New projects

The year 2009 was an intensive time for writing funding proposals in our group... and sometimes a nerve-wrecking time waiting for the decisions to be made.

We were lucky this year. Funding was granted for two new projects for 2010-2012: "Vegetation Structure and Functioning from Imaging Spectroscopy" (PI: Matti) and "Seasonal Reflectance Changes of Boreal Forests" (PI: Miina).

Action will start next week.

The art of canopy image processing

Since 2004, I’ve spent countless hours in taking and analyzing a special kind of photographs: skyward looking images that display tree crowns. Back in 2004 I managed to get a summer job at Metla, so I spent six weeks at Puolanka photographing tree crowns with a digital camera (back then it was not obvious that all cameras are digital). As a continuation project, I was hired to analyze the data: there were something like 1500 images, and emailed instructions how to analyze them with Paint Shop Pro. I needed to separate the sky and canopy pixels in the image so that the percent canopy closure could be calculated as the proportion of canopy pixels. Basically the job was a continuous torture for the keyboard and mouse (not to mention the analyst!), as most of the images needed some manual tuning before the conversion to binary format succeeded.

In spite of all this, I ended up using similar data in my master’s thesis, which meant more of the same cake. In addition, I manually painted the small gaps inside the crowns crowns black so that proportion of between-crown gaps could also be derived. Having gained some hard-earned expertise in this area, I came to contact with Hannu Ilvesniemi, who was planning a large-scale inventory in which crown photographs should also be taken. Fine, but who would analyze all those images? Luckily that wasn’t me: Jaakko Heikkinen happened to work for Hannu at that time, and he knew how Matlab could be used to repeat automatically everything that I had done manually. I was not familiar with automated image processing back then, so it looked almost like magic how he could obtain the same results than I just by typing the name of program into the Matlab command prompt. The trick is actually quite simple – using just the blue RGB channel helps to get rid of problems with clouds and contrast, and an automatic algorithm can be used to select the threshold value consistently. Even better, Jaakko could also separate the between-crown areas automatically with morphological image processing operations. He implemented this all so that results ended up neatly in excel sheets without any human interference, and an additional check image was printed for every image so that any problems could be spotted just by browsing them.

I started to feel that we had done something worth publishing – we had a nice method of analysis, images, and validation data that showed a reasonable correlation. So just the work of putting it all to paper remained. Review process went through quite smoothly, so now you can read it all from this article, download current version of our code here, and everything should work out of the box. This study is really one of the most satisfactory things that I’ve been part of during my career as a canopy researcher – I know that I’ll never need to work with canopy images using such elementary methods as I did five years ago. And the story is not over –I still use different versions of the same code for different tasks, such as estimation of LAI from hemispherical or even aerial images. As a summary: a programmer is the master of the computer, whereas the end user of the software is more or less its slave. So all the students out there – take your programming classes, someday it’ll pay back.

Field work completed

Last week Eeva and I spent a few days in Hyytiälä. The four-month long field campaign is now over, and we have a good looking seasonal LAI time series to analyze (thanks to Eeva!).

I had already forgotten how difficult it is to make LAI measurements in September (not to mention October). The sky is not uniform and the sun sets and rises 'too fast' - the time for making our measurements is very short each day and it seems that the campaign proceeds at a glacial pace. Anyway, we did get nearly everything we had planned done, and even had the time to eat a few blueberries when rushing from one plot to another.

The trip was memorable for another reason too. The roads at the study site are horrendous, and I ended up driving into a rock and breaking the oil pan of my car. The roads of Hyytiälä now have an oil track for several kilometers... and my car was towed 25 kilometers to the closest car workshop.

Two weeks in Boston

Miina has already written about her visit to Connecticut for the Multitemp conference at the end of July. Actually, she was not alone in the US. We were traveling together from Helsinki to Boston and while Miina was visiting the town called Mystic, I was having a good time working on p and having lunches with prof. Ranga Myneni. A large part of justifying the transatlantic flight was to meet the Climate and Vegetation research group at Boston University.

Heat wave in Boston

Boston was hot and tropical, air conditioning in BU was fierce, and welcome was warm. Thus, it was good two weeks. Eventually, prof. Yuri Knyazikhin also arrived from Spain and during the second week the theme of the visit closed in on the spectral invariant, photon recollision probability, or just p for short.

