Thursday, 6 December 2018

Night at the museum ....

Last Friday, we were at the Natural History Museum Lates event, the monthly NHM public 'open house' events showcasing new science: people drop in, have a drink, chat to scientists, talks, interactive sessions etc. This one was showcasing NERC science, and in particular the 2018 Impact Award nominees. My NCEO colleague Shaun (Quegan) was up for the Economic Impact award for leading the ESA BIOMASS mission, and I was helping out on the stand, showing the TLS stuff we're doing for BIOMASS cal/val. BIOMASS is being built by Airbus in the UK under a 180M contract from ESA. So, definitely impact, and Shaun went on to win the award on the Monday - yay! We had a stand with a film produced by Sheffield University, a model of the sensor from the Airbus team, some tree discs, my 3D movies and the ZEB-REVO, and movies of deforestation impacts from Joao Carreiras (also from Univ of Sheffield).

My son Rudi came along for a mooch about and I got him to make himself useful and collect some ZEB data in the NHM main hall. He did a great job.

Section through the NHM main hall, whale in view, with people milling about below. Scan R. Disney.

Looking down from the balcony. The NCEO/BIOMASS stand is on the opposite side, just above the whale's head. The giant globe is the Earth installation by visual artist Luke Jerrans - which was also spectacular! Scan by R. Disney.

Walk-through of the ZEB-REVO data collection. Animation by Phil Wilkes.

The sketchfab models are pretty nifty too (as always).

We had a lot of visitors to the stand - Shaun and I literally didn't stop talking from 6-9:30. Not *that* unusual for me, but definitely for Shaun! We had lots of great discussions and questions from visitors and I really enjoyed it (which is the main thing). The event seemed really successful, with about 3500 visitors on the night, and capped with Shaun's win at the award dinner on the following Monday.

And meanwhile, congratulations to the NASA GEDI team - successfully launched to the ISS on 5/12/18 - let the lasering of forests commence! Great news.

Friday, 30 November 2018

You can't make an omelette without .....

Destructive harvesting in Brazil

A few updates on some of our activities over the past month or two. Most excitingly, this involved a destructive harvest experiment in Caxuianã, where we first scanned in 2014. Andy and Matheus led the experiment to scan, cut down and weigh four large tropical canopy trees. The aim of this work is to provide the best TLS estimates of tree volume we can, and to compare these with the harvest values. We also wanted to make measurements of wood density, as a function of tree diameter and with height. Wood density is critical in going from volume to mass of course. But it can vary a lot within and between species and even within a single tree. In the hyperdiverse tropics, the relative lack of wood density measurements may be one of the big uncertainties in forest biomass estimates based on allometry - size-to-weight relationships - that convert tree diameter (or height from satellites) to biomass. That's ALL the estimates then.

Here is a 46 m tall, 20 ton tree coming down. The team did an amazing job of clearing around the tree to give a fantastic, clear view with the TLS - some of the best data we've ever been able to get for a tall tree like this. This is a highly-skilled job as you can see.

I very much have mixed feelings about this - it's hard to watch a tree like this coming down and knowing you're responsible for it. The flipside is that if we can show how TLS can work in weighing trees like this, we can massively improve our estimates of global forest carbon stocks, particularly in the tropics where few trees of this size have ever been weighed - and none have been done like this with TLS in the Amazon.

The tree weighed over 20 tons wet, probably half that dry, of which half again (~5 t) is carbon. Early results show the wood density is a lot more variable than we'd ever expected - a problem for converting volume to biomass with a single value, but really interesting in scientific terms. Regardless of the mechanical properties, it's easy to see why these trees are so commercially valuable just on the basis of the beauty of the wood.

Prof. Lola da Costa (far right) and the chainsaw team weighing a large. and beautiful, piece of hardwood trunk.

