Wednesday, 21 December 2016

The shortest day ....

Here we are on the winter solstice - I can feel the day(s) getting longer already. It's been a busy year for lasering stuff, and next year looks even more so. Which is of course a good thing. Meanwhile, Phil's been busy summarising some of the adventures we've had, from Ghana to Gabon, Manaus to Morpeth (well, Harwood), Wytham to ... well, woods far and wide. His post for the NCEO blog is an excellent summary of our activities. Phil has also written a blog guide to airborne lidar for the BES journal Methods in Ecology and Evolution, where Kim's Eucalypt biomass paper is still getting lots of attention - 58 citations so far, and a nice little feature on the BBC Science page after the 2016 BES meeting in Liverpool.

So... next year - Borneo, Brazil, deepest darkest Peru, California for some of these (*very* excited about that!)
A giant redwood: image Michael Nichols, from
 Closer to home, we'll be working on some London-based tree mapping and modelling. Including this rather striking Hardy Ash, so-called because the odd skirting of gravestones were added by a young Thomas Hardy during railway works in the 1860s (where he earned his living long before he became a writer). The tree is tucked away in one of London's many, many little hidden gems, St Pancras Old Church, apparently one of the oldest Christian places of worship in England (may be 7th century). And incidentally with several other literary connections, including featuring in A Tale of Two Cities, one of my all-time favourite books. Camden Council are interested in measuring the tree and getting a view on how to best preserve it. Which is where we come in for our first work of 2017. From the old to the new.

Monday, 26 September 2016

FACE time

Our latest trip was to the Amazon again, this time to the ZF2 forest site, north of Manaus, central Amazonia.
Hellooooo Amazonia!

Field station at the ZF2 research site.

The Brazilian government are funding an extremely ambitious new Free Air CO2 Enrichment (FACE) experiment at the site, to try and answer the question "What will the Amazon rainforest response be to elevated CO2 levels over the next century or so?" See the Science feature on the experiment from May 2016.

Model projections of change in the Amazon over the next century. From Lapola et al. (2009).

These FACE experiments are a well-established, if logistically challenging way to take a peek into the future and look at large-scale ecosystem response to climate. FACE experiments are an attempt to duplicate the kind of treatment/control replicate lab experiments we are all familiar with. But full scale! There have been a wide range of these projects over the last 20 years or so, in a range of ecosystems, but never in the Amazon. Until now.

Upward-looking panorama of the FACE ring tower and canopy.

AmazonFACE is establishing 8 30m diameter rings, each with a tower in the centres, which will have CO2 piped into the canopy, raising the ambient CO2 to around 600 ppm (50% or so above current normal levels) for the next 10-15 years. The rings span a range of forest conditions, and have paired plots fairly nearby which will be the controls. Within the rings, and at the wider site, the climate and wide range of soil, plant, biotic responses will be measured, as the rings are established and the CO2 is switched on (planned for start 2018).

We were very privileged to be invited by Prof. David Lapola and his AmazonFACE team to come and use our lidar to scan the FACE rings at the outset of the experiment, to try and characterise the plot biomass and structure. We also aim to establish a baseline of the canopy structure against which future changes can be compared, as well as to try and unpick the structural differences between the rings at the outset.
A single scan from our Riegl, centred on the middle of one of the AmazonFACE rings (colour is vertical height, from blue to green).

A close up of a single scan within the ring above, showing the tower at the centre. Some of our reflector targets can be seen in bright red to the right of the large tree in the centre (colour represents return intensity of the laser pulse, from blue to red).

Top view of scan taken using our ZEB-REVO mobile laser scanner, with the tower visible in the centre (colour represents vertical height, from blue to green).

After some amazing logistical and paperwork help from David and his team, particularly Bruno Takeshi who is the guy who does everything (including driving through and over and fallen trees!), Matheus and I spent a very busy few days scanning the FACE rings with our lidar. We had a great deal of help from Dr. Florian Hofhansl, the resident ecophysiology expert, and other station researchers. We collected 8 rings with our Riegl and I also managed to scan them with our GeoSLAM ZEB-REVO. Florian's overview of the experiment is really informative, with detailed maps and plans etc. Check it out.

Despite some minor travel hiccups (losing not one, but both our laptops, on different flights; we got them back, albeit one only on the way back out), the occasional unseasonal tropical downpour, fallen trees and getting savaged by some tiny horrors (me), the expedition has been a great success and I'm really excited about the results. It's also been great to establish some new research collaborations with the Brazilian AmazonFACE team and their colleagues from elsewhere. Huge thanks to the team and cNPQ, INPA and the colleagues, for bringing us out and organising the trip.
Cross section (few cm in depth) of the ZEB-REVO scan, showing some of the tree trunks.

