Friday, 8 December 2017

Judi Dench: My Passion for Trees

It's not often you get to use lidar and Dame Judi Dench in the same sentence. But we've been lucky enough to work on a new documentary presented by Dame Judi, to be shown 20th Dec BBC 1 8pm, and featuring some of our lidar work. The program follows Dame Judi on a journey to some iconic English trees and woodlands, to find more about their history and biology, what goes under the ground, under the bark and up in the canopy. It's a very beautiful film with some very interesting science: the sounds of transpiration, canopy response to predation, and the fungal communities that seem to facilitate communication of resources and even 'information' in some senses, between trees.

We visited Dame Judi's garden last summer and scanned a 200 year old oak tucked away in a wild corner. We then estimated the mass of the tree, and its leaf area/count - 25 tons and 260k if you're interested! We then generated a nice fly-through of the garden and around the tree, which then talked through with Dame Judi - she was suitably impressed by the detail. Interestingly, our estimate suggest the tree has 12 km of branches, more than any other tree we've come across, even in the tropics.
Press shot of Dame Judi in bluebell wood, from: 

Phil and I working Dame Judi's garden. The oak tree in question is in the background.
The program was made by Atlantic Productions, and is beautifully done - not too heavy on the foley sounds either :-) Anthony Geffen, CEO of Atlantic, gave our lidar a nice plug before the preview screening at Kew, and the whole event was introduced by Richard Deverell, the director of Kew. Alchemy VR also made a fantastic VR fly-through of our lidar data, which they had running at the drinks reception after the screening. Phil and I were blown away - *THIS* is how you have to view all lidar data! Dame Judi also seemed suitably impressed by that - who wouldn't be? BBC Arts have handily put the extended version of this up on their FB page:

Dame Judi looking at our VR lidar, watched by Anthony Geffen, CEO of Atlantic. Thanks to Alchemy VR.
The screening was also a fascinating chance to meet some of the people who were involved in making the program, particularly Tony Kirkham head of Kew's arboretum. We'll be back at Kew in January scanning one of Tony's icon trees.

Meanwhile, here's a 3D model of an example oak tree scanned by us.

Wednesday, 11 October 2017

BBC docs featuring our work

I've just noticed that two BBC documentaries featuring our work are available in HD on youtube. "Nature's Greatest Survivor" from 2015, presented by Dr. George McGavin, describes a year in the life of an oak tree on the edge of Wytham Woods. The upload seems to have been slightly speeded up in compression, so unfortunately sounds a bit Mickey Mouse, but hey, the visuals are still great ;-) Our work features from the start.

Life and Death on Your Lawn screened earlier in 2017, presented by Chris Packham, and describes the hidden world of biodiversity in suburban gardens of Welwyn Garden City. Our work features from about 1:15 in.

Saturday, 30 September 2017


I've been in Kourou in French Guiana this week, at a workshop on Remote sensing for tropical biodiversity mapping and management across scales, organised by Jérôme Chave from CNRS, Toulouse, and Grégoire Vincent, IRD, Montpellier. The thematic workshop is funded as part of the CEBA Centre for Study of Biodiversity in Amazonia programme here in French Guiana, and the idea is to bring together early-career scientists, interested in these topics and selected based on a proposal to work on a specific application, with a cross-disciplinary 'faculty' including David Coomes (Cambridge), Maria Joao Ferreira dos Santos (Uni Utrecht), Jean-Baptiste Féret (IRSTEA) and Sassan Saatchi (JPL). The aim is that by bringing together a relatively small group, and addressing specific, focused topics at an almost 1-1 level, rapid progress can be made by sharing tools and methods, adapting/trying new code and methods, as well as for thinking about some of these areas in new ways. From what I've seen, the workshop has been extremely productive and successful - ideas mulled and tried out, papers proposed, data munged, connections made.....

A fuzzy view of afternoon discussions in the lab. As seen by the ZEB-REVO in double quick time.

Paracou field station, from lidar from above.