Matheus (front left) and the team with the results of cutting up the tree above. Giant heavy beermats.
An interesting aside - when we came back, Feng Yin pulled down the Sentinel 2 satellite data covering the period the harvesting was going on - a few days before and over ensuing couple of weeks. Amazingly, the gaps due to felling 3 trees can be seen from space at 10 m resolution! The NDVI images highlight this even more. A sobering thought - 3 trees and some clearing leaves a hole that can be seen from space.
Sentinel 2 images showing the site and the tree harvest area circled: dates are 26/09, 1/10, 6/10, 26/10.

NDVI generated from the images above, highlighting the holes in the canopy.

Early analysis by Andy and Matheus already shows some amazingly clean point clouds from the TLS, which will allow for high quality reconstructions and estimates of volume from the TLS. The wood density is also showing some very interesting variations!

Huge thanks to Lola da Costa who organised the local teams - without him this wouldn't have worked at all. Also huge thanks to Patrick, Lucy, Ingrid and the local crew.

New papers

Our leaf angle distribution (LAD) paper came out in AFM, which shows a new way to get at LAD from TLS and comparing this to a photographic method. LAD is an important parameter in understanding canopy photosynthesis. But it's very hard to measure so it's often assumed to be simply distributed to make life easy (and because we don't have any other info). This work was largely led by Matheus and Jan Pisek, applying Matheus's leaf-wood separation to TLS data from Kew, and comparing to Jan's photographic method. It shows that the TLS method does surprisingly well even for small leaves and odd morphologies.
Figure 8 from Boni Vicari et al. (2019) showing the TLS point cloud, separated leaves and extracted leaf angles.
Here is a 46 m, 30 ton tree coming down. The chainsaw team did an amazing job of clearing around the tree to give us a fantastic clear view with the TLS - some of the best data we've ever had of the upper part of a tree like this. This is a highly-skilled job as you can see.
Two other papers accepted for publication are Andy's paper on treeseg, his tree extraction tool for TLS data; and Matheus's paper on leaf-wood separation, as part of his lidartf tool development. These are both potentially really useful tools for anyone working with TLS in forests. More on both those soon. 

Lastly, my Tansley Insight piece in the New Phytologist, on the potential for TLS in plant science, has come out. I've had some very nice feedback from people on it, mostly to do with figure 1, the montage of trees sketched by my daughter's primary school class! People really seem to find it relatable - which was the original idea, but you never know if these things will work or fall flat.

Monday, 17 September 2018

Summer sun, rain, wind and trees

**UPDATE 18/9/18** Ollie Baines won the RSPSoc President’s Prize for the best oral presentation of his MSc Remote Sensing dissertation project, estimating London’s urban forest cover, at the NCEO annual conference, Birmingham, 5-7 September. See below for more details.

**UPDATE 2**
See Phil's beautiful Sketchfab model of the Curtain Fig at Yungaburra, scanned by he and Allie during the recent work in Aus. That is an *amazing* tree.

It's been a busy summer for the various teams we have out there measuring trees. It started in July with Andy and Allie off to Malaysia, with nary a hiccup. Oh, other than our kit going missing for 2.5 weeks in transit. It got there in the end, but that wasn't in the plan - Andy and Allie just got started than had to come back, to be spelled by Phil. This is part of our NERC project measuring large tree architecture to understand the relationships between form and function, with Yadvinder Malhi, Lisa Bentley and Brian Enquist.
Allie and Andy, trying out the new tree QR codes for automatic tree recognition from the lidar data. 
Allie with our collaborators in Malaysia.
So in this case, the aim is the structure of a smallish number of specific trees, for which there are traits measurements, rather than 1 ha plots. This involves making sure we can ID the specific trees, so Phil developed some fancy new QR codes. We've always thought that being able to ID the trees automatically from the lidar *must* be the way to go, but Phil's worked out a good way to do it - QR codes that are big enough to be recognised automatically in image data form, even as point data.

