth, temperature, and salinity in many of the tidal marshes that they monitor, but we think there are many more eco-research applications for this sort of open-source ruggedized electronic outpost.
NerdBuoy sensor and geolocation data is saved to a local memory card and also uploaded to the ManyLabs data server via cell phone and/or wifi link when within range, and mapped using a beta version of ManyLabs data mapping software. Over time other methods and services can be explored. For more details please review the preliminary google doc description, and to see some of the sensor data we collected as we carried the NerdBuoy along on our short bioblitz out-and-back hike, look at the map and data set.

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Map view of some NerdBuoy windspeed data collected at the NerdFest, as viewed on the ManyLabs Data Hub.

 

This design is the first proof-of-concept prototype for a versatile technology exploration platform.  It will serve as an environmental sensor, attitude and position, and wireless signal telemetry unit, and can be placed in various spots around pilot test areas to gather data on a regular schedule for a few days or weeks at a time. It can also be carried by hand, bicycle, vehicle (or possibly even by drone in a stripped-down version) to profile a given area’s suitability for various technologies and protocols.

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The NerdBuoy electronics module gets passed around for inspection — photo by Ed Brownson

 

For example, a major issue for most remote sensor projects is figuring out what wireless methods should be used for reliable yet cost-effective communication. Cell phone modems might provide adequate coverage, but ongoing service and data charges are likely to be expensive for even a moderate number of locations. Experimentation with various wavelengths and protocols might indicate that a local mesh or other dedicated RF link system would provide comparable bandwidth for a much cheaper ongoing cost.

In other words, this platform will allow variations on many technology themes to be developed quickly to explore the general problem space, then more refined design work can commence. The first version is built with circuit modules available off the shelf — Arduino boards and shields, Grove sensor boards. A mounting scheme using laser-cut plastic sheets as a “skeleton” to hold these various modules together has been customized by Peter Sand to make efficient use of this cylindrical instrumentation housing.

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Once the NerdBuoy acquires data, the ManyLabs Data Hub provides lots of ways to look at it — composite screen capture by Ken McGary

 

This project is also an exercise in imagining the data structures and network software that will be required to accommodate a variety of envisioned smart buoys/remote environmental sensor platforms in the future. Multimedia features beyond GSM cellphone audio and perhaps very low-res video or still jpeg photos are not generally envisioned for this particular platform, but we expect these options will be explored in related projects soon.

We’ll have more information here on the NerdBuoy project as it develops, but for now join us on the Networking Nature Google Group to explore these ideas further.

What’s Next?

Now it’s time to start thinking about our next NerdFest! We’ll no doubt be back to Mare Island soon, but maybe there are other possibilities, too. Do you have connections at an outdoor venue that might be perfect for field-testing drone ideas or for exploring NerdBuoy operation, like one of the relatively abandoned air bases scattered around the Bay Area? Do you know of other research groups or agencies that we might collaborate with on similar problems? Throw out your ideas on our Google Groups or Meetup page and we’ll see what happens!

Posted in Uncategorized by Ken. No Comments

N4N Takes Flight For Nature

Reposted from the Nerds For Nature Blog:

[Don't miss N4N Project Night on Tuesday, Oct. 29 in Oakland]

A new Nerds For Nature working group is on the wing! Flight For Nature is bringing Unmanned Aerial Vehicle enthusiasts and remote imaging, GIS, videography, and other technology experts together with biologists, geologists, and naturalists, to inspire and develop new remote flight applications that benefit ecological research and education. We want to consider and include every possible sort of non-piloted flying machine, from quadcopters to kites to fixed-wing R/C airplanes and beyond.

