An update to the automated species identification debate: 

A paper has recently come out which used deep learning ("very deep convolutional networks") and managed 89% accuracy for the Snapshot Serengeti Zooniverse dataset, IF the image was first manually cropped around the animal. Seriously, who has time to do that? If the image remained uncropped they managed a woeful 35% accuracy. 

Perhaps we have a long wait ahead of us for this to become a practical reality?

There's also GitLab. Again, it's probably not perfect as it's designed for coding, but I'm currently using it with a conference organising committee.

I personally think a wiki would be best. 

People in this thread might be interested in this special issue of remote sensing in ecology and conservation, looking for papers on "New Approaches to Citizen Science". Submissions close 15th July 

http://zslpublications.onlinelibrary.wiley.com/hub/journal/10.1002/(ISSN)2056-3485/journal-menu/call-for-papers.html

A new article by Lyndsie Bourgon in the Smithsonian magazine highlights recent innovations that may be of interest to members of this discussion. The article is a fascinating read in its entirety, uncovering the loss of ancient trees from protected areas around the world. 

How Thousand-Year-Old Trees Became the New Ivory

Ancient trees are disappearing from protected national forests around the world. A look inside $100 billion market for stolen wood
 

It was a local hiker who noticed, during a backwoods stroll in May 2012, the remains of the body. The victim in question: an 800-year-old cedar tree. Fifty meters tall and with a trunk three meters in circumference, the cedar was one of the crown jewels in Canada’s Carmanah Walbran Provincial Park. Now all that remained was a minivan-sized section of its trunk, surrounded by shards of wood and dust, with broken heavy equipment chains lying nearby... Lately, these living ecosystems have been disappearing across the province. In the past decade, forest investigators have found themselves fielding cases in which more than 100 trees were stolen at once.
...

Global timber theft has grown into a “rapidly escalating environmental crime wave” according to a 2012 report by the United Nations Environmental Program (UNEP) and Interpol, titled Green Carbon, Black Trade. The report estimates estimate that somewhere between 15 to 30 per cent of the global timber trade is conducted through the black market and linked to organized crime outfits that wouldn’t balk at trading weapons or humans. Now with armed “timber cartels” as part of their operation, these groups have identified profit in the immense value of ancient nature.

...

Two main factors have made timber so appealing in recent years. First, the pay-off: One massive old growth cedar can fetch close to $20,000. A report released in 2000 from the Canadian Forest Service’s Pacific Forestry Centre noted theft of Canada’s timber as a growing problem, costing B.C. $20 million annually. Red cedar is especially at risk, with thieves often specifically targeting its ‘high grade’ old growth. Even smaller parts of trees can be incredibly valuable: In 2014 there were 18 cases of thieves hacking out chunks of burl from 1000-year-old California redwoods.

Second, stealing trees is low-risk. In a globalized economy, timber is exceptionally easy for thieves to get their hands on, says Cameron Kamiya, Canada’s only full-time forest crime investigator. And the Carmanah is the perfect place to commit a crime: a remote rainforest sanctuary on the Canadian west coast, thick with damp air and spearmint canopies of moss. It is so vast and so sparingly visited that park wardens only patrol the area about four times a year.

...

CITES, a convention that many countries follow, regulates the trade of plants and animals, including about 600 timber species. About 400 of these species—including rosewood, bigleaf mahogany and Asian yews—are actively, commercially exploited. In theory, countries that participate in CITES agree to subject exporters to trade regulations, including requiring that they show a permit for the wood they are trading.

But Chen Hin Keong, head of the Global Forest Trade Programme at the wildlife trade monitoring organization TRAFFIC International, says that permits often aren't requested. “There is a good chance that they won’t ask. No one bothers,” says Keong. “If I’m a retailer selling furniture, I can ask my supplier if it’s legal, but he might buy the materials from 10 different sources and he’ll have to check. He might buy his plywood from one place, his dowels from another, planks from somewhere else.”

...

IV. Fingerprinting the Forest

As global tree researchers get more savvy, they’re figuring out how to fingerprint wood products back to the ancient trees they came from.