Discussions with Yuri. The photo is misleading: it is actually me who is at a loss, not Yuri. I manage to hide my confusion well, but this is (as I have heard) a common side effect of talking to Yuri about the eigenvalues

Spectral invariants: one of the hot spots of vegetation remote sensing. Everybody knows what they are, but I guess that only a few understand what they (or it, in case there is just one spectral invariant) mean. I have some publications on the subject, but why the spectral invariant approach works so well has remained a mystery to me. I understand the idea behind using the eigenvalue and why the radiation field should be reasonably well approximated by the first eigenvector. Still, sometimes points fall on the line with magical accuracy, and not just for canopy absorption, but also for reflectance.

The discussions we had with Yuri were fruitful, at least for me. I think I am a bit closer to some sort of an understanding. However, it will take some time before I can write this understanding down with sufficient accuracy.

There some other good things about traveling besides meeting interesting people. It is often about the little things, like having morning coffee and a croissant in Paris during a six-hour change at CDG. Some praise for such an opportunity has to go to the global recession: our original flight from Boston to Paris was canceled and we had to take an earlier one. Thus, what is usually considered a nuisance can be turned into a possibility -- to be in Paris before the tourists wake up, sit on a terrace of a boulangerie in the Latin quarter surrounded by a haze in the head created by the time difference watching Parisians cleaning the streets and opening up their businesses.

Paris in the morning

The jet lag, of course, had its revenge once we were back in Helsinki.

Cajanus tube conquers Norway

I returned last Friday from Norway, where I participated my first ever field measurement campaign outside Finland. Svein Solberg from Skog & Landskap contacted us to ask if some Cajanus tube experiments in Norway could be arranged. As Miina was busy with her travels, I volunteered for a substitute. And so after the usual flight and train travels I found myself in a farmhouse guest cabin, sitting nicely above a river valley near Svarstad in Southern Norway. And the river Lågen seemed to swarm with fisherman and salmon, wish I had known to bring my fishing tackle…

River landscape

The plan for next days was to make some Cajanus tube measurements and compare results to terrestrial laser scans obtained from the same plots. So I headed to forest with the TLS team, and had some time to follow their work before Svein and others arrived to discuss how the measurements should be arranged. We decided to do very typical dot count sampling but record also gaps inside the foliage, which is more difficult than usual between-crown gap measurement.

Terrestrial laser

Following days were typical field work with small differences to Finnish conditions, like climbing up to 30 minutes before arriving to the plot, cow dung and sound of the bells in the forest, and a Norwegian Cajanus tube that was considerably sturdier than the Finnish ones. Norway spruce forests were quite similar to Southern Finland, except usually more sloping. Also the rain that hindered our attempts was a very familiar experience… All in all, even though the final plot result remained once again smaller than planned, the campaign was definitely a success: also Norway now belongs to the international Cajanus tube family.

Two Cajanus tubes and an American implementation, GRS densitometer.

Towards hypertemporal remote sensing

I just attended a conference on multitemporal remote sensing images in Mystic, Connecticut. The conference was already the fifth in a series of workshops focusing on the analysis of time series imagery - for me it was the first one. The topics covered in the meeting were quite diverse, and included also radar images. Various methods for change detection and data mining were presented. There was discussion on cross-calibration of data from different sensors, accuracy assessment and detection of land cover changes and vegetation dynamics (the most interesting part for me). From many of the talks it was evident that we hope to be going towards hypertemporal (and not only hyperspectral) remote sensing - especially if we want to monitor environmental processes continuously and near real-time.

Tiit recommended this conference to me already last winter. I was interested to attend, and so we decided to prepare a presentation on our seasonal reflectance time series of birch stands. We used a radiative transfer model to identify the key factors which influence the seasonal pattern of stand reflectance in medium resolution satellite images (Landsat, SPOT), and briefly compared our results to 'landscape level' MODIS LAI and phenology products.

Signposting

Muutama viikko sitten löytyi meille uusi koeala. Nimi on "Parasmetsa" ja sijainti Saarenmaalla. Voisiko parempaa ollakaan PARAS-mallimme testaamiseen?

ALS, ALS, ALS

This blog has been too long without a decent Airborne Laser Scanning post. After a few months of laser data processing and one week on an intensive ALS course at Mekrijärvi research station, it is a good time for me to correct this deficiency.

In case that somebody not yet familiar with ALS happens to read this, the idea is that an aircraft equipped with laser scanner and inertia measurement unit flies above a forest area, measuring XYZ coordinates of laser return echoes. This way the 3D-structure of underlying forest can be measured very accurately. Here at University of Joensuu's forest inventory research group, ALS has been the main topic of research since 2004. First Finnish experiment with originally Norwegian area-based laser inventory method started then with the collection of the famous Matalansalo dataset. The idea in this method is that the height distribution of pulses hitting a pre-measured plot can be used to predict predict practically anything, from stem volume and LAI (easy cases) to biodiversity indicators (very difficult). Alternative approach is to detect individual trees in a stand and use allometric models to predict their dimensions, which requires higher pulse density.