Oblique slice through a Riegl scan.
Thanks all!

We were faster, but maybe not by much.

Wednesday, 13 July 2016

Mondah plots done!

2 weeks, 2 hectares, 484 scans, many billion points, several hundred trees including way more 40+ m beauties than I've seen in one place before, some ants in the pants, some blood & definitely sweat, but fortunately no tears. Got some additional 'bonus' data to collect in the time left over with the ZEB, some high res scans of single trees but we got what we came for. We've acquired an additional member of the team for a few days in Melina, a stagiare with ANPN, who has already done some great work manually verifying which tree is which in the lidar stem maps. We're very happy about that and hope she can carry on with us in Lopé (if she wants to!). An example of one of these maps is here.
An example stem map, from plot MNG-04, showing the NE-most 20 x 20m quadrant, with tree sections from the lidar labelled with their tree IDs from the tags. Good work by Melina.
And we really couldn't have done this without the huge help of Leandre, who has been amazing - guiding, carrying, organising, driving and generally being the oil in the wheels of progress. Thanks!
There's nothing like getting that last scan done, and getting the heck out of Dodge for a shower and a nice cup of tea ;-)

Saturday, 9 July 2016

Mondah plot snaps

Andy has been working through the Mondah data from the first two GEM plots, and here are some examples of what they look like. First up is a transect through the MNG-03 plot, which covers 1 full row of 100m, and is about 20m deep. The plot shows the scanner locations on the 10m grid along the bottom (3 rows of them). The colours represent points coming from different scanning locations, with each colour corresponding to the colour of the scan location 'dot' - it's quite hard to see those for any other than the nearest ones on the black background, but you get the idea. For example, the purple points in the upper part of the tall tree in the centre come from scans to the far left and right in this case, showing how scan locations far from a given tree can often reveal the most detail at the top, due to being able to see through the surrounding crowns more easily.
Transect through MNG-03 showing the points from 3 rows of scan locations. There are 121 locations in each plot in total i.e. 11 rows of 11 locations, starting at 0, 0 and moving up to 100, 100 in 10m spacing. The point cloud here is drastically reduced (by factor of 1000) to allow easier manipulation.
 The image below shows a fill resolution example of a typical large tree with very grand buttressed roots, in the centre of the MNG-04 plot. In this case the colours represent the reflectance (returned energy) of the points, so the reflectance of points from the nearby broad trunk and roots is very high (near white), while the reflectance from the leaves and from points further away is much lower (orange through to dark red and black).
Reflectance image of small section of MNG-04 plot. This shows the full point cloud density.
Meanwhile, some more results from the ZEB-Revo scan are shown below. First, a height map of the whole plot, which shows the ZEB sees around 30m in some cases. So we can see the lower parts of the trees well, up to the crowns of the taller trees, but no detail in the upper part of the canopy. There are ~130M points in the 1ha cloud in total. Note that the heights aren't relative to the ground level but to the total height variation across the cloud. So the highest points (upper right) are still only 20-30m above the ground, but are on a raised area and so 30-40m above the lowest points. So the red parts here are largely a map of underlying topography. 
ZEB-Revo scan of MNG-04 plot, with the colour representing height, from 0 (blue) to around 35-40m (red).
Another view of the ZEB scan of the plot, from above this time.
View from above, looking down on the ZEB-Revo scan of the MNG-04 plot.
And a zoom in on one section in the diagonal gap towards the left of the plot. This gap may not be real - I think it may be a function of my scanning pattern going haywire during my walk of the plot. Staying on the grid is hard when you're struggling to walk, not fall down the slope or large holes, trip over logs and vines and hold the scanner at the same time!
Zoom in of small section of the ZEB scan of the MNG-04 plot.


Friday, 8 July 2016

Return to Gabon

So we're back in Gabon, returning after 3 years to scan Yadvinder's GEM plots at Mondah where we previously scanned. And then on to Lopé where we'll revisit 2 previously scanned AfriTRON plots, and then a few more new ones established by Simon for the ESA BIOMASS cal/val campaign. This will be the first time we can look at possible changes over 3 years, against a backdrop of the recent very large El Niño event.

Andy is leading the field campaign, over 6 or 7 weeks, with Matheus, myself, Ewan and Joanna coming in and out over the duration. We've had huge help from ANPN Gabon, via Kath Jeffrey, Lee White, David Lehmann and others in organising permits, kit and logistics. Without them it's safe to say this wouldn't be happening. And they've also organised great local help, Leandre and Hector in particular, who are really helping to make the operation much more efficient.