Initially, we are collaborating with the Western Ecological Research Center (WERC) of the USGS, but we hope that our activities will inspire other efforts, as well. These concepts include HD videography for habitat surveys and educational films, high-resolution photography using various wavelengths and formats for determining vegetation cover and stress, and precision geolocation and range-finding techniques for mapping tidal marsh landforms over time. The coastal areas that WERC monitors are often literally shifting sands, marshlands, salt ponds, river deltas, and so on — they have a lot of work just keeping track of geomorphology, much less living things.
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HD video camera on a quadcopter — image courtesy of KopterVision

The prohibitive expense and potential danger of small fixed-wing manned aircraft for ongoing tracking projects has made this once-standard protocol a rare extravagance. Satellites are too distant to get the resolution they need (centimeter-sized pixels are the tantalizing goal). Tromping through on a regular basis to map out vegetation is time-consuming, tedious work, and disruptive to wildlife habitat.

There’s plenty of uncomfortable news these days about military drones, but like any technology, there is an abundance of more hopeful applications as well. UAVs and drones are no different, and their rapid adoption by researchers will help solve many of these vexing ecology-monitoring problems. Check out ConservationDrones.org to learn about exciting conservation-oriented projects around the world, and visit PublicLab to see some amazing citizen-science balloon and kite mapping and photography efforts.
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Balloon mapping of wetlands near Clayton, NY – via PublicLab

Clearly, the Bay Area is a hub of aeronautic innovation, as well as a locus of conservation research. Flight For Nature, then, is a natural extension of Nerds For Nature’s mission of “bringing together technologists and environmental professionals to collaboratively build awesome tools to understand, protect, and revive the natural world.” Join us and help push forward the state of the nature-flying arts!

Our goals include:

  • Discuss technologies and concepts, while growing the “drones for nature” community.
  • Collaborate on proposals and projects.
  • Collect and share resources, links, and other information on these topics.
  • Plan demonstration flights for a “Nature Nerd Field Day” at the WERC field office on Mare Island, possibly in early December.

We’re working on a Flight For Nature Meetup some time soon, stay tuned for more info. In the mean time,

  • Jump into our group discussion on Project Night (and bring your drone/UAV/pics)
  • Send an email to Ken for more information and to get on the FFN email list

 

Ken McGary

Nerds For Nature Organizer
Flight For Nature facilitator

Nature Nerds, Crowdsourcing, and the Bioblitz Explosion

My last post left me walking blissfully in the park, but I’m an electronics engineer, right? I’d better get back to my workbench, those circuit boards aren’t going to solder themselves. Except that I started noticing things in the park I hadn’t noticed before…

Ken snaps a close-up of some nice ripe blackberries near McLaren Park’s Gray Fox Creek. — photo by Matt Ball

Wildflowers, in particular. Not all that many years ago, I happened to be the proud owner of a newfangled iPhone, and I was looking for clever ways to justify my purchase. When I was much younger I fiddled with photography and even developed my own prints a few times, but I hadn’t really spent much time with a camera since — it was always too much trouble to keep one handy. Of course smartphones have largely solved that problem, and so I found myself taking wildflower photos with my shiny new camera-phone and posting them online, hoping someone could help me figure out what they were.

Then I figured out how to add a magnifying lens in front of the iPhone’s then non-macro-capable camera to get some fairly nice close-up shots. Like many other frustrated wannabe botanists and naturalists out there, my efforts to catalog and comprehend the wildflowers and other interesting plants I found using Flickr were fun at first, but found limited success.

Then I started paying more attention to birds. I was largely inspired by my sister Thana, who got her undergrad degree in wildlife biology and is a serious and lifelong birder. Her latest visit out west a few years ago sealed the deal, as we went birding and wildflower hunting from King’s Canyon to the Kern River Valley to Joshua Tree National Park to right here in McLaren Park. I was thrilled at her ability to just glance at a bird and know what it was, or to hear a commotion in the distance and say “oh, those are Cedar Waxwings over there”.  I was hooked, and started to seriously observe our avian friends whenever I got the chance, joining local bird walks and even the Christmas Bird Counts. I still struggle sometimes to ID even the obvious ones, but I’ve also had some amazing experiences just watching and trying to figure it all out.