It's been a fantastic week - a real privilege to be invited and to catch up with some old faces, and meet many more new, particularly the incredibly bright and enthusiastic participants. It's certainly provided food for thought for me, even if that isn't the main aim :-) I've seen new work on demographics, different ways of considering diversity & species richness, the wide range of conceptions of forest 'structure' (there's so many ways to look at it!), acoustic mapping, wood density and growth rates, overstory, understory, lidar, hyperspectral, modelling and on and on. I can't wait to follow some of this up. The one downside? During a day visit to see the work at the long term Amazonian tropical field station and Guyaflux tower at Paracou, I managed to pick up some very unwanted and irritating passengers in the form of Trombiculidae, or chiggers. Aaargh.

Lidar view of the Guyaflux tower at Paracou.

As a serendipitous bonus, we were lucky enough to get a last-minute tour of the Ariane spaceport just up the road (the main industry around here), the day before a scheduled Ariane launch! This had been delayed from a few weeks ago, apparently just for our benefit, on a balmy Friday evening. Sitting on the beach with the sun going down behind us and watching a spectacular launch was a fitting end to a great week. Props to Jérôme, Grégroire and Jessica (the tireless organiser) for sorting that out. The only slight hiccup was the small earthquake yesterday morning which surprised us all - no harm done though.

The gang - at the space centre.

Friday, 22 September 2017

They might be giants

So, here's the first example of one of our Sequoia sempervirens TLS data. To say I'm excited would be somewhat of an understatement. No one has seen these trees like this before, and there will be so many things to look at from these data. The data are just stunning, and this doesn't do data to them but still .....
I get a cricked neck just looking at this!
The tree is ~80 m tall, and 16 m across the crown. Phil generated a first estimate of the volume which suggests it's ~80 m3, meaning it weighs about 40 tons! And 50% of that volume is in the lower 20 m of the trunk, perhaps unsurprisingly given its shape.

Meanwhile, here's a great example of Dave's 14 GoPro 360 photo setup.
Can't say we look good, but the trees certainly do. Remember, never go full lumberjack Andy.

Dave developed his Terrestrial Recording of 3D 360 Surveys (TR33S) system under funding he was awarded through the Universities Space Research Association (USRA - Columbia, Maryland) Internal Research & Development Program. The TR33S collects pictures in every direction by linking the 14 cameras together. The 360 photos are great, but more generally Dave is aiming to capture 3D point clouds using structure-from-motion (SfM). SfM is a photogrammetric technique that can model a 3D space from 2D images. It's widely used for UAVs but this is the first time I've seen it used like this, and there are some potentially great applications in forest research like this! Dave has written about his work with the camera on the NASA blogs: Below the Mangrove Canopy; and Mangrove Carbon With a Grain of Salt.

Saturday, 16 September 2017

Everything's bigger in America

... or so my kids have told me. Andy and I have been having an amazing time scanning here in CA, with our NASA/UMD colleagues Laura Duncanson, David Lagomasino, and John Armston. We've managed to scan 8 x 0.25 ha plots as part of the NASA Carbon Monitoring System project, following Laura's protocol for the GEDI cal/val. The others have been measuring stems in 25 m fixed radius plots (i.e. single GEDI footprint-sized) overlapping within each 0.25 ha. Meanwhile, Andy and I have been doing the TLS - 1ha in two locations, and then in Armstrong Redwoods State National Reserve, using smaller 0.25 ha plots due to the constricted nature of the site (paths, valley, road).

These trees really are amazing. It's perhaps too easy to bandy around words like 'majestic' or 'spiritual' and so on, but there is something quite primal about being here. And amazing (and sad) to think that this whole area was covered with giants like this not much more than 100 years ago. Also incredible to think about the effort required to fell and remove one of these things, with nothing more than handsaws and some horse-powered carts and trucks. And a lot of labour of course.
"That's not a tree maayte, THIS is a tree"

"We're going to need a bigger DBH tape"
Some of these trees are HUGE - approaching 100m tall and 4m in diameter or more. They have amazing structures, roots, fire damage and I literally can't stop looking at them - my neck hurts from looking up.

Interestingly, the largest/tallest trees as noted on the maps and guides may be taller/shorter than measured - we're waiting on the TLS to find out for sure. The recorded sizes are from 20+ years ago in some cases so that may explain some of the differences, but we already think we may have found a taller tree than the apparently tallest one, just off the beaten track a little bit. We'll see!

