Thursday, 11 May 2017

Urban nurban

https://en.wikipedia.org/wiki/Non-uniform_rational_B-spline
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!https://en.wikipedia.org/wiki/Non-uniform_rational_B-spline

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 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 fusiondatascience.com 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.



And here's the Sketchfab interactive model: