Notes from the Field: Yunnan, China

Dr. Peter Fritsch, BRIT’s VP of Research and Director of the Herbarium, is on a visiting scholarship from the Chinese Academy of Sciences, based at the Kunming Institute of Botany in Kunming, the capital of Yunnan Province. Peter went on a brief (8-day) field trip in late October-early November to far northeastern Yunnan Province and the bordering area of Guizhou Province. Below are some photos from his trip.

1yunnan

The arrow on the map above shows the location of my field work, in Weixi and Yiliang counties.

 

2river

Typical scenic shot in this region—limestone mountains blanketed with native forests in the least accessible parts.

 

3symplocos

One of my specialty groups, Symplocos of the Symplocaceae (sweetleaf family). It’s mainly a tropical family—we have one species in Texas, S. tinctoria. This one is S. setchuensis. Flowers resemble that of a small version of Camellia, but are usually white instead of pink.

 

4cornfield

Hazy but otherwise beautiful day. Overlooking a valley, with corn in the foreground (no rice grown in these parts).

 

5pass

Pass between Yunnan and Sichuan provinces. Apparently the weather is always like this here. So, unknown to us, it was one of the more brutal and rather dangerous “hikes” (actually climb) that I have done in a while. No real trail, average 70% slope. One false step in some places…

 

6dovetree

A real treat to see this, the Dove Tree (Davidia involucrata in the dogwood family Cornaceae), one of the only places left where it occurs in the wild. Spectacular when in flower.

 

 

Another rare treat: Rehderodendron macrocarpon, in one of my pet families, the storaxes (Styracaceae). Has one of the oddest fruits you’ll see, football shaped and ca. 2.5 in. long. Inside is a hard bony center surrounding the elongated seeds, with radiating parts to the edge, and in between is a corky material. I can’t imagine what disperses this, and we found all the fruits dropped right under the tree.

 

10lowhills

Low limestone hills. The beginnings of what farther east will become the bizarre landscape of Guilin. I guess Guilin will have to wait ‘til next time!

 

11fieldteam

Field team, out of the cold—and onto those short stools (you need good knees in Yunnan). From left to right, Ren-Fu Lu, Hong-Hua Liao, our driver Ting-Xun Liu, and Dr. Lu Lu, my colleague from KIB. Ren-Fu Lu is Dr. Lu Lu’s father, and he’s a sharp-eyed plant collector and incredible mountain climber.

 

12dinner

Colorful dinner—the plants in the upper left dish are grape ferns (Botrychium). Sorry, tasted terrible. Those in upper right are fungi—much better.

 

img_8876

Me at the Kunming Institute of Botany herbarium in Yunnan, China, where I’ve just finished annotating their Styracaceae (storax family) collection. About half the specimens were mis- or unidentified—the family is a challenging one taxonomically, but I’ve been studying these plants for over 20 years and know them well. The annotated specimens extend in front of the image to all the way to the back wall behind me, and total around 800 specimens, including some rare and endangered species. The work took five days and was conducted as part of a visiting scholar fellowship gratefully received from the Chinese Academy of Sciences.

Share Button
Posted in China, Field Dispatches, Herbarium, Notes from the Field, Research | Tagged , , , , , , , | Leave a comment

Youth Range Workshop 2016

by Dan Caudle, BRIT Resident Research Associate

 

2017-yrw-participants

2017 workshop participants

Just imagine trying to keep up with 25 energetic, enthusiastic, inquisitive high school students for a week in the middle of a hot, dry summer in the semi-arid country around Junction, Texas. Well, I accepted that challenge even though it had been 35 years since the last time I did it!

I served as workshop director and instructor for the 62nd Texas Youth Range Workshop this year. Not only did I survive the experience, I enjoyed it so much I’ve volunteered to do it again for many years to come!

Caudle2

Mr. Caudle sharing his wisdom…

The Youth Range Workshop is held annually at the Texas Tech Center at Junction and is an activity of the Texas Section of the Society for Range Management. As you might expect, it’s evolved through the years as research and technology have advanced and natural resource issues have emerged.

 

learning-to-burn

Learning to burn.

