Searching for an elusive orchid pollinator

Orchids are, of course, flowers, and flowers generally need pollinators in order to reproduce. A seemingly offhand comment about the unknown nature of the pollinator(s) for a species of orchid in Western Australia has led Paul Hamilton to undertake a multi-year citizen-science project to try to fill that hole. He came to Everything Open 2023 to give a report on the progress of the search.

Helmet orchids

Hamilton lives in Busselton, Western Australia, which is near the southwest tip of the country. There are 117 native terrestrial orchid species in his area, some of which he displayed on a slide that can be seen in the video of his talk. A photo of the slide is below, on the left, as well. There are various kinds of pollinators for these orchids, mostly insects, including ants and wasps. The orchids in his area do not have powdery, granular pollen like many other flowers, but instead have pollinia, which are waxy blobs of pollen that stick to the backs of insects that enter the flower.

He had a picture of a thynnid wasp with two pollinia on it, as well as another of a wasp on his finger. They are a fairly small, around 20mm long, native wasp that does not sting. They pick up the pollinia at one flower and drop them off at some other, thus helping to propagate the species.

"Quite a few years ago now", he was on a walk with Professor Mark Brundrett and they were discussing pollinators and why they were important. Brundrett pointed out that the pollinator for the helmet orchid is unknown. That got Hamilton thinking "how hard can it be?"; he set out to try to find the pollinator of this type of orchid, which is not rare in his area and also lives all along the east coast of the country.

Ten years earlier, he had been shown a large, slowly rotting, downed tree with lots of helmet orchids on it, so he decided to try to find that log to use as the focal point of his search. Over the next few years, when he was in the mood for a walk, he would go back to that area to search for the log. He crisscrossed the area, logging his GPS tracks, but it turned out that his memory was bad—the log was actually a little ways outside of his search area.

In the meantime, though, he found an "even more spectacular" log with helmet orchids; it was elevated "like a bench", which made it easy to photograph. There were around 60 flowers of one species (Corybas recurvus) all growing together in the moss layer on the rotting wood. He showed a close-up of the orchid, which has a roughly 20mm-wide leaf and a 10mm-wide flower; the location inside the flower where the pollinia are is around 5mm wide, "whatever goes in is small", Hamilton said.

The flowers come out in July and August (Australian winter) "in a dark, wet forest". It may not sound all that daunting, but if you go there at that time of year, you will be attacked by hordes of mosquitoes. There is a second helmet species (Corybas despectans) in that same area that he is also targeting, which is even smaller than C. recurvus. The two orchids bloom for two or three weeks in succession, with a bit overlap between them.

Traps

He and Brundrett constructed some traps, one of which did actually catch some insects. It was raised up a few centimeters above the flower, but none of the insects they captured had the pollinia on them. Next up was using a sticky paint-on substance on transparent flexible plastic (from overhead transparencies) for trapping insects; most of what they trapped using this first generation of sticky traps were fungus gnats that "look like mosquitoes, but they're a little bit smaller".

The next generation traps were laser cut from sturdy, clear plastic, each with grid marks for reference purposes along with a place for the date and site name. Each was around twice the area of an index card; they were sticky-painted and placed in the field. At lunch, after he and Brundrett first put out the traps, they realized they were going to have a real problem storing the traps. Some "quick thinking" led to a 3D printer design for a storage box for the traps; he now has many of these boxes, from multiple years, all filled with the traps and their stuck insects.

They did have some success with this technique. He showed pictures of three fungus gnats, each with differently shaped pollinia on their backs; "Fantastic!" But there is a problem: even though the traps were positioned just above the orchids, there is no way of knowing that those pollinia came from the orchids; "maybe they came from over there or maybe from a kilometer away".

At that time, DNA testing was around $2,000 per sample. Doing a test was discussed, but, as a citizen-science project, that was too steep for citizen Hamilton—his wife was even less keen on the idea, he said with a chuckle. The collected pollen is still available, though, so if prices for DNA tests fall low enough, perhaps that testing can be done.

Instead, he went around and collected samples from helmet orchids as well as other orchids in the area. The pollinia are quite small; he showed pictures of them on the ends of toothpicks. But trying to work with individual pollen grains would be far more difficult. However, the pollinia for the two helmet orchids were around 1mm wide and had no real discernible shape. "Time to go high tech", he said.

Photography

He was in a "Raspberry Pi phase" a year or so later and thought he could use that device to help in the search. He put up a block diagram of the Raspberry-Pi-based camera system that he built. It uses an infrared camera to continuously take pictures of a target flower. It is powered by two "very heavy, unfortunately" sealed lead-acid (SLA) batteries using a power distribution board that allows him to swap batteries in the field without shutting down. He also designed a companion board with a realtime clock, small display for power monitoring, and that could drive an infrared floodlight at night.

He started out taking full-resolution photos, but "it was taking too long to take a photograph, relatively speaking"; he reduced the resolution to 1920x1080, which allowed him to take a photo every 0.8 seconds. The "3.2 million photographs" from the title of his talk referred to what he gathered in a normal month-long season: a bit over 100K photos per day for roughly 30 days. Over a season, five different flowers were monitored in succession.