Day 1 and we had this visitor following us on the road!
No you can't have my lunch.

A 'typical' view of the second GEM plot.
Leandre carrying the Riegl out of the plot. A job for a younger man than me these days!
One of the giants we're here to scan, in the centre of our plot. Photos just don't do these trees justice - this one is 50+ m tall, with the enormous buttressed root system and a canopy that seems to be in the clouds.
One thing we're doing here is testing out our new Geoslam ZEB-Revo handheld scanner, to see what it can do. In particular we want to see how well it can capture the tree trunks and diameter, given its relatively short range, and how quickly we can do plots. First results are very encouraging. I scanned our 1h plot in about 80 minutes, generating 500G of data, which took ~6 hrs to process. But Andy and I were surprised at the level of detail and how well the tree trunks were captured. The snapshots here don't really do the detail justice, but this looks very good indeed. It opens up the possibility of us covering many ha at this level of detail, for trunk diameter and shape, to augment the more detailed Riegl data.
A very small slice through the 1ha ZEB scan of the plot.
I also scanned a single large tree in the corner of the plot, looping around it 3 times. The results from this are also very encouraging indeed. Here's a slice showing the tree with 2 slightly smaller (but still huge!) trees next to it. The white points are a second horizontal slice through the cloud, shown in plan view below.

Scan of single large tree (well, 3 really).
A slice through the trunk of the large tree, at about 4m above the ground, with the other two smaller trees next to it, and the rest of the point cloud in gray around them. The larger tree diameter is around 1m.
So, good progress and some interesting results so far and I'm really looking forward to seeing what we can get from the ZEB in combination with the Riegl. It's hard work doing the high density scanning in this landscape though! ;-)

Saturday, 25 June 2016

New papers from the group

Three new papers from our group, either from our work directly, or members of the team working with colleagues elsewhere. First up is Phil's paper written when he was in Australia, on characterising the vertical structure of forest canopies using airborne lidar data via a new metric, the Number of Strata (NOS). Phil et al.'s analysis shows that NOS can be a useful descriptor of canopy structure to complement canopy height and cover. They also propose this might be useful as a candidate Ecological Biodiversity Variable (EBV) for characterizing habitat structure.

Next we have work led by Sébastien Bauwens in University of Liège, and involving our own Kim Calders and colleagues from Wageningen University, comparing mobile hand-held and static TLS for forest inventory work, such as estimating canopy DBH rapidly across field plots. Their work shows that low-cost hand-held scanners can be a useful tool to supplement more expensive, longer range TLS instruments for DBH, particularly if speed is a key constraint, but struggle with height due to their much lower range.  

Lastly, we have a paper in PLOS One by former UCL postdoc Aida Cuni-Sanchez, with colleagues from the Agence Nationale des Parcs Nationaux and the Institute de Recherche en Ecologie Tropicale in Gabon and myself, Andy Burt, Kim Calders, Jose Gomez-Dans and Simon Lewis from UCL. Aida's paper presents work quantifying forest-savannah boundary dynamics over 20 years. Our contribution was to use our TLS to characterise the vertical forest structure quantitatively, allowing differentiation of forest types across these boundaries. Aida shows how colonising forests show much slower changes in biodiversity than structure or AGB. Aida also shows that all the forest types studied store substantial quantities of carbon.

Friday, 3 June 2016

Name-checked by Chris Packham and Frank Skinner!

Nic Stacey, who directed the Oak Tree documentary for Furnace TV we were involved in, alerted me to the fact that our work on that got a very nice mention by Chris Packham on Frank Skinner's weekly  On Demand With ... roundup of BBC highlights on the iPlayer. Both of them picked up on the number of leaves and seemed amused by the thought of me counting the leaves by hand. In practice, counting leaves like that is anything but amusing ;-) Hey ho, that's what the lidar is for I guess! Link to the program here, and from about 02:20 in: It was also great to see that the documentary won a Royal Television Society award for Best Science and Nature programme. It's good to see Nic, Paul Sen, George McGavin and Furnace getting recognised for this, a really gripping and beautifully-made programme.