Now five years have gone, and forest inventory is going through greatest revolution in its history. Numerous ALS papers have been published during this period, and Joensuu has become one of the leading knowledge centers in this field. Airborne forest inventories have entered commercial stage, first in company and state-owned forests, and next year also first private forest-owners can order a forestry plan that is based on laser inventory. National land survey of Finland has already started gathering data for laser-based elevation model, which will eventually cover entire country. This means that huge amounts of data will be available for practical applications of ALS research.

Personally I've been in great place to see this all happen, but my own start with laser data (which I've had since 2006) has delayed and delayed as other more urgent projects have moved forward. Now I actually feel that I'm a bit late - so many scientific papers concerned with laser measurements of canopy structure have already been published that the remaining job is to figure out how all those studies could be done a little better. Luckily I think I have some new ideas to try... So the last winter months before the yearly travelling season in may-june were quite intensive laser data processing, which will now continue for a few weeks before the start of the holiday season.

Last week's Nova course was certainly one of the highlights of Univ. of Joensuu's ALS history. PhD students and teachers, mostly from the Nordic countries, came together to study basics and more advanced topics of ALS in forestry, and also to have a good time in the peaceful countryside. For me the most interesting part was Ilkka Korpela's photogrammetric/physical approach to ALS, and especially his work with LiDAR-vegetation interactions. I totally agree with his view that also ALS research should next turn to a more physically-based direction, which will however require plenty of work and technological developments. But that's what science is all about - mapping the unknown.

Field work

We started our field work season on May 14th. Eeva has stayed at Hyytiälä since then, others have visited twice. This week has been our "intensive" measurement campaign, and we've been able to produce at least a few spectra, tree coordinates, hemispherical images and LAI-2000 readings.

Lauri hugging trees and Pola giving out instructions.

Measuring tree variables and coordinates.
Time for (another) coffee break.



Calibrating our camera at Tartu Observatory.

The night shift.

Establishing plots.

Planning
& checking
data.

Eeva learning
to use the camera
- four
'experts'
supervising...

Estonian-Finnish vegetation remote sensing seminar

During the last four years, I've had several chances to visit my friends in Tartu. There have been courses, recreational trips, and like this time, scientific seminars. Tartu is a beautiful city and always worth a vist, even though getting there means way too early wake-ups and traveling well around the clock by foot, train, ferry, taxi, and bus. The world is just too far away from Joensuu.

This year the Estonian-Finnish vegetation remote sensing seminar started with two UAV presentations. It seems that these remotely controlled mini aircrafts will become very useful in small-scale remote sensing. Jouni and Juha from FGI even arranged a show flight with their helicopter just in front of the university main building, which attracted some interested audience also from passers-by. In a nearby park we found more space, so also an aerial group photo of the seminar participants could be taken.


Image by Juha Suomalainen

The seminar continued with radiative transfer session, which have always been a bit too physical to my understanding... But after the lunch there were several less theoretic but just as interesting presentations, including Mait's new method for hemispherical image analysis, Terhikki's winter LAI flights at Sodankylä, and also my own laser scanning stuff in a traditional Joensuu style. The day ended with an evening party with sauna, excellent fruit board, and lots of chocolate.

Next day I, Janne and Eeva visited Tartu observatory to participate in the calibration of our LAI camera. Determination of lens distortion and vignetting functions was done very carefully - actually I was quite stunned by the level of precision (=calculating individual photons) in which physicists can (and bother to) do these things. After that was done we had free time, and ended the night by celebrating Barcelona's UCL victory together with Tartu's seven Barca fans that crowded the streets at midnight. But the morning started with a long return back to normal routines: bus, taxi, ferry...

Organizing & emails

Field work season for LAIDetectives is about to start in two days.

I've spent the last couple of weeks trying to recall everything I should take care of, coordinating the acquisition of satellite images and writing lists of equipment I need to find or purchase before going to the field site in Hyytiälä. At the same time I've been organizing a conference trip to the US and arranging the relocation of my personal (and office) belongings from Estonia to Finland.

After all this, I feel like an 'Expert in Emailing'. Time to get new business cards?

What motivates us?

Last week I attended a PhD students' workshop. The final part of the workshop was dedicated to discussing motivation and supervision issues. The simple question was: what motivates you to work on your PhD (or, for older guys, on your research)?