Once again, *who* chose this plot? Some "challenging" terrain shall we say. 
Allie and the team in the field. 

Allie and Phil then moved on to Australia, northern Queensland, to some of the plots where Kim Calders and the Ghent team are also working. We're working with them to double up on TLS measurements, along with Harm Bartholomeus and the Wageningen Ricopter team. Although again, some shipping issues have led to a few delays. What is it with UAVs, batteries and paperwork??

The methods we're using here involve destructive branch sampling. So first of all some bowskills are required - Phil "Katniss" in action here, so end up a line and snag a branch for climbing and cutting.

Then the branches are placed in a lab, or the lounge of your AirBnB, to get no wind & stable lighting conditions, to capture high resolution lidar scans as well as 360 photography for SfM point cloud reconstruction. Allie prototyped this method back in the UK and it seems to work really well thus far.

Meanwhile, all these measurements have led to us thinking about 'extreme' trees - what the drivers of morphology are. So, while soil type, terrain, competition, herbivory, snow, rain etc. all have their place - wind can do funny things. Here's a 'tree' from a Pembrokeshire clifftop that kind of illustrates just how plastic this morphology is. A few 100 m away, in a more sheltered part, these hawthorn trees grow quite straight, up to 10 m or so in height.
Any way the wind blows, doesn't really matter.
Andy and Matheus are preparing to go off to Caxuianã to do some destructive tree harvests. We have axes, tarps, straps, logging tools. And this. Can hardly even lift the weighing scale it's so heavy!

Meanwhile, we have had various MSc students working with us over the summer on a variety of lidar-related topics (not all TLS for once!). Wanxin Yang did some very nice work using our PiCUS sonic tomography instrument on some trees in and around UCL to try and understand if and how it can be used to make more quantitative measurements of wood density. This approach has been used for quite a while by forestry professionals to indicate the status of trees (damage, hollows etc). But if we can use relatively quick, non-invasive measurement like this quantitatively, this would be very useful for biomass and structure studies more generally. Wanxin's work has shown some very interesting results - more on that soon.
Measuring wood density of Plane trees (L, R) and lime (Centre) in and around UCL. Picture: Wanxin Yang, UCL 2018.
Quantifying how hard the nail is being hit with the sonic hammer (yes, really). Picture: Wanxin Yang, UCL 2018.
Meanwhile, Oliver Baines was doing some excellent work mapping London's trees in terms of number, height and % cover, by combining the EA lidar data with Landsat, and some up-scaling. More on that later too. Olivers' headline figure is just over 9 M trees, which is slightly higher than current best estimates but very much in line with our recent work in Camden on this. 
Trees per unit area, at 30m resolution across the Greater London Area. Picture: Oliver Baines, UCL, 2018.
Oliver's work is something we want to take further, with other lidar and EO data and comparing to ground-based TLS estimates particularly for height and crown-size validation. The numbers on tree height and canopy cover have some quite important implications for valuing and managing (& hopefully expanding!) urban green space. More on that soon as well.

Both Wanxin and Oliver presented their work to the NCEO National Conference in Birmingham early in September, and generated lots of interest.
Wanxin Yang presenting her work on the PiCUS and wood density.

Oliver Baines talking about London's tree cover.
Phil's poster on the ZEB-REVO work in Peru.

Tuesday, 26 June 2018

The Amazon on your doorstep

Our first slice of urban work, led by Phil, is out this week in Carbon Balance and Management (Open Access). We used a combination of TLS and the UK Environment Agency open lidar data to estimate the C density over the London Borough of Camden. We show that the 85K or so trees in Camden have a median C density of 50 t/ha, rising to 380 t/ha in spots such as Hampstead Heath and Highgate Cemetery.
Map of London Borough of Camden, showing the study area.

These are values that wouldn't be out of place in the Amazon, albeit over very small areas. The figure below show the C density over the whole borough.
C density across Camden.