Meanwhile, Dave was deploying his cool 14 GoPro 360 shape-from-motion-on-a-stick set-up. Here's a 360 picture of us in the plot from the system - but I'm really interested to see some of the point clouds from this. He's got some excellent results from mangroves, so this is a liiiiiittle different.

I've even managed to rope the kids into doing some work - it's educational! 
Roots. Or as I like to call them "someone elses' problem".

Andy in classic fieldwork with TLS mode.

Never let people who aren't *doing* the TLS lay out the grid. Precarious.

Strange fire history - possibly due to a large 19th C fire caused by an explosion from an illegal whisky still - but hard to see how (or if) that caused the scarring, other than the burn.
It's been a stunning field visit and I can't wait to see the data. It will be fascinating to see where these very large trees sit on the allometry line - how variable they are and then to think about some of the issues of density and hollowness.

One of the interesting things about working in a very public location like this has been the interest shown by people walking past. I've given the "Weighing trees with lasers! Carbon! NASA! Science!" spiel so often that the kids have started calling me Steven Spielberg. School groups, retirees, local cops & park volunteers, runners, walkers, cyclists - the response has been almost overwhelmingly positive. People have been interested, enthusiastic universally extremely supportive of what we're trying to do, particularly in view of the current political and funding climate. It's rare to get such instant, positive feedback on your research! People *are* interested in science, particularly if they can see it in action and you can explain why it's cool and important.

Thursday, 7 September 2017


So this time we've come to California, to scan the largest organisms on Earth, the giant sequoias of Northern California. And what a sight they are.
Feeling very insignificant.
I always find big trees can have an overwhelming sense of scale - perhaps it's their size, coupled with the often (but not always) wilderness of the surrounding environment. But these are genuinely breathtaking - and at 60+ m are actually on the small side. Next week, we'll be in a grove with some of the 100+ m real giants. I can't wait! Meanwhile, myself, Andy, Laura Duncanson and David Lagomasino from UMD, will be working here.

Everywhere you look - just outside the front door.
We're here as part of a NASA-funded Carbon Monitoring System project led by colleagues Lola Fatoyinbo and Laura Duncanson of Univ. of Maryland and NASA Godard, and Amy Neuenschwander, from the University of Texas. The project, Future Mission Fusion for High Biomass Forest Carbon Accounting, is using data from Gabon, Costa Rica and here in the US to help calibrate and validate estimates of C stocks from a trio of new spaceborne sensors which will be launcched in the next 2 years, GEDI, ICESat-2 and NISAR. With ESA's BIOMASS mission also being launched around the same time, there is huge potential for combining these complementary new observations to dramatically advance our understanding of forest state, structure and biomass. We're working with the GEDI and BIOMASS teams, using our TLS work to provide key new observations of biomass and structure in a range of forests, but particularly forests with large trees and high biomass. Providing better measurements of biomass and structure will allow the GEDI and BIOMASS science teams to test their retrieval algorithms, and potentially develop better ones.

Even Andy is impressed by 3m DBH. A bit.
It's a lovely place to work - not just the forest plots themselves, but the surrounding landscape of hills, vineyards, rivers, and the coast just a few miles away. Fortunately we missed the heatwave of last week - 43 C isn't much fun in anyone's book - the landscape is totally parched after several years of drought and low rainfall.
Not much swimming here.
I've hired a bike to ride some of the amazing roads in the early mornings. I mentioned to the hire guys that the forecast mentioned it might even rain. They laughed: "Hasn't rained in 6 months. It's not going to start now". This morning?
Eerie, atmospheric. And wet.

I rode 40 miles and got absolutely soaked. But it was still beautiful - eerie and quiet up in the forest groves. At the risk of sounding corny, being among so many very old and very large trees and yet seeing so many charred, or rotting rotting hulks - remnants of even larger, older trees that were logged out and sold, does remind you of how fragile this all is. You can see why they were so attractive to the lumber men but once they're gone, they're gone.

Obligatory lidar forest shot.

And getting a 2.8m DBH. We've had 3+ already.
More pictures of the giants in Armstrong to follow. And David's cool 14 GoPro 3D camera setup, for capturing 3D data via SfM (niiiice!).