As usual, the students in the 2016 workshop group came from across the state – from the Panhandle to the Rio Grande and from the Trans-Pecos to the Gulf Coast. Sponsored by various organizations in their home counties, students arrived on a Sunday as total strangers with limited knowledge about natural resource management and left the following Friday as lifelong friends with the potential to be the leaders of the next generation of Texas land stewards.

The majority of this intensive week of training was conducted in the field and included instruction on native vegetation, soil, water, wildlife habitat, livestock grazing management, prescribed burning, and stewardship of natural resources. Public speaking, personal development, and team building were also an integral part of the program. Hands-on activities included data collection and monitoring techniques, plant identification and plant collection, on-site participation in an actual demonstration prescribed burn on a ranch with an opportunity to become an active member of the fire crew for the day, carrying out demonstrations of water infiltration and runoff, measuring transpiration rates from various types and species of plants, and many other activities.

 

The group visited four ranches where they were able to meet and talk with the landowners and learn about their management objectives and conservation strategies. The group also went to the Kerr Wildlife Management Area where they discussed wildlife habitat management, endangered species, and the interactions of fire, wildlife, and livestock with Texas Parks and Wildlife Department biologists.

 

Blue Mountain Peak Ranch

Blue Mountain Peak Ranch

Each student had to make a plant collection of 25 plants from the official lists of plants used for the state 4-H and F.F.A. high school plant contests. They were each given their own plant press. They had to learn to identify the plants, collect the plants during the week while on field trips, press the plants, accurately describe the characteristics of each plant, prepare a label for each specimen, and organize their collection by categories for grading. After grading, the collections and presses were returned to the students for them to take home. They were all encouraged to keep collecting and building their own collections.

Caudle7

A plethora of plant presses!

 

The final exercise of the week was when the students had to work in teams to develop plans to resolve conflicts between agricultural, environmental, commercial, recreational, and governmental interest groups concerning some fictional land in the Texas Hill Country. The teams each had to present their arguments and defend their positions to a mock regulatory board made up of workshop directors representing each of the different interest groups.

caudle4

Hopefully BRIT will become more actively involved with the educational and plant collection aspects of the workshop in the future. It’s a rewarding and exhausting experience for the students as well as the instructors!

 

Share Button
Posted in Education, Herbarium, Notes from the Field, Research | Tagged , , , , , | Leave a comment

The changing plant life of small islands in the Sea of Cortéz

Exploring the plant ecology of the Bahía de Los Angeles Island Archipelago, with staff and students from the Ocean Discovery Institute 

With Dr. Drew Talley, Quinn Heist, Leslie Torre, Ndekey Kahindo, Samantha Gaeta, Aurora Figueroa, Joan Flores, and Joel Barkan.

img_401300004

Saturday, July 2nd

We met at the office at 6:30 am and proceeded to spend about two hours packing the truck with food. 40 mouths are many to feed, and after hundreds of pounds of coolers, boxes, bags of rice, and beans, stuffed in between with fresh fruit, we load up and hit the road. It’s a lengthy drive (via Mexicali), and we switch drivers in San Felipe, before embarking on the long (~40 km/ 23 mi) dirt road south. Our vehicle wants to go faster, but we slow down to botanize and try to stay light-hearted through the painfully slow crawl. I’m delighted to be traveling with two rock star scientists from NOAA—Dr. Tina Fahy and Stephanie Nehasil—whose conversation I enjoy immensely. We reach our destination at sunset, and it’s spectacular! We rush to unpack the trucks, and I somehow accidentally lock the keys in the car. Luckily we’re now in a town, and a locksmith comes to save the day.