Comparison of Camden C density values to other biomes.
The important aspect of this is not the total storage - clearly we are talking about small areas here! - it's that we are probably undervaluing the C storage capacity of trees in urban areas. And because we can choose where and how to plant them and can manage and protect them, they can grow very large and live long (and prosper). The other aspect we've found is that using allometric (size-to-mass) relationships for non-urban trees to estimate the mass of urban trees is problematic: due to their environment, urban trees have their own weird and wonderful shapes. TLS is the way to help quantify those differences.

I've written a piece for The Conversation on this work, which seems to have gone down well, and there's been some excellent coverage of the article including the Times, and then online science and tech blogs (, Metro, Reddit - 15K upvotes and counting!).

Various people who are involved in actually planning and implementing policy on protecting and managing urban trees were kind enough to provide quotes about our work:

Sir Harry Studholme, Chair of the Forestry Commission:
The trees in our cities are important. They matter because they are close to people and are a key component of our urban environment providing beauty, shade and homes for myriad species as well as absorbing carbon and pollutants. The work being carried out at UCL is adding colour and detail to this understanding.

Dr. Kieron Doick, head of the Forest Research Urban Forest Research Group:"Urban trees are a very important resource for all those who live in, visit or work in towns and cities, for they provide us with a plethora of health and well-being benefits, and they keep these places cleaner and more attractive. Canopy cover values released last year show that for some areas the abundance of trees is also higher than in the countryside (averaging: 16% (towns) and 10% (pan-England in 2016)). This means we should expect our urban trees to also be providing us will an important carbon sink, helping to combat the global trend of increasing carbon dioxide in the atmosphere. This new work by UCL is a welcome development in advancing this understanding, and I look forward to hearing how the work continues to develop."

Councillor Adam Harrison, Cabinet Member for Improving Camden’s Environment :"Camden is really pleased to partner with UCL, based in the borough, in order to unlock the benefits of trees not just for our own residents but for people's benefit round the world"
We want to expand this work to other cities, both in the UK and elsewhere. Clearly, C storage is just one of the ecosystem services provide, and by no means the most important. But, if we can assess their value more effectively in all ways, hopefully it will help us plan and build better, greener cities.
Scanning in the urban forest, Hampstead Heath.

Wednesday, 9 May 2018

The Future Starts Here

The new V and A exhibition "The Future Starts Here", which includes some of our lidar work, had its preview and VIP opening yesterday. It's quite a spectacle, with some amazing exhibits. The opening also had its fair share of VIPs and famous faces. And me. :-) 

Museum director Tristram Hunt opening proceedings.

And here we are! Our lidar animation from Caxiuanã, originally generated by Andy.
I was approached by Rory Hyde, one of the curators of the exhibition along with Mariana Pestana, who wanted to include our 3D lidar work from tropical forests, as an example of how new technology is allowing us to understand and hopefully manage our world better.

Other work included in the exhibition includes: a chargeable shirt which can power a phone; a drone ship which can clean up oil spills; an autonomous flying wing intended to cruise the skies using solar power and broadcasting internet access to remote areas; AI bots intended to help mediate and hopefully improve political discourse and democratic process. Lots of fun, thought-provoking and definitely worth a visit if you're in London between now and November.
Aquila, the flying broadcast drone: as being developed by Facebook, obvs.

A man-made leaf that photosynthesises.
Our work also features in the glossy accompanying book, and it's quite a thrill to see it amongst all the other incredible ideas and technology. I got to speak to some very interesting people whose work was also featured, as well as people passing who were interested in my work. There may be more connections arising out of this yet!

Point cloud included in the glossy (£25!) book accompanying the exhibition.