Friday, 20 May 2016

Karen's blog post on our recent lidar paper

Karen Anderson has written a really nice blog post on our recent paper "A comparison of LiDAR approaches for vegetation and landscape characterization" (published in the open access Remote Sensing in Ecology and Conservation journal). Karen's blog "Weighing up the benefits and costs of waveform LiDAR", and hosted on the ZSL blog site, outlines some of the benefits of waveform lidar for ecology. Our work shows how waveform lidar can provide habitat measurements that just aren't available any other way. Karen concludes that the next few years are likely to see an explosion in applications of waveform lidar in spatial ecology.
An image from Karen's blog showing our TLS work in suburban Luton (taken from:

Friday, 13 May 2016

First results from Ankasa

Andy's been busy processing the Ghana data. First cut from this is a flythrough - low res at the moment but you can see the tower at the start, and the topography towards the end. This was ..... a challenge shall we say.
Andy's also pulled out the 17 largest trees in the ESA AfriSCAT RADAR footprint - and the poibt cluds, and the resultiung models, are shown below. Our initial estimate is that there's around 150 t C in these 17 trees, probably close to half of the total for the whole plot!
Point clouds of 17 largest trees in the plot, extracted automatically from the co-registered full point cloud. Colours are just to differentiate each tree (same below).

Initial results from fitting cylinder models to point clouds. Mostly looking good, and the volume estimates seem robust from the parameter variation.
More tree models to follow!

Thursday, 28 April 2016

Winter, summer, ground, air ....

Kim has been working on the airborne lidar data over Wytham, provided by David Coomes and co at Cambridge, and originally collected by NERC ARSF as part of the AIRSAR campaign. The data were collected on 24th June 2014, so leaf on and a year before our ground campaign. The image below shows the airborne lidar data over a ~100m transect across Wytham wood.
NERC ARSF lidar collected over the Wytham site, 2014.
 It's immediately obvious the difficulty that even this dense, high quality airborne lidar sensor has in seeing through the canopy. But this is also a lovely example of the power of lidar to show the vertical structure and density of the canopy the layering, and the range of heights over the ground. Below we see the same airborne data overlain on to the TLS summer (leaf on) data. It's worth emphasising what a good job Kim's done in manually overlaying these datasets to get the agreement we can see.

TLS data (green) collected summer 2015 (leaf on) overlaid on to the 2014 summer ALS data.
 Now we can see: how well the two datasets match up, but also the massive amount of detail that is missed when you look down. Clearly, the trade-off is the time and area you can do this. But what a fantastically rich dataset illustrating the canopy structure. We also have of course the leaf off TLS:
TLS data (red) collected winter 2015/16 (leaf off) overlaid on to the 2014 summer ALS data.
Again, this shows beautifully the profile of the canopy, but also how much more we see in winter than in summer of the upper branches. Unsurprisingly! As far as I'm aware no one's ever collected a dataset quite like this with the detailed TLS, ALS and then the spectral and biophysical data. We're all looking forward to exploring these data in more detail in conjunction with the spectral and spatial analysis with David's group, even radar, and the ground-based trait data collected by Yadvinder. And even the aerial photography is a thing of beauty ;-)
Aerial photograph of the Wytham site, with the lodge visible in the centre and the walkway just visible directly above the lodge towards the edge of the image.

Friday, 15 April 2016

Zebedee arrives

While we were away in Ghana, our new "toy" arrived, the ZEB-REVO hand-held TLS instrument (or Zebedee). I say "toy" because it's not - it's a highly-portable laser scanner, developed by CSIRO in Australia, with much lower power and range than our Riegl but with correspondingly much lower weight, hence the much greater portability. It's designed to be used on mobile platforms - cars, UAVs and the like; the platform in this case being our legs. The idea is that we can use it to augment the Riegl, combining both to provide additional information in environments where we may find it hard to move the Riegl around and/or where the understory causes a lot of occlusion. First tests show it's *very* easy to use, which is a key point. Also, so far I'm impressed with the SLAM software that automatically co-registers all the data into a single point cloud. It seems to work well as long as you capture enough objects & targets that the software can identify in post-processing. I'm really looking forward to getting it out into a real forest environment with the Riegl to start experimenting.
The Ginkgo trees in the UCL quad, done in around 1 minute, with ghost Lewis's everywhere.

A rather more careful and complete scan done by Phil of you know where.

An animation of a walking down Gower Street, done by Kim. And below, a quick look inside the Dept. from a walk out of the lab and down the stairs.

And finally .... Ewan's nice picture of two great minds at work. Look, how hard can it be, just switch it off and on again.

Kim's BES prize

We're all very proud of Kim, who was recently announced as the winner of the British Ecological Society Methods in Ecology and Evolution (MEE) RobertMay early career researcher award (see Kim won for his paper "Nondestructive estimates of above-ground biomass using terrestrial laser scanning" (see The paper was the culmination of Kim's PhD work, and involved many of our long-term collaborators, and it was a key piece of evidence vindicating our approach to using TLS to estimate biomass. Kim's paper received quite a lot of attention when it was published, featuring on the UCL News front page amongst other places (see, and has already been cited 30 times in less than a year. I'm not surprised, and I've no doubt it will go on to be cited many times, given its groundbreaking demonstration of the maturity of TLS for biomass.