We wolf down a tasty dinner and make introductions, and I set up a cot outside the staff house and fall asleep almost instantly, not waking again until the first light of dawn with a beautiful bat circling above my head. I smile to think no insects or mosquitos will be near me thanks to this scenario, and as I sit-up a little I see the most spectacular sunrise beginning on a horizon of black islands and an inky sea.

img_423700013

Sunday, July 3rd

Today is my free day. As I walk to breakfast I see the Mobula rays jumping, and my heart soars. I quickly seize an opportunity to go snorkeling, and by 7:30 am we are off, heading out to the bay to look for whale sharks. We find a small one, but the action is slow, so we head out to a great snorkeling spot at Isla Pescador. It’s wonderful—I swim around the point in the shallows seeing large numbers of yellow fin (jurel) and a ton of friendly puffer fish that I can almost touch. At the point, the marine environment changes, seems more productive; shallow boulders have miniature gardens of algae that in turn host a plethora of tiny fish, anemones, crustaceans, corals, sea stars, and other treasures. There are small fish that behave like snakes and tiny fish that flit like gobies. It’s a magical place, and I assume the waters are nutrient-rich as a result of some upwelling on the outer side of this mini-peninsula. The chasms are much deeper on this side, and although the water is warm at the surface, it’s pretty cold in deeper water, and I soon realize that I am too cold to continue.

I make it back to the boat barely able to pull myself out of the water (!). I don a borrowed shorty wetsuit, and we move to an area known as the drunken rocks. Currents are strong so we don’t stay long. And now we’re looking for whale sharks again. I decide I’m not interested, but when we pull alongside a monster and the captain yells “Go on! Get in!”, I abide. It’s amazing! I’d forgotten the absolute majesty of swimming alongside a creature of this size. It is magnificent. I can see the cleaner fish on its tail and back, and if I swim as hard as I can, I can reach its head and swim alongside the main dorsal fin. Suddenly it turns towards me and dives down, passing directly underneath me. An amazing three minutes. I’m exhausted! We head in for a lunch of making your own spring rolls, and an afternoon pow-wow about the week ahead.

img_443600029

img_440100028

We’re here to work with a group of 24 under-represented kids in the Bahia de Los Angeles, Baja California, Mexico. The Ocean Discovery Institute has organized a five-week camp for these kids, with 30+ scientists visiting over the course of the summer. My stint is just six days (plus two days driving), and today is my only day off. I feel like I made the most of it. Dinner is served at six-thirty after a talk by Dr. David Sandstrom on sea-slugs. The talk is fascinating. I had no idea that there were animals that steal chloroplasts from the green algae they eat. They store this contraband in their own tissues, where the chloroplasts continue to produce sugars for some time.

The rich green color of the photosynthesizing sea slug, Elysia chlorotica, helps to camouflage it on the ocean floor. Credit: Patrick Krug

The rich green color of the photosynthesizing sea slug, Elysia chlorotica, helps to camouflage it on the ocean floor. Credit: Patrick Krug

After dinner, I’m able to contact an old friend, Karina Rubio, who lives near town. She and her husband (Pancho Murrillo) drive out to say hello, and I have brought them a packet of photos from our last trip together, which is now more than two years ago. I’m delighted to see her, and heart full, I walk back to camp just in time for the “family meeting” that celebrates the achievements of the week then looks forward. As we walk back, the wind is whipping around us, and scores of tiny mesquite flowers are flung into our hair, making it look like we’d just walked back from a wedding. Then we have a team meeting—I’m so excited about my team! Five bright young students, a project manager who couldn’t be more excited about plants, and Dr. Drew Talley from the University of San Diego as a Co-PI. Team Perfect.

img_420100011

Aurora, Sam, Leslie, Ndekey, Joan, Quinn

Aurora, Sam, Leslie, Ndekey, Joan, Quinn

Our plan for the week is to resurvey as many of the small islands in the bay as possible, comparing the abundances of perennial plants to those documented in 2002 by the thesis of Patty West. One of the students asks me if I’m planning to do a lot of extra research without them. I answer that I hoped we could do as much as possible all together and be a team and have the best project ever. They seemed to like that answer!

I’m oh-so-tired again tonight and find time for just one beer before crashing. The winds are so strong that we all have our cots on the porches of the buildings in little rows.

img_4092

Monday, July 4th, Independence Day – first day of field studies.