Thursday, 3 May 2018

The Colonel Armstrong Tree

This is the biggest tree (well, tallest) we've scanned and processed so far - the majestic, huge Colonel Armstrong Tree, in Armstrong State Park, CA. The tree is apparently 308 feet tall, although our lidar measurements suggest it's slightly shorter (90m or around 290 ft). Either way, it's MASSIVE. The point cloud is incredible, particularly the detail of the lower trunk. Andy has left the sign in at the lower part of the point cloud for scale - the sign is about 1.5m high.
The base of the tree: (image Roy Tennant,

Here are some quick screengrabs of the point cloud showing the amazing detail.

Event horizon. Or inside the giant.

Close up of trunk about 1/3 of the way up.

Another trunk close up showing some of the small epicormic branches.
Finally, here's the link to the Sketchfab point cloud. I can't get the smile off my face when I look at this. For anyone who wants to find out more about these extraordinary trees (and they really have some amazing ecological secrets) I thoroughly recommend Richard Peston's The Wild Trees, an account of a band of climbers, ecologists and enthusiasts like Steve Sillett and others, pioneered the climbing, measurement and understanding of these trees in the 1980s and on.

Wednesday, 2 May 2018

Ham and High: May Day fun

Activities close to home this week, with some scanning on Hampstead Heath to measure some of the coppiced oak woodland with our Riegl VZ400, on a gorgeous clear spring day. As befitting May Day and notwithstanding the ridiculous wintry temperatures and torrential rain the day before, this was as good as it gets. Hiding away in the well-heeled suburbs of Highgate and Hampstead, this is a real oasis in the city. Most of the trees are relatively young (20th C), but a couple of them, slight hill in the background below, are more than 200 years old.
One of the lovely secluded oak stands, within earshot of the busy Spaniards Road. Crystal skies.

Looking up through the crowns. Is that a cloud?
We're aiming to compare our estimates of biomass in the woods here with those from the local surveys done by the estate management. This has to be one of my favourite bits of London.

Earlier that morning, I visited my daughter Lotta's school to talk to the Year 3s about trees. It's their Science Week and they're studying trees in and around the local area, including Epping Forest, which has the famous Gilwell Oak, the UK's 2017 Tree of the Year (yes obviously it's a thing!) and a nominee for European TOTY 2018. I showed the children some of our work, some of the oldest and largest trees in the world, and the UK. They seemed to enjoy finding out about the people and animals that live in forests around the world very much! I even took our ZEB REVO in to scan them while they 'stayed still'.

ZEB Revo scan of the Jubilee School Year 3s listening intently with the adults sitting at the back (left).

Sunday, 25 March 2018

Inside and out

The last few weeks we've been without our Riegl TLS which is being serviced. It's survived being dragged through forests all over the world, but it obviously needs a bit of TLC, particularly the batteries. This has given us a chance to work on processing some of the backlog of data we've already collected, as well as look at using our Picus sonic tomograph to look at the inside of some local trees, and think about the whole issue of wood density. We've had Oscar, a high-school student, with us for the past two weeks, doing work experience as he heads into his GCSEs. We've had Oscar manually pruning some of our tree point clouds from Gabon - tiring work but he's done a bang-up job. We did allow him out from behind the desk for a bit though, to look at some of the trees in Russell Square. It's certainly a good way to meet some interesting people who want to know what we're up to. And as anyone who knows me can confirm, I'm always reluctantly prepared to talk about what we do. Cue mildly curious passers-by backing away with glazed looks on their faces.
Oscar fixing the Picus to a large plane tree in Russell Square.
This one appears to be sound, as are most of the trees in and around Camden. This isn't surprising given that they are carefully monitored just in case they do develop imperfections, weaknesses and so on, which might require surgical work, or even felling in extreme cases. We're on the look-out for trees which do have imperfections, to try out our analysis of the Picus data. We have a number of UCL Geography MSc students working on our tree data this summer. Hopefully they will make some good progress on various aspects including: urban biomass from ground-based and airborne lidar, inter-species differences in tree form between urban and woodland, crown structure and filling, uncertainties in allometry due to imperfections in tree density and extrapolating biomass estimates from Camden and Islington across London and beyond using satellite data. More on all this soon!