Eleanor White, a retired molecular biologist with the Canadian Forest Services, was the first to develop a way to “fingerprint” trees. In the late 1990s, she developed a method that has since played a key role in advancing a database of red and yellow cedar DNA in British Columbia. White’s method uses a mixture of solvents to isolate short, repeated DNA segments “microsatellites” from samples of wood. Like fingerprints, each tree has a unique pattern of these microsatellites.

Tree fingerprints are just one promising innovation in a relatively new field: forest forensics. New scientific developments are being used to raise the stakes of this kind of lucrative, difficult-to-trace theft. The goal is to dissuade both individual poachers—those who take trees for firewood, or harvest a Christmas tree from preserved land—and large-scale timber thieves alike.

In Oregon, U.S. Fish and Wildlife has developed its own forensics lab to investigate cases of poaching and timber theft. Ken Goddard, the lab’s director, has been working in park crime since 1979. He wrote a manual for environmental crime scene investigation and is also a bestselling serial novelist, having written books like Double Blind, which follows a U.S. Fish & Wildlife special agent into the wilderness.

Today he runs the only lab in the world dedicated to crimes against wildlife—“though we sure don’t want to be,” he says. They tackle some of the most bizarre crimes in America: illegally imported caviar, poached bear gall bladder, plants coated in banned pesticides, and of course, tree poaching.

“When we first started looking at it”—tree theft—“we were stunned,” says Goddard. “We were starting to hear stories from agents in other countries, about entire forests being clear-cut and ships filled with raw trees in containerized cargo. At that point we couldn’t make an identification if it was milled into planks, so we had to come up with something.” Right now they spend a lot of time handling the illegal import of agarwood, which most often makes its way to the lab in the form of wood chips or incense sticks. Known for its dark, aromatic resin that provides the musky, earthy smell common in manufactured scents, a kilo of agarwood can sell for up to $100,000.

The lab guides investigators who intercept these shipments on how to get samples. It isn’t exactly glamorous. The work includes digging through shipping containers filled with raw material and extracting single logs or planks to take back to the lab. “It’s pretty horrendous work, the mechanics and science of it,” says Goddard. “You’re supposed to take a random sampling for results, but imagine a container full of 2x4s and you’re supposed to take the 412th 2x4 in the bunch. It’s a tremendous amount of physical work, to get that sample.”

Very little of the work that the lab’s criminologists, Ed Espinoza and Gabriela Chavarria, do is actually based in the forest. Rather, they most often examine evidence that has already been manipulated; that is, the tree has already been turned into a product. The team will receive boxes of wood chips or shipments of milled, kiln-dried planks from Fish & Wildlife agents or border inspectors, and get to work hunting around for specific ions to determine the species of wood.

They use chemistry to nab tree poachers after the act, because by the time the samples get to them, the wood is almost unrecognizable. On rare occasions, they have been asked to study full logs or planks that have been misleadingly labeled or declared. “With all the shows today, they mix up CSI with forensics and it really isn’t,” says Espinoza.

Espinoza has done groundbreaking work when it comes to developing a method to identify tree genuses: “Up until a few months ago, as far as anyone in the world could go was family,” says Goddard. Espinoza’s work has since been applied to a species of trees called aguilaria, in which agarwood falls. “It’s a mind-boggling discovery,” says Goddard. 

Espinoza uses mass spectrometry to identify chemical compounds, essentially by turning an unknown liquid (in this case, oils from bark) into a gas and then injecting it into the dart instrument. The chemical compounds then show up on a screen a few seconds later.

In addition to forensics, there have been some attempts by non-governmental organizations to push for a customer-driven solution. The World Wildlife Foundation is working with companies like Kimberly Clarke, Hewlett-Packard and McDonald’s to help identify places in their supply chain where they may be inadvertently part of the world’s illegal timber trade. McDonald’s, for instance, is focusing entirely on the origins of its paper packaging.
 

@victoria from Global Trees Campaign just flagged an event for us over on twitter that might be of interest to this thread in particular. Starting in jus ta few hours, the Forest Governance Project at Chatham House will be hosting a livestream debate: 'What challenges and opportunites are pos3