I wake up very early, with terrible allergies. I can’t seem to stop sniffing and sneezing, so I get up early and tiptoe over to the staff building. The sunrise is again magnificent, and I enjoy watching the local fisherman circling around and making bait on their pangas. I check my emails, change my clothes, and pack my field bag. Breakfast is at 6:30 am, and we’re in the boat by 7 am. I have a field press, and we have several gallons of water with us. Our first island stop is Cerraja, my first taste of the Bahia de Los Angeles Islands. She’s beautiful! The students rush off to check the pitfall traps they installed six days ago, and I marvel at the wealth of cacti and totally crispy annual plants. I quickly realize that (unsurprisingly) we would have to exclude all annual plants from our analysis—there had been no new growth here in quite a while. We see cardónes, barrel cacti, hedgehog cacti, fishhook cacti, and more. In fact, we even record a second species of fishhook cactus for the island. I’m delighted—we can really see some changes in the perennial flora over the past 15 years, and we’re able to document the abundance of all the perennials. The students seem pretty engaged, and they’re keeping up with all the names and methods; it’s going well.

fishhook cactus 1. (Mammillaria dioica)

Fishhook cactus #1 (Mammillaria dioica).

Fishhook cactus #2 or strawberry cactus (Mamillaria insularis, we think).

Sam, Leslie and Ndekey with Stenocereus gummosus, the pitaya agria

Sam, Leslie, and Ndekey with Stenocereus gummosus, the pitaya agria

The second island is Llave. It’s smaller and less diverse, which makes life easier. We split into teams here, and the plant team surveys while the insect team measures the surface area of the chollas and the spider diversity that each one supports. We can see several dead cardónes, and their abundance seems to have dropped to rare. We also find the other fishhook cactus here (new record), but we’re unable to locate the hedgehog cactus, and we speculate on its disappearance.

We get back on the boat, and our amazing panga driver Martín, long-term friend of the program, has caught several bass and made ceviche for us. DELICIOUS!!

Now we’re rushing to our third, much bigger island, Ventana, which has a lot more plant life. I’m excited to see agaves (Agave cerrulata) and the torote (Bursera microphylla) from the water. We land in a hurry, and I’m amazed how many of the perennial species on the list we find in 30 minutes, right there at the landing. We don’t have time to do extended abundance estimates, but we do press a couple of fertile specimens, and I point out a few of the botanical highlights to our team of budding plant ecologists.

Lunch is tostadas. I’m exhausted!

 

Tuesday, July 5th

Though it’s not as hot as yesterday, the afternoon heat was endless and without reprieve, so I sat in the shade with a small fan and worked quietly for a while. The evening’s festivities included some face-painting and Zumba—which I really quite enjoyed—and finally a good night’s sleep in a cot by the ocean. I awoke before dawn again, and quickly it was hot.

Today we visited another three islands. Coronadito was small, and the plant team did a great job recording all the perennials with some interesting differences in the numbers of cacti. A treat for me was getting fairly close to a large colony of my name-sake birds, the blue-footed boobies (Sula neobouxii), nesting in the cliff.

img_4274

A blue-footed booby (Sula neobouxii)

Coronado/Smith Island was huge and somewhat barren for an island of its size. I collected an “asteraceous” shrub that was unknown to me and made a few notes on the flora while the students checked their pitfall traps for beetles. It’s not enough time to make an exhaustive study of the perennial flora, so instead I search for the endemic barrel cactus, Ferocactus gatesii. It’s the only plant known to be endemic to these islands, but my search on this particular island was not successful. I’m sure it’s there somewhere, just not where we landed.

I’m anxious to move on to the next island, Mitlán. It’s smaller, and we should we able to conduct an exhaustive survey. We’re moving slowly in the heat but still feeling positive, and we land on Mitlán around 11:30 am. We split into teams, and the plant team again is covering ground, identifying plants. We make an exciting discovery of a fagonbush (Fagonia sp.) which might be a new record for the island, but there are several perennials noted in the 2002 thesis that we are unable to relocate, including the senita or old man cactus (Lophocereus schotti), which had been noted to be rare previously, and the fishhook cactus (Mammillaria insularis) which was formerly noted as scarce, but couldn’t be found. Both these plants are of particular interest as one (the old man cactus) is listed on the Mexican Endangered Species List (NOM 059) and the other is one of the rarer regional species.

img_419800010

Mitlan.