Much of the journey of building the camera "trap" is documented in a series of posts on the South West Makers forum. The designs and code are also available in Hamilton's GitLab repository.

He would go daily after work to the camera site in order to swap batteries, so it was dark—and generally raining at that time of year. The electronics and batteries were housed in a plastic bin, which he tried to shield with his poncho when he switched batteries, but eventually water got into the housing and corroded some of the contacts on his hand-assembled board. That led him to create a printed circuit board for the project, which has worked out well; it can be used for other projects too.

He did some more 3D printing for various parts, such as a camera sun/water shield and flexible battery terminals. He also needed a housing for the camera that would keep out the water except for a small hole over the lens. He prototyped it with laser-cut MDF, then created the final housing from acrylic. The camera focused at 2m, which was way too far for his needs, so he carefully removed the glue that held the lens from changing focus. Then he could adjust the focus through the hole in the housing using a 3D-printed tool that he created, which allowed him to focus at around 6.5cm.

The plastic tub eventually got waterproof connectors for USB, HDMI, and power, which allows him to connect to the sealed box in the field. The housing is just externally connected to the camera and light when it is in use. The camera and light are positioned near the flower and the "rig" is covered in a waterproof camouflage poncho. People do walk through the area with their dogs at times, so the camouflage is to try to disguise the $300-400 worth of equipment.

The camera generates around 100GB of data each day. He showed photos from both day and night, which are washed-out looking due to the nature of infrared light. Next up, he needed to figure out what to do with all of this data that he was gathering.

Software

"OpenCV to the rescue." He said that there are some fantastic OpenCV tutorials available from Adrian Rosebrock, which Hamilton used to come up to speed on doing motion detection. There are some tricks, though, like figuring out how to ignore things moving in the wind. He identified an area of interest for OpenCV and had it look in that area for motion with certain characteristics. For example, if the item moving was too large, it could be a cockroach or other larger insect and thus would not be of interest.

When OpenCV found a match, it would copy the photo to a folder. That would reduce the number of photos he had to look at greatly; instead of the 100K photos generated, he would only need to look at 500-2000 or so. Every day, he would swap out a 128GB USB flash drive when he swapped batteries.

The basic pipeline consisted of copying the data from the USB drive to his home network-attached storage (NAS) server. Then a script was run to use the data in the photo log file to annotate the date, time, and frame number directly into each image. It also creates an 800x600 version of the file, which helps make OpenCV run faster; those images are turned into a video using FFmpeg. OpenCV was run on the video and would copy the files of interest to another directory for him to examine.

He showed some photos of the results, with various insects in and around the flowers. Over 1.5 seasons, he has detected two bush flies entering the flower, one stayed for seven seconds and the other for 36, which was a surprising amount of time he thought. There have been seven brown ant visits, for five or six seconds each, and two fungus gnats for 13 and 20 seconds. At the outset, it was thought that fungus gnats were the mystery pollinator, "so it is interesting to see so many ants going down inside there". He has yet to capture the "smoking gun" of an insect entering without pollinia and leaving with one or more. He plans to try again this year.

When you visit the site, "you see nothing, it's just barren", Hamilton said, which makes you think the site is kind of boring. But the camera captures that, roughly five minutes after the human leaves, all sorts of life emerges. "It is fascinating" to see the insects, worms, spiders, ticks, mites of various sorts, and so on. He showed some pictures of those as well; the spiders are particularly impressive, he said, as they look like something out of a horror movie in the video.

He has more data to analyze, including temperature readings from the site. It might be interesting to correlate insect activity with temperature, for example. As he was putting together the talk, he realized that gathering rainfall data might also be interesting, so he may look into adding a way to do that at some point. Another tidbit is that he had little trouble making the housing waterproof, but making it ant-proof was a real problem; it turns out that ants love a dry place and can get around the seal on the plastic bin, almost no matter how much effort you put into sealing it further.

In 2017, he was invited to give a talk about the project at the Maker Faire Shenzhen. He and his wife also set up a booth, where some 50,000 people walked by over the three days of the event. The orchid-pollinator project led him to Shenzhen, which also led to another interesting project—with the inevitable add-on maker projects thrown in as well.

His wife wanted to have her own activity at the booth, so she brought fabric squares and pens that attendees could write or draw on; over 650 of those, with stories, poems, pictures, and so on, were collected. "As one does", he then created a scanner to photograph each of the squares, which were processed with OpenCV for edge detection and auto-rotation; they plan to put them on the web somewhere so that others can see them too. The squares themselves were incorporated into a quilt over the next two years, which they donated to the Maker Faire organization at the 2019 event.

Over the years of the project, which has gone in fits and starts at times due to various glitches, life happenings, and so on, he has gathered some 2.7TB of data, which he is happy to share—though his data plan is not up to a direct transfer, he said with a chuckle. At this point, it sounds like he has most of the "bugs" worked out of the process; one hopes that a smoking-gun photo is in the cards for the coming season. If so, it seems likely that Hamilton will find another way to combine electronics, 3D printing, and FOSS, perhaps with a different orchid—or a completely different citizen-science objective.

[Thanks to LWN subscribers for supporting my travel to Melbourne for Everything Open.]