Wednesday, 16 August 2017

Scan you at the cemetery gates

Highgate Cemetery in North London is a grand, Grade I listed site, rightly known as much for its architecture, trees and wildlife as for its various famous residents. The latter include novelists George Eliot and Douglas Adams, political writers and activists include Karl Marx, musicians, poets, historians and scientists including Michael Faraday.
The Riegl scanner among the gravestones of Highgate Cemetery (P. Wilkes; K. Calders).
Perhaps less well-known is that, by our reckoning, Highgate Cemetery has some of the highest biomass per unit area in London. As a result, Phil, Kim and Matheus spent a day there recently using our Riegl VZ-400 to scan the highest biomass parts of the cemetery, so that we can capture the structure and biomass of some of its magnificent and unusual trees. They are unusual both in terms of some relatively exotic (by urban standards) species, as well because of the landscaping and architecture by which have helped to shape them, and which in turn they also shape.

Ivy roots (I think) clinging and enveloping a tomb, as well as a nearby tree.
The resulting data look good already, and the team have been producing some more elegant visualisations of the resulting data. Below is a flythrough of the TLS with the RGB from the camera; and following that, a nice timelapse of the scanner in action.

As we generate the results of the biomass estimation from the TLS, it'll be interesting to compare with the Environment Agency lidar tree locations and heights. I'm also intrigued to see where these trees sit in terms of their shape and size, compared to the ones from 'natural' woodlands as well as their definitively urban counterparts.

Tuesday, 18 July 2017

No ordinary view

Phil and I (and my put-upon son, on his birthday no less) spent a day last week scanning part of the Queen Elizabeth Olympic Park, to characterise the 3D structure of the vegetation in the park. The park is a legacy of the 2012 Olympics, and provides the first new parkland in London in over a century. Extensive landscaping has resulted in ".... over 35km of pathways and cycleways, 6.5km of waterways, over 100 hectares (ha) of land capable of designation as Metropolitan Open Land, 45ha of Biodiversity Action Plan Habitat, 4000 trees, playgrounds and a Park suitable for year-round events and sporting activities." (Legacy Communities SchemeBiodiversity Action Plan 2014-2019, LCS-GLB-S106-APP-BAP-001-V01, 2013). UCL has ambitious plans for expansion into UCL East. As part of this, our colleague Prof. Kate Jones and her team have been doing some amazing work using in situ sensors to map bat populations in the area, in real time. See more details of the project here.

By measuring the 3D structure of the park, we're hoping to be able to provide Kate and her team with information they can use to help understand the paths and activities of the bats in the park. And while we're at it we hope to be able to map and monitor changes in the trees and shrub cover of the park over time. Phil has produced some stunning fly-throughs of the data we collected. Given that we only scanned along about 200m of path in the centre of these animations, the far detail still amazes me! The views of the Arcelormittal Orbit, the London Stadium, and the front of the late Zaha Hadid's amazing Aquatics Centre, are pretty spectacular.

Fly through of Queen Elizabeth Olympic Park from Phil Wilkes on Vimeo.

Fly along the Lea River at Queen Elizabeth Olympic Park from Phil Wilkes on Vimeo.

Lastly, our work at Wytham Woods also features briefly in a series of short films showing the range of measurements going on using new technology in the so-called Laboratory with Leaves.

Wednesday, 12 July 2017

Life and death on your lawn

The new BBC4 documentary on Britain's Gardens that we featured in aired last night (available on iPLayer until August 2017). And slightly melodramatic title aside, it was excellent (despite me being in it) - really well-put together, thoughtful, and with some beautiful footage. Beyond the usual British garden staples - hedgehogs,  foxes, blue tits - there were some fascinating bits on snails, spiders and pond-dwellers.

The 3D fly-through that Phil produced from our lidar data looked really good on screen. Various HD versions of them are on vimeo:

LiDAR scan of back garden featured in BBC 4’s “Life and Death on the Lawn” from Phil Wilkes on Vimeo.

LiDAR scan of back garden featured in BBC 4’s “Life and Death on the Lawn” from Phil Wilkes on Vimeo.

LiDAR scan of back garden featured in BBC 4's "Life and Death on the Lawn" from Phil Wilkes on Vimeo.