Thursday, 15 February 2018

Royal Society Super Special Issue on TLS

The special issue of the Royal Society Interface: Focus covering our meeting last year, is published today. The special issue has many excellent papers from our colleagues and collaborators, check it out - it's great! :-)  Special mention should go to Mark Danson, who proposed the meeting in the first place, secured the funding for it, and then has written the issue intro paper. Well done Mark and well done all! I've been doing various press interviews in advance of publication today, so hopefully will be able to collate some of those here later.

The image below from our work at Wytham Woods is on the cover, and the various papers led by meYadvinder and others, have examples of our work from Wytham, Gabon, Ghana, Brazil and Borneo.  

Top down view of 1ha of Wytham Woods TLS data (Fig 2a from our paper); image produced by Kim Calders, then at NPL (who funded that work through EU METEOC-II), now at Ghent.
It also has some of the amazing plots of point clouds including the sycamore with 11 km of branches.
Figure 3b from Disney et al. Sycamore from Wytham Woods.

and Yadvinder's paper has the huge 60 m wide, 100 ton Gabon moabi, alongside a much taller but narrower dipterocarp from Borneo.
Figure 7 from Malhi et al.

Some of the press coverage from these papers is here:

we also had interviews on Sky Radio, BBC Wales and various others.

Wednesday, 17 January 2018

Celebri-tree ....

Back to Kew on a chilly morning with Phil, to meet Tony Kirkham, Kew’s hugely knowledgeable and accommodating Arboretum Director. Tony invited us to come and scan one of Kew’s Champion trees - the tallest Chestnut-leaved oak in the UK. And it’s quite a specimen - I’ve not seen Quercus castaneifolia close-up before and this one is over 35 m tall and with some amazing secondary stems and boughs.
Quite the character.
It was a classic chilly London morning, but there’s worse places to work. I always learn stuff when I’m at Kew, particularly when I'm with Tony, about the trees themselves and their history and ecology but also about how trees like this need to be so carefully managed: air-blowing the soil around the roots to aerate them; pollarding the middle of the crown so it acts less like a sail in high winds, reducing stress on the trunk. And today’s word of the day 'Balanocultures: people that depend on acorns as a staple diet'. Also found out that the word Druid means ‘to know the oak’. Trees eh?

UPDATE: check out the beautiful 3D model Phil has produced, showing the tree in all its glory. Turns out it's 36.5 m tall.

Good times.

Phil and I also scanned a sweet chestnut of unusual shape, which apparently featured as the model for the Whomping Willow in the first Harry Potter film. It’s not a willow, but it’s still a cool tree.

Funny looking willow.
UPDATE: closeup visualisation of the trunk of this sweet chestnut.

Wednesday, 3 January 2018

Trees and champagne

Happy New Year and welcome to 2018. Well, 2017 was a doozy and finished off with the very enjoyable aspect of seeing our work appear on the Judi Dench: My Passion for Trees. The programme seemed to go down extremely well, with seemingly universal outstanding reviews (see here, here and here for example, as well as my personal fave: "Come for the lols, stay for the poignant thoughts about death."). We've already had some interesting feedback. As well as some "interesting" feedback 😁. It was certainly quite entertaining following #MyPassionForTrees trending on twitter on the 20th December! There's definitely some new possibilities opening up as more people see this work. More to come this year I think!

Meanwhile, Andy's been busy pulling out trees from the California plots. This is a snapshot of the 20 largest stems from the Grove of Old Trees, the first plot we scanned there, and an absolutely stunning place to work. These trees range from
Twenty sequioas from the Grove of Old Trees, Sonoma, California.
Meanwhile, we're off back to Surrey, Kew and then plans for trips back to Malaysia, Brazil and elsewhere. Onwards and upwards. Trees and champagne for everyone!