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 RenĂ© Viviani, next to the Saint-Julien-le-Pauvre Church, also one of the oldest in Paris.
The Robinier False Acacia, Square RenĂ© 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.

Friday, 3 February 2017

Back to Kew ....

Back at Kew, this time to try and scan some of the 'civilian' Planes and limes outside the Herbarium, and around the grounds. The weather didn't play ball on the whole, so we spent some time in the wonder that is the Palm House. Mainly this was so Florian could learn how to use the ZEB, but the resulting scans have proved rather elegant and striking. So here they are, variously produced by Florian, Phil and myself.

The outside on a rainy day - much warmer inside. Goose giving me the evil eye.

ZEB-REVO data collected by Florian over about 20 mins inside the Palm House (F. Hofhansl and P. Wilkes).
Section through the centre of the building scan (rendered by Justin Moat, Kew Gardens).
Another rather nice slice (rendered by Justin Moat, Kew Gardens).
Section through the centre of the scans, coloured by height (M Disney).

Friday, 27 January 2017

Historic London trees

We've been looking at working a little closer to home recently. Not that tropical forests, ancient woodlands and the like aren't interesting enough, just that in an old city like London, there are some pretty incredible trees. These are tied intimately to the history and development of the city itself. The availability of new data sources, in particular the UK's Environment Agency open sourcing their extensive airborne lidar over urban areas, has led to us thinking about how we can use this.

London has a *lot* of trees, many of them large and spectacular London Planes,  Platanus x hispanica. This is arguably THE iconic London tree, with its mottled bark, huge leaves and (sometimes problematic!) seed pods. They line so many streets, parks and avenues, providing shade, cooling and habitat for birds and insects. They can occasionally take a chunk out of unwary double decker buses too.

We're looking at using the EA lidar data, in conjunction with colleagues at in Liverpool, and the GIS Unit at Kew Gardens, to identify and measure trees across London, and then use our ground-based lidar scanning to assess the size, volume and structure of a range of these. We're interested to see whether we can apply the same methods we do to tropical trees to urban/street trees in London, with their wide range of managed histories and shapes. We'd like to assess the amount of Carbon they store, their structure and how this relates to their environment.

As part of this work, we've started close to home, looking at trees in Camden, in collaboration with the Camden Council tree department. The first tree we've looked it is amazing - not a Plane, but an Ash. It's in the cemetery of St. Pancras Old Church, a very old (C11th) church tucked away behind the very modern and redeveloped Kings Cross. The Church history is interesting in itself, but there's an Ash tree in the yard with a very unusual back story. The railway being built in the mid C19th led to part of the cemetery needing to be excavated. A young Thomas Hardy was (supposedly) put in charge of moving displaced headstones, and placed them around the trunk of an Ash tree by the church. The tree and the headstones are now entwined, leaving a strange and rather haunting growing monument. The tree is struggling a bit, partly due to the unusual roots but also due to footfall around it. We are using our NERC NCEO-funded Riegl and ZEB-REVO lidars to scan the tree to build a detailed 3D model snapshot of it to help the Camden team plan their management in order to preserve this historic tree.
Scanning the "Hardy Tree". The railway line, and the modern world, is behind the wall.
A view of the scan data collected by Phil, of the whole church yard with the Hardy Tree to the front centre.

The tree, with the hedgerow surrounding it.

A closer view of the strange, leaf-like headstones around the trunk of the tree.

And this is how it looks 'for real'. Image: David Edgar.
Phil's path around the churchyard, carrying the ZEB-REVO handheld scanner. The Hardy Tree is the one at the front left of the Church with the loops around it.
Phil did a great job of capturing the tree with the ZEB and Riegl, and is currently processing the Riegl data - first example of a fly-through from those data is below. We will be extracting the 3D model of the tree and looking at the structure in detail, and then revisiting over the coming months to capture it leaf on, and then over time if we can.

Here's an additional animation that Phil produced, showing his walk through the church yard, alongside the ZEB data.

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.