Hot and tired we walked back to the boat and took a quick trip around the coast to check for any plants we couldn’t see from the higher points of the island. Still no sign of our cactus. We start the fairly long ride back across the bay, which is surprisingly choppy, and I get soaked with salt water. This was not disheartening as dolphins were jumping clean out of the water and amazing us all on the ride. Arriving to shore I rush to change, and we head straight to the local CONANP office. CONANP (Mexico’s National Commission for Natural Protected Areas) is responsible for the management of these islands and are working with on this research. The meeting goes well and I am inspired, but stay indoors to beat the heat for the rest of the afternoon.

Careful!

 

Wednesday, July 6th

Well, I was surprisingly tired again yesterday. Enjoyed hearing Richie play the guitar at sundown and got an early night. Today another early start and out to the magnificent islands of Flecha, Jorobado, and Pata. The first two I just loved—great hikes, great views. Super plants on Flecha, a total of just 4 perennial plants on Jorobado (so that was a quick visit), but Pata blew us away! LITERALLY! Two of the students were blown over (!),my hat blew off, and we had to turn back from the peak. Very disappointing, as we were close to re-documenting all the perennial plants that Patty West had recorded in 2002. One exciting discovery was the true elephant tree (Pachycormus discolor, Anacardiaceae) which I can only assume was formerly ID’d as Bursera microphylla (an easy mistake to make), since it appeared to be more than 15 years old. Luckily it was flowering, and I was able to grab a small piece for the press.

The elephant tree or Pachycormus discolor (photo by Andrea Schieber, via Flickr).

We had some delicious fresh rock-bass (cabrilla) ceviche in the boat between Jorobado and Pata, and that definitely compensated our sore legs and sticky bodies for their efforts. The ride back seemed long, and the students were sleepy. Once back at camp we ate, cooled off with a quick dip, and headed to the local museum which Carolina Espinoza had kindly opened for us. Wonderful museum, great tour, excellent souvenirs!

I feel a sense of sadness that this is my last day in the field with the students. I’m very fond of them and will miss them very much tomorrow when we head out without them (they have a field trip to go clamming and snorkeling).

 

Thursday, July 7th

6 am. Wow—staff meeting last night was interrupted by a whale-shark swimming past, and then my night was filled with lightning strikes over the water behind my head and shooting stars above. Magical! My allergies get worse every time the wind blows, but otherwise it’s pretty divine now. The nights are finally cooler, but the sun is hot hot HOT! First views of the day were the fishing boats with the ocean as flat as a pond. Today is my last field day.

6:38 pm. So many highlights today! We left at 7 am again, first going to the lovely island of Gemelito West where I was thrilled to hear the fish-eating bats roosting in the rocks. Their chirps were amazing, and although we never saw them, I was delighted to know they were there. We also got very close to some frigate birds and blue-footed boobies. The next island was Cabeza de Caballo, which was too big to thoroughly inventory, but which Drew had wanted me to see because of the amazing plant life (which included many old succulent friends). There I saw my first chuckwalla (Sauromalus)! What an amazing animal! He looked so reminiscent of the iguanas of the Galapagos Islands (which I have only ever seen on the television). He made no effort to escape my hands, and I was again overwhelmed by the diversity of these special islands.

Drew and the Chuckwalla

Drew and the Chuckwalla

Next we drove past the back side of Ventana, to check the abundance of the barrel cactus, and then we went back to Pata to finish checking the plants of the high peak that we couldn’t reach yesterday. A long hike revealed that we had basically missed very little yesterday! Still the views from the peak were spectacular.

Next we went to Bota, a new island for me again, small enough to quantify fairly accurately, but a patch of green shrubs at the bottom of the west end led us down a very long, steep scree slope. We were well-rewarded with two new records for the island: Santa Lucia (Trixis californica) and the whitestem milkweed (Ascelpias albicans).

Ascelpias albicans

Ascelpias albicans (photo from SEINet).

Trixis californica

Trixis californica (photo from Wikimedia Commons).

Finally we decided to take the boat around Coronado Island in a last attempt to locate the barrel cactus, which was previously recorded as scarce here in 2002. The boat ride was long, and the oceanward currents were strong, creating bigger waves than I had anticipated. After an hour or more circuiting the perimeter, we realized that the barrel cacti were nowhere to be seen, and we headed back to shore, stumbling across a whale shark on our way back to field station.