Tuesday, 15 March 2016

Ghana, March 2016

So here we go again! This time we're scanning in Ghana, as part of the European Space Agency-funded AfriSCAT project, using our lidar to characterise the 3D structure of a piece of the Ankasa Forest reserve. AfriSCAT is designed to provide RADAR measurements of tropical forest, in preparation for the launch of the ESA BIOMASS Earth Explorer satellite mission in 2020. BIOMASS is a P-band (70cm) RADAR mission, which will allow it to 'see' through dense canopies to the larger trunks and branches; shorter wavelength RADAR (and optical signals) can't see through the upper part of dense tropical forests. So the ESA team want to know what their RADAR is seeing, and that's where we come in!
The AfriSCAT P-band RADAR instrument on the tower in the Ankasa forest.

 We visited the site, with the help of collaborators from CMCC in Italy, along with our colleagues from Wageningen University, Alvaro Lau Sarmiento, Cornelis Valk, Harm Bartholomeus and Martin Herold. so we could operate two lidars of the same type, in order to move faster and reduce risk. This is the first time we think anyone's deployed two lidars simultaneously in a tropical forest like this. It involved a bit of planning and synchronising so we all use the same protocols, but it seems to be paying off in terms of what we can cover. Also visiting was Yadvinder Malhi, our colleague from Oxford, who's been working at the Ankasa site for some time (and in Ghana more generally), establishing several large permanent plots in overlapping the one we were scanning and nearby. Yadvinder is working with with Harm and Juha Suomalainen, also from Wageningen, to collect UAV data over the site. Yadvinder is particularly interested in the relationship between tree traits, and structure, and is using the hyperspectral UAV data combined with detailed measurements made by his ground team, to try and understand these issues. See some lovely examples of the UAV footage of the site on Yadvinder's blog.
L to R; Justice, Cornelis, Alvaro, Andy and Phil (standing).

The view from the Ankasa tower is pretty stunning, if a little hot in climbing.

The team, sitting on a buttressed root with the two lidars.
So far, data collection has been looking good, despite some pretty challenging terrain. The image below shows a slice through the plot, which illustrates the nature of the terrain in the plot. Scanning on slopes like this is hard.  The weather has held up - no rain and not too much wind so far - and other than a bit of sunburn, so far nothing too tricky in the way of hazards. We didn't see a single mosquito in a week. Result!
An example of a slice through the AfriSCAT footprint plot showing the scan locations on the slope. The colours are reflectance i.e. brighter colours represent higher scattered lidar energy.

Below we can see another example of the lidar data from the AfriSCAT plot, from two scan lines, and joined together by Andy.
A slice around 70m long and 5m deep through the plot, coloured by height up to around 40m for the tallest trees.
Our research here has been funded primarily by ESA as part of the BIOMASS mission, but also in part by NERC through our involvement with NCEO and a recent Standard Grant award for tropical forest measurements.

Wednesday, 24 February 2016

More scanning at Kew ....

I went back to Kew yesterday to scan the Oriental Plane with its leaves off. It was a glorious sunny day, with almost no wind so ideal for scanning.
There's really not many more beautiful spots in London on a sunny day.
The famous Kew Orangery. 
The Oriental Plane is still standing, as it has for 250 years or more I guess. Albeit with a little help these days, in the form of wires and guys.
Oriental Plane at Kew Gardens.
Here's a first look at the lovely tree. Points are a bit large so it looks leafy, but it's not.

View up through the trunk from below the point cloud. Note the guy wires to the left and upper centre.
Viewing it like this makes me think 'brain'. Thanks to Andy for pulling the data off the lidar and registering it - literally within a few minutes of me getting back to UCL! This image highlights a couple of things - first the precision of the measurements that easily catch the 5mm diameter guy wires. And second, the accuracy of the registration in that the wires are not 'ghosted'. The fact that there was no wind certainly helps in this case.

The other reason for being at Kew was to film some more footage for the latest ESA MOOC (Massive Open Online Course), this time on optical remote sensing. The last one, Monitoring Climate from Space, seemed to be successful. So I've been asked by the production team to contribute to this new one, and scanning trees in Kew makes a great backdrop to talk about forests, land use and how we can use EO and other new technology to make sense of it all.