Ithurial’s Spear in McLaren Park — photo by Ken McGary

And then butterflies! Save McLaren Park has helped gather volunteers to help with the McLaren portion of the annual SF butterfly count for the last few years, and they have been a revelation to me. Birds are generally skittish around humans (and some of their more adventure-seeking canines) but butterflies flitter around in their own universe, not really seeing or hearing us anthropods unless we get right up in their antennae. There are only a handful of species to keep track of in local open spaces, so after you’ve been paying attention for a little bit you start identifying the regulars on sight and tuning your senses for the more unusual ones that might pop up. Every walk in the park became a treasure hunt:  ”Hey look at that butterfly!” “Hang on, I’m taking a picture of this wildflower…”

Earlier this year, a newly-formed group calling themselves Nerds For Nature contacted us to see if Save McLaren Park might be interested in helping with something called a bioblitz. So what’s a bioblitz, we asked? Well, a bioblitz is an attempt to observe and catalog as many species as possible in a certain geographic area within a set period of time. The Nerds were eager to use a new crowd-sourced software platform called iNaturalist to supercharge the effort.

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Field Crescents spotted on a bioblitz in McLaren Park — photo by Ken McGary

So we brainstormed and organized and walked the park together to figure out the best way to proceed. Bioblitzes aren’t a brand new idea, National Geographic pioneered the concept over a decade ago. But using the crowdsourcing power of iNat was fairly new to the bioblitz experience. The developer of iNat, Ken-ichi Ueda, was on board, as was his new colleague Scott Loarie, and we rounded up a few local naturalists to help lead the effort.

I wrote a guest post for the new Nerds For Nature blog, Saving McLaren Park: Urban Parks Need Nature Nerds. Others on the Nerds team, especially co-founder Dan Rademacher, who was at the time managing editor of Bay Nature Magazine, publicized the heck out of our upcoming field event. Then we anxiously watched the EventBrite list slowly but surely rack up the reservations.

The Big Day was nothing short of epic! We had a clear sense of making history, but we were also worried silly that all the fuss would somehow fall flat. By the end of the day, we were exhausted and giddy, but no longer worried. Our results had wildly exceeded our expectations, and we had almost 200 species noted, and well over 1000 observations.

 

The excitement didn’t stop, as the results continued to trickle in over the following few weeks. By the time the counting was done, we confirmed 250 species within the four designated bioblitz zones of McLaren Park, largely by folks who didn’t really have an idea of what they were observing. Here’s how I explained it to Dan Rademacher for his KQED Science Blog post on the event:

“When the city developed the [San Francisco] Natural Areas Plan back in the 90s, there was this huge project to get all these professionals mapping out all this stuff,” said Ken McGary, a leader of Save McLaren Park who lives nearby. “Now 15 or 20 years later, we did something similar with a few experts and volunteers. And we’re also inspiring a new group of naturalists.”

How is this even possible, one might wonder, but the results speak for themselves. Crowdsourcing, or distributed problem solving, has come to the public’s attention due to projects like Wikipedia and KickStarter, but iNat takes the concept a few steps further. It solves several problems at once — the observer gets to learn about her natural surroundings, local park visitors get to take advantage of the newly collected knowledge through electronic field guides like this one for McLaren Park (that I am the curator for), and local park managers get a better idea of what’s really going on in the park’s wildlife areas.

Ken explains the origins of the Electronic Field Guide to McLaren Park in a KQED Radio news brief:

 

But that’s just the beginning, really. The other naturalists who are helping you ID your findings are also honing their observation skills, having fun chatting with other experts about whether it really is this or that, racking up their species scores, and feeling really good about helping along all of these newbie nature nerds. And for the meta-icing on this big biodiversity cake, all of the confirmed observations wind up in both the Global Biodiversity Information Facility (GBIF) and the Encyclopedia of Life, where researchers all over the world can make use of it.