And the resulting garden model, with RGB from the lidar camera, is on sketchfab:

Not bad for a day out in Welwyn!

Friday, 16 June 2017

Off to see DC .... as an artiste!

I was fortunate enough to be invited to Washington, by Prof. David Lapola and the AmazonFACE team, to show some of our images and data from the September 2016 trip to the Manaus plots.
Not a tree.
The meeting was hosted by the Inter-American Development Bank (IDB), and I was there primarily as part of the 'cultural', outreach aspect of the project, using our TLS data to show the forest in a new light, to other project partners, policy-makers and the public more generally. Matheus put together the lidar data, and we generated some animations and images which formed part of an installation in the IDB foyer. I was blown away to see the trees in the large banner formats, and in such grand surroundings. The pictures seemed to be very popular - I definitely wasn't the only one taking selfies, honest!
Some fool.

One of our trees, printed 3m tall.

The 4 piece banner and the fly-through Matheus and Phil produced.

People looking at the movie and the trees in the IDB foyer.
It was also nice to be able to get out and about in DC on the last afternoon, to take advantage of the sun and the DC bikeshare scheme (same bikes as London!) to see some bits of DC I've not seen before. I stopped in the leafy quad of Georgetown University - there's always time for a good tree pic.
Oak tree in the quad of Georgetown U.

How green was my valley?

In a slight departure from the usual applications of the TLS, I took the ZEB-REVO to Wales and scanned some places local to our house in Stackpole. The scan below is from the Stackpole Estate, a National Trust property with an interesting history going back several hundred years, and to the Thane of Cawdor no less!
Bosherston Lily Ponds from Stackpole Court.
Along with the iconic Bosherston Lily Ponds, the Estate has some beautiful woodlands and unusual trees, planted by the landowner in the 18th and 19th C. The Estate is a beautiful place to visit, in a breathtaking landscape. The scan below is of the front of the Stackpole Court itself, including two large, old oak trees. The old bell tower in the centre can be seen - these days a habitat for some rare Greater Horseshoe bats. There may be opportunities for scanning more the NT woodland here as part of a new citizen science project - watch this space.

Stackpole Court, scanned using the ZEB-REVO, coloured by height.

Thursday, 11 May 2017

Urban nurban
In amongst all the tropical work, we've been looking at some more urban and suburban trees. Phil has been leading work looking at London trees - more on that soon, but he's posted some great 3D models on Sketchfab including this amazing scan of Russell Square.

Some of these trees are pretty stunning - here's a montage of some of them extracted from the scans above. Particularly striking is the fact that they're all London planes, but they have such different crown shapes. So what makes a plane a plane or an oak an oak? It's the old nature v nurture / genotype v phenotype debate again - how plastic are these shapes?

A range of Plane trees extracted from the Russell Square scans above, ordered by size, with the estimated mass below. (Phil Wilkes)
We've also been looking at the now public Environment Agency lidar data over London, so we can try and pull out all the trees, to estimate numbers and even heights, to assess this firstly in Camden - where we're working with the tree specialists - and then city-wide. Early results are looking promising.
Trees located in the Environment Agency lidar data over Bloomsbury, coloured by height from brown to dark green (Phil Wilkes).
Meanwhile, we've been doing some scanning for a new BBC4 documentary, which aims to uncover the overlooked biodiversity of suburban gardens. The production team have spent a year monitoring and filming all aspects of life in a row of 7 contiguous back gardens in leafy Welwyn Garden City, one of Sir Ebenezer Howard's original New Towns, arising out of the Garden City movement. We've scanned one of the gardens in early Spring, to show the new leaves and the 3D 'bird's eye view'. Phil's lovely 3D view is great, with fly-throughs to come.

Meanwhile, Matheus has been running his leaf / wood separation code on the point cloud, to extract the leaf points, so we can estimate the leaf area on the trees. Here's a rather elegant little apple tree.

Thanks to Pat and Steve for letting us trample in their lovely back garden. We'll be back there soon to film with the team and discuss the results, and this will be aired in summer 2017. Exciting!

Deepest darkest Peru

The team are off to Peru this time, to the plots in Tambopata in the Madre De Dios region. As you can see, the site is in the Western end of the Amazon Basin, in the foothills of the Andes.