The afternoon activities included a question and answer session with the students. The highlight for me was when one student was asked “If you could have any job for one day, what would it be?” and she answered, “I would be Sula. I would be a botanist!”

img_423000012

Friday, July 8th

Getting ready for a super-early departure tomorrow. Great morning entering data with the students. After some heart-felt goodbyes and a very sweaty Zumba session, I went for a quick “midnight swim” by myself in the dark, and the water was full of phosphorescence. What a lovely way to end the trip. Looking forward to next year!

img_415200007

Ahhhhhh…

Share Button
Posted in Mexico, Notes from the Field, Research | Tagged , , , , , , , , | 1 Comment

World Record Largest Myxomycete Found On BRIT Campus

The lead photo in the article featured in Fungi magazine about the world-record myxomycete found on the BRIT campus.

The lead photo in the article featured in Fungi magazine about the world record myxomycete found on the BRIT campus.

bioswale-3

Fuligo septica, otherwise known as scrambled egg slime mold. And yes, this IS actually eaten in some cultures, though we don’t recommend it.

And there it was—a myxomycete fruiting body about 30 inches by 22 inches, round like a pancake and filled with spores, found in BRIT’s front yard growing on bark mulch in bioswale #3. This discovery was recently published in the 2016 Summer Issue (Volume 9, No. 2) of FUNGI magazine, a popular publication for amateurs and professional mycologists (people who study fungi and fungal-like organisms). There were more than 20 smaller fruiting bodies scattered on the surface of the bark mulch, but this fruiting body eclipsed the former world record by several inches.

resized1

What is a myxomycete? They are often referred to by mushroom collectors as “slime molds” because of a soft, jelly-like, amorphous stage called a plasmodium that creeps over the surface of bark mulch feeding on microorganisms, mostly bacteria, eventually developing into a fruiting body structure that forms spores. There are animal-like life cycle stages that are motile, tiny amoebae or swimming cells as well as plant-like or fungal like stages with spores. Most of the species have fruiting bodies that are tiny, less than 0.1 of an inch in diameter.

resized3

This myxomycete species, Fuligo septica, is common in the Fort Worth area, growing on piles of leaves, compost heaps or piled grass clippings, wood chips, decomposing tree stumps, living grass in yards, and bark mulching around the base of trees. It is not a disease pathogen and poses no problem attacking and killing lawn grass or shrubbery. It is sometimes a scary nuisance as in the case of a Garland, Texas, homeowner that discovered the plasmodial stage growing and getting larger, that was called “the Texas Blob,” portrayed as a mutant bacterium that might take over the earth, and made newspaper headlines throughout the country.

resized4

How did this myxomycete get to this site? The spores are wind-blown and probably were already present on the oak bark mulch when it was placed in the bioswale around the trees. This article has weather data compiled from a BRIT weather station that includes the temperatures, precipitation, and the time course of fruiting body formation for the period March 1st to April 15th, 2016.

The discoverers by the now old plasmodium.

The discoverers by the now old plasmodium.

Left: The world record Fuligo septica measured a length of 30 inches. Right: The same specimen two days later, showing more weathering and exposure of black spore mass and breaking up of cortex.

Left: The world record Fuligo septica measured a length of 30 inches.
Right: The same specimen two days later, showing more weathering and exposure of black spore mass and breaking up of cortex.

Keller, H.W., B. O’Kennon, and G. Gunn. 2016. World record myxomycete Fuligo septica fruiting body (aethalium). FUNGI 9(2):6-11.

Share Button
Posted in Research | Tagged , , , , , , , | Leave a comment

BRIT’s Computer Vision(aries)

This summer, four high school students from Trinity Valley School interned at BRIT through our Junior Volunteer/Intern program. These students were given the task of applying their computer science background to the challenge of helping BRIT create a quick and easy way to determine the fullness of our herbarium cabinets. By better understanding the details of the capacity of the cabinets, BRIT will be able to strategically plan for future growth and management of the herbarium collections.