Medium

Elegant rein orchid observed in a field of ice plant at the Fort Funston Bioblitz — photo by Ken McGary

I was so thrilled with the results of the event, and so impressed with the caliber of folks in the Nature Nerd cadre, that I jumped in with both feet! I starting going to Nature Nerd meetings and helped plan and publicize several more events. Then we joined up with California Academy of Sciences and the Parks Conservancy to blitz Fort Funston, part of the GGNRA in San Francisco’s southwest corner. This was another wild success, as I detailed on the Nerds blog, with quite a few interesting discoveries and another very impressive plant and animal list of about 200 species confirmed.

Then just a few weeks ago we joined with Sequoia Audubon to bioblitz Laurelwood Park/Sugerloaf Mountain, in the peninsula city of San Mateo. Sandwiched between El Camino Real and the 280 freeway, this 200-acre slice of open space was saved from development just a few decades ago, so there had been no official wildlife surveys.  The Laurelwood/Sugerloaf bioblitz literally put this park on the biodiversity map.

I’m no statistician, but even I know that three huge successes like this in a row is a long way from a chance occurrence. So we’ve compiled some ideas for how others might do their own bioblitz events, both in a longer version and most recently condensed into 10 Steps to Bioblitz.

So what’s next? I predict that 2014 will go down in history as “The Year Bioblitzing Went Viral — In A Good Way”.  Remember, you heard it here first! As initial evidence, we’re still a few months away and there are already several Bay Area events in the planning stages, from Oakland’s Lake Merritt and other East Bay parks to San Francisco’s downtown green spaces, to the entire Golden Gate National Recreation Area at the end of March (where ” iNat-ing”  will be one of many cool nature activities).

And that’s just the beginning! The California Academy of Sciences has been sponsoring citizen science forums among land managers and naturalists and hopes to eventually help bioblitz open spaces across the entire state. We also hear that Sequoia Audubon is planning to eventually bioblitz every park in San Mateo County, and hopes to hold several events next year. We’ve also heard from groups in Chicago and Washington, D.C. who have recently done iNaturalist bioblitzes with similar results.

Nerds for Nature logo

Nerds For Nature has even been in recent discussions with DIY biology group Counter Culture Labs around the idea of collecting tissue samples at future bioblitzes to perform DNA barcoding, something like the Barcoding Alaska project. This is an exciting prospect! Taking pictures of plants and animals to ID them is pretty nifty. But having your name on the very first DNA barcode sample ever taken of a particular species is quite another thrill.

So how do you jump into this exciting new trend of observing and understanding the biodiversity all around us with just the phone in your pocket? You might as well start by installing the iNaturalist app. Then check out the following videos to get oriented, and peruse the iNat Help pages for more information. Or send me a note on my iNat homepage and I’ll try to point you in the right direction. By the way, I understand that there’s a super duper new iPhone-friendly version of the field guide iNat app coming soon, so we’ve got even more fun to look forward to.

If you’d like to join us in the Nature Nerd revolution, sign up for our N4N meetup group and show up at an upcoming Project Night like the one scheduled for Tuesday, October 29 in Oakland. Or join our Google Group. Bioblitzes and a whole lot more are being planned as I type, so don’t miss out on the fun!

 

 

Creating an iNaturalist account (youtube)

How to use the iNaturalist app (youtube)

 

 

 

Posted in DIVERSIONS EVENTS NATURE by Ken. No Comments

Actrino X2 In The Design Pipeline

The fact that this blog hasn’t been updated in a while is in part attributable to the fact that I’ve been busy updating everyone else’s blogs –I’m the cobbler whose children have no shoes. So just what is Ken up to these days? I’ve been busy, let me tell ya. I’ll play catch up with a flurry of blog posts, here’s the first one…

Through mid-summer I concentrated on building up a few more Actrino X1 prototypes and shepherding the design towards it’s next incarnation.  I went to quite a few meetups and tech gatherings and got feedback from several trusted engineering friends and finally decided on some new features and formats for the platform.  I’ve been distracted by other projects the last couple of months but I’m getting back to laying traces recently. The schematic for the X2 version is complete, board layout is maybe 75% done, and I hope to have some prototypes together by the end of the year. Here’s a 3D rendering of the design at the moment:

 

 

You might notice a few changes from the X1 version. Where the X1 used an Atmel AtMega328 microcontroller chip in a DIP package, the X2 upgrades to an ATmega640/2560 pinout in a TQFP 100-pin surface-mount package. You should NEVER run out of I/O pins — OR MEMORY — on this board!