The results were diverse. For some young people, starting a PhD had been "the easy, lazy choice" to earn an income - no need to go through the trouble of finding "a real job" and the possibility to continue the lifestyle of a student for a few more years. A few students were also motivated by the feeling that their research is important.

However, the most interesting replies came from senior scientists. A well-known male scientist said that the driving factor for his research was pure interest in his research question - the social framework was less important. A well-known female scientist, on the other hand, argued that group synergy and an inspiring atmosphere created by her colleagues (or students) was a key factor driving her research.

I am certainly not trying to suggest that men are always interested in technical details and women in other people and social issues. Nevertheless, the contrast between the answers was clear and has, in my mind, fundamental consequences in the way our research team is currently run.

What motivates me? A dynamic group. The chance to work with sharp, kind or inspiring people. To be honest, the research theme is less important than the social framework. Many, many research questions are important enough to deserve my attention - as long as I work on a diverse team.

I would never have started working in research if I had not been offered a chance to work in an international environment with people having different backgrounds (both professionally and culturally). When I entered university, my goal was to be back in the tropics or mild climates of my school years by the age of 25. I was not aiming for a PhD, only for an MSc. Well, here I am, still in the North and with a PhD and more than 25 years of my life completed. And I would not be here, if it had not been for the international MODIS LAI campaign I was employed to work in as an undergraduate student nine years back in June 2000.

So, what am I trying to say? I think supervisors should not only offer interesting measurements or research questions to their students, but also go through the small trouble of organizing social contacts or providing an international framework. In the end, that might prove to be the most important thing in attracting the attention and dedication of many students. For me it was.

A conference trip to Israel

I spent last week in Tel-Aviv attending an imaging spectroscopy workshop organized by the European Association of Remote Sensing Laboratories, Tel-Aviv University and the Israel Space Agency.

At first I wasn't too eager to travel to Israel, but in the end the trip was a success. The conference was perhaps a bit too sensor-oriented for me - imaging spectroscopy applications, especially concerning vegetation, received less attention than I had hoped for. On the other hand, I did learn about new hyperspectral missions, enjoyed excellent Israeli food, followed discussions on whether we should call it "imaging spectroscopy" or "hyperspectral remote sensing", and also got a few new references to articles I need to look up. The workshop also included spectral measurements in Maktesh Ramon in southern Israel and an excursion to (and bathing in) the Dead Sea.

The next conferences for me this year will probably be the annual Finnish-Estonian vegetation remote sensing workshop in Tartu (in May?) and the MultiTemp meeting in Connecticut in July. Lots of work to be done before them..

The Maktesh Ramon imaging spectroscopy calibration site.

Springtime optimism

The beginning of this year has passed very quickly for me. I haven't had an inspiration to continue our blog until now. So, here it is: an update of the past few months.

I returned from my four-month research visit to Australia in December and had problems coping with the cold and short days of my native country. In addition to that, December has always been the shortest month at work for me: just a couple of seminars, an office Christmas party and then the holidays. It was no surprise that my research didn't really progress during December. I was, of course, full of optimism and sure that things would start advancing once the year 2009 arrives.

January always brings about perhaps the toughest time of the year: proposal writing time. This year, it was my job to write two and assist preparing a third funding proposal. I've learned the routine of writing proposals, but it still feels tough planning the work of others - it is easier applying funding to support my own work.

In February, I spent a week in Helsinki planning this year's scientific agenda with Pola, Janne and Matti. We are planning to find a new MSc student to work with seasonal LAI and/or phenology issues. There was also a lot of discussion on using (national) forest inventory data to create a LUT for boreal forests using forest reflectance models. Things are not supposed to be easy, but (at least for me) it was good to realize how many problematic steps are involved with the project...

Anyway, once the proposals were submitted (well in advance this year! :) ), I started to think of more scientific activities. I've attempted something I'm not so familiar with: forest albedo simulations. It has been motivating to do something different for a change. However, I don't know yet how things will turn out and if I get any useful results. I'm also hoping to do some work with spectral invariants and hyperspectral data later during the spring.

I guess the best thing about this winter-spring was realizing that (for once!) I don't have any old, unfinished projects still hanging around and reminding me of their existence every now then. I'm still surprised that I actually managed to finish in time everything I had planned for 2008. As we say in Finnish, I don't have 'to pull a sleigh full of rocks behind me' for the next couple of months. I'm feeling quite optimistic at work :)

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PS. I'm also being quite optimistic when I call the season outside my window spring. We've just experienced a snow storm and there have been cuts in the heat supply - it is quite cold even indoors.