CompVis1

L to R: Ashia White, Kevin James, Jason Best, and Jacob Haydel

I worked with students Grace Beasley, Jacob Haydel, Kevin James, and Ashia White to explore the process of using computer vision technology to analyze images of the open cabinets. We set out to extract details of each cabinet’s structure and the height of each stack of specimens within the cubbies of the cabinet to determine how much space is available for use in the cabinets. The students also created a powerful graphical interface for visualizing the cabinet data once they are generated.

The students already had experience with Processing, a software platform which facilitates the creation of software with rich and dynamic user interfaces, so we chose this as our primary tool for the project. Fortunately, Processing also has a number of additional modules which helped the team manipulate and analyze the images. In particular we used two modules that are focused on computer vision technology: OpenCV and BoofCV.

faceswap

The popular app FaceSwap involves similar technologies as those being used for this project. Photo credit: John Woods (Woodsie TV @ YouTube)

Computer vision technologies are used for many applications ranging from self-driving cars, to robotics, to entertainment, and much more. For our particular challenge, we used computer vision techniques to analyze the images of open cabinets to first find the boundaries of the cabinets and the cubbies, then to identify and measure the spaces that were filled with specimens. The computer vision modules provided all the tools we needed to do this, but we still had to experiment a lot to find the right combination of tools and methods to get consistent and accurate results. We haven’t yet found the perfect formula, but we are very close to a solution that we hope to start using soon.

 

To perform a full herbarium capacity analysis, we’ll need to capture an image of every cabinet in the herbarium (something we hope to recruit our loyal volunteers to help with), then process them with our computer vision solution. In the end, we’ll have a dataset with a record for each cubby and the percentage fullness of that cubby, as well as a total fullness percentage of each cabinet. With those data, we’ll have a much better idea of how much room we have to grow and how to strategically organize our collection to more easily adopt orphaned collections. To better understand this huge amount of data, the team also created a graphical interface that helps visualize the data in a more intuitive format. In particular, we created a herbarium “heat-map” using Processing which can read all the capacity data and superimpose color-coded cabinets on a herbarium map (pictured below). The interface also lets you click on a cabinet and see the details of each cubby and eventually we’ll combine this with the herbarium inventory data to let you see what species are in the cabinet.

A heatmap of the BRIT herbarium showing cabinet fullness.

A heat-map of the BRIT herbarium showing cabinet fullness. This was created in Processing and uses simulated data, but the interface itself is fully functional.

The project still has a ways to go before we have a final, polished tool ready for use by the herbarium, but several of the students are eager to continue their efforts beyond the end of their summer break. Below, Jacob and Kevin share their summer experiences.

Jacob Haydel

Going into this project for BRIT, I didn’t really know what to expect. I hadn’t really done any work with computer vision, but I was eager to get started. The main thing I have learned from the project is that programing as a team is very different from working on an individual project. When working as a team you have to make sure everyone is on the same page and agrees on the direction the project should go. I also learned a lot about the problems that face BRIT in the digitization process. Taking a written format and converting it to a digital one can be a very tedious process; however there are huge benefits to digitization.

Working on the program, at first we had a really simple goal, to figure out how full the cabinets were. As we progressed we slowly started adding other goals to our original goal and expanded our idea of what this program could do. Despite this we were able to incorporate most of the ideas we came up with, and I think when the final program is done it will be much better than we initially imagined. I have really enjoyed working on what I would consider my first real world project in programing. It has definitely solidified my desire to pursue computer science as a career.

Kevin James

Going into this project, I wasn’t too sure how we were going to approach a project on such a large scale as this one. To begin, we learned the basics of computer vision and data visualization. Over the summer, we mainly worked on the data visualization aspect of the project, using fake data to test our program. We now have a heat map of the BRIT Herbarium, as well as a program that lets us view the fullness of individual cabinets. We hope to continue to expand this program, and we also hope to find a reliable method to obtain accurate data from the herbarium.

Our group faced the challenges that come with working on such large code as a team. This included changing specific parts of the code without unintentionally altering the entire program. We eventually learned how to work together more efficiently, and we managed to make a working program to display our herbarium data. This project was a very rewarding experience for me because I got an opportunity to use my computer skills in the real world.

 

Share Button
Posted in Herbarium, Research | Tagged , , , , , , , , | Leave a comment