The X2 also includes some extra power output transistors, which upgrade the original 4-channel current sink output to a fancy precision DC current and PWM-controlled dual H-Bridge that can drive loads in the sub-100W range in some very clever ways. There are also copious jumper pins to provide a plethora of operating options, including current gains and error/alarm signals per output channel. The power supply circuitry is completely redesigned, with options for a back-up DC supply input, sophisticated real-time current monitoring and overload shutdown for both 5V and load power, and a replaceable microfuse socket for fail-safe over-current protection.

Click BoardsPerhaps the biggest change is the adoption of the Click™ board format. The new X2 design provides four mikroBUS™ sockets that can accomodate the more than 50 expansion functions perofrmed by the ever-expanding line of Click boards. And the format is perfect for developing custom functions as well. Developed by MikroElektronika a few years ago to address their need for a standardized “breakout board” format for various I/O and interface chips, the mikroBUS™ form factor provides just the right balance between small size and having sufficient and rational I/O per breakout function (I2C, SPI, TTL serial, interrupt, analog, reset, and 3.3 and 5VDC power pins). Since the ATmega640/2560 chips have four serial ports, each mikroBUS™ socket will have it’s own TX and RX signals.

Now MikroElektronika makes some cool stuff but it is not directly “Arduino-compatible”. But the cool thing is, most of the chips used on these boards are the same as those used on other breakouts by AdaFruit, SparkFun, and others, so there are Arduino libraries floating around for most all of the Click chips.  And it’s a much more svelte form factor than Arduino’s shield format. I’ve played with some of the Click boards on the breadboard and they’re pretty nifty, so I’m looking forward to using them soon on the Actrino X2. mikroBUS™ and Actrino together are bound to be a powerful and versatile platform for open source research apparatus and lab instruments — stay tuned!

 

Actrino Says “Hello World”

If it looks like nothing’s been happening here on the KSF blog, it’s because we’ve been insanely busy inventing a brand-new twist on open source hardware.  On Thursday, Feb. 7, I presented Actrino proof-of-concept prototypes to the tech community for the first time at the SF Hardware Startup Meetup. The event was held at IDEO‘s Pier 28 space under the Bay Bridge, and drew a typical overflow crowd of over a hundred curious hardwarians.

If you find this product concept interesting, I’d love to hear from you. We’re looking for potential end-users and alpha testers, as well as business and technical partners, so drop me a line (ken a t ksflabs dot com), sign up for our mailing list, and watch this space!

 

The Actrino X1 Base Board — 3D rendering from KiCAD design files

The Actrino X1 Base Board — 3D rendering from KiCAD design files

 

The Arduino™ form factor has thankfully brought microcontrollers to the masses. But it also comes with limitations. Frankly, we’ve gotten a bit tired of fiddling around with all those awkward little square wheels — so we decided to invent a round one.

Actrino brings a modular systems approach to the open-source world, integrating electrical, mechanical, thermal, and even aesthetic aspects of a design. This frees you to focus on your application rather than shield compatibility, mechanical mounting schemes, heatsink placement, and other common headaches.

10W RGBW LED mounted on center pedestal, coupled to heatsink base below.

Features

Compatible with Wiring/Arduino™ & other AVR software environments
Four bullet-proof high-current low-side drivers

  • Controls over 100 watts of DC power (24VDC @ 5A per channel, 8A board max)
  • Drives DC and stepper motors, high-power LEDs, heating elements, thermoelectric coolers, solenoids, relay coils, fans, and many other loads
  • 16-bit PWM, 12-bit analog current control, and thermal protection for each channel

Flexible serial interface slot — MIDI, DMX-512, RS485, RS232, USB, IrDA, etc.
Sixteen status LEDs
Several spare analog & digital I/O pins
I2C and SPI peripheral bus
Modular enclosure system and expansion scheme based on elemental forms

  • Mounting holes in a grid and around the perimeter of the board
  • Inherent heatsink base with many options including center mounting pedestal
  • Can often be fabricated from common raw material (rod stock, acrylic/Lexan tubing, etc.)
  • Custom bases, brackets, and other accessories can be modified from templates using online CNC services

10W LED prototype illuminating a magnifier lens. Higher power LEDs can be used with a thicker heatsink base and/or forced air cooling.

Applications

Research

  • Hot/cold/stir plates, incubators, peristaltic pumps, valve manifolds
  • Fiberoptic/microscope light sources, fluorescence imaging, slide coolers, optogenetics
  • Operant conditioning, neurobehavioral rigs

Photography

  • LED flash/camera control/intervalometer mashups
  • Linear or matrix flash arrays
  • RGBW LED beauty dishes and soft boxes

Art & Design

  • Table lamps, color organs, status indicators, mood lighting
  • Theatrical lighting, stage mechanisms
  • Large LED/actuator arrays for interactive installations
  • Display/architectural/club lighting

Robotics & Automation

  • Rovers
  • Smart motors and actuators
  • Process control

 

10W RGBW LED prototype configured as a fiberoptic light source. The translucent Delrin rod on top is used as an integrating sphere and adjustable attenuator.

 

Actrino spin table prototype on the bench

~ Click image for brief video of stepper motor action modulated by a light sensor ~

RaspberryPi @ Noisebridge — Sept. 29

Rob Bishop from the RaspberryPi Foundation is touring popular hackspaces in the US throughout September 2012, giving talks and workshops about the exciting new RaspberryPi $35 credit card-sized, ARM-based GNU/Linux computer board (FAQ). He’ll visit Noisebridge (2169 Mission St, SF) on Saturday, 29-September-2012.

Here’s more info on the event…

RPi news and views

Posted in Uncategorized by Ken. No Comments

Comic Science, Eyeball Edition

Yes, science is often comical (“where did THAT number come from?”) but we’re referring instead to the science nerd comic strip xkcd. Most installments poke fun at science and technology’s never-ending absurdities, but every once in a while creator Randall Munroe gins up an entertainingly informative panel like the one below. Behold, the miracle of sight!

Posted in Uncategorized by Ken. No Comments

KSF Labs joins Science Exchange

KSF Labs is pleased to announce that we are now a service provider with Science Exchange! If you don’t know about this new start-up, we suspect you will soon. This group of researchers and entrepreneurs are trying to solve a big problem that affects most every corner of academia — effective allocation of expensive but necessary research resources. 

Science Exchange aims to be the brokerage for a new age of research collaboration. So you’d really like some scanning electron microscopy done on your latest samples but you don’t have access to one? Or perhaps you’d like a custom electronic gizmo designed and built for your research and you don’t have access to an electronics shop? (Hey, that sounds like us!). You gotta have it but you don’t have local resources to get it done – what to do, what to do?

First, you search Science Exchange’s service provider database of institutional core facilities and other specialized labs, instrument shops, and the like. Then after you are matched up with a provider, Science Exchange handles all of the inter-institutional paperwork and makes sure everyone pays and gets paid as promptly as possible, and in exchange takes a small commission on the transaction for their troubles. Perhaps the best explanation of Science Exchange comes from this Scientific American article by one of the founders, Dr. Elizabeth Iorns. If you’d like more information about Science Exchange, their Help Center answers your questions about requesting services and evaluating estimates, as well as their purpose and history.

You can request a work estimate from KSF Labs by visiting our Science Exchange Profile Page.

Posted in Uncategorized by Ken. No Comments