Andy and Kim set off in early May, and the expedition will be for another 6 weeks, with the aim of scanning some of Simon and Oliver Phillips' plots along an altitudinal gradient in the region. This is one of the areas where Alvaro, Jose et al. went to scan and harvest trees for the new MEE paper, as well as an area we will be retuning to for the new NERC structure grant with Yadvinder.
The last leg of the journey out (Kim Calders)
Walking to one of the plots, with a little bit of rain along the way (Kim Calders).

Intrepid science guys. Travelling light.

Wednesday, 29 March 2017

Borneo giants

This past month we've been working in Borneo, at a couple of sites including Sepilok and now Danum Valley. Both sites lie within the Sabah region of Malaysia, on the island of Borneo - somewhere I've always wanted to visit. Andy and Matheus started things off, and then I joined Andy, along with Toby Jackson from Yadvinder Malhi's group at Oxford. Toby is looking at the structural response of trees to wind flex measured using accelerometers, and by building CAD models. Toby is using our TLS data to help to build more realistic models, and he was helping us out with our scanning at Sepilok, and in return we are scanning some of his instrumented trees at Danum Valley.

The site at Sepilok has some of the largest trees I've seen in the tropics so far - we don't know yet hoe large the largest are, but I'm guessing a tree like this one will be nearly 60 m. Once we have processed the TLS data, we'll know for sure!

One of the large trees in a Permanent Sample Plot at Sepilok.

Another pretty large tree.

As for Danum, this is the location of the so-called 'tallest tree in the tropics'. There's been a bit of to and fro over the title of late. David Coomes, a colleague from Cambridge, found a Yellow Maranti tree of 89.5 m (dubbed the 'Minecraft Tree') using NERC ARF airborne lidar data collected for our teams in 2014. Then, along comes another colleague, Greg Asner from Stanford, with his Carnegie Airborne Observatory and finds many more trees over 90 m in the same area, including one of 94 m

The tallest tree in the tropics, another Yellow Meranti, shown in the CAO lidar data. Image: Nick Vaughn, Carnegie Institution for Science.
The tree's location has been kept quiet (for obvious reasons) but Toby managed to get out to see it - and here it is. It's very hard to judge the size without scale, but it's incredible how straight and even the trunk is. It's easy to see why trees like that are prized for their timber.

The largest tree in the tropics. Photo by Toby Jackson.
Not a tree, but a rather magnificent palm next to the field station.

 It's warm work, and on some of the steepest terrain we've worked on so far - slopes of 50 degrees at times. Who on earth would put a sample plot in such a place?? Simon ..... I'm looking at you.

Another tropical forest selfie - with Andy and Toby. We're dripping with sweat and we've only just arrived in the plot. I wasn't even carrying the lidar - I'm too old for that now ;-)

Friday, 10 February 2017

Lumps and bumps

Here is a short article in GeoConnexions based on the possibilities for using low-cost lidar for doing fine-scale DEM building. I should add that Phil and Andy did the scanning, so this is very much me taking credit for their work - sorry! The original PDF is here.

Wednesday, 8 February 2017

Ghostly stairs, and old Paris

A number of people have commented on the ghostly nature of the images that Justin pulled out of our Kew Palm House scans, particularly with the combination of the spiral staircase, the vaulted roof and the exotic trees. The combination of man-made and natural architecture seem to complement each another in an aesthetically appealing way. The fact that we were able to scan from the walkway at roof level is what gives the great detail of the Palm House roof, and the detail of the upper part of the trees in the centre. If only we could do that everywhere.

The full-length cross-section through the Palm House at Kew.
The ghostly staircase.

Meanwhile, on his way back to Vienna, Florian stopped off in Paris and managed to grab an opportunistic scan of the oldest tree in Paris. It is a Robinier pseudoacacia (false Acacia), or locust tree, planted in 1601 in the Square René Viviani, next to the Saint-Julien-le-Pauvre Church, also one of the oldest in Paris.
The Robinier False Acacia, Square René Viviani (from Wikimedia).

Overview of the scan of the square, church to the left and tree in the centre.

The Robinier False Acacia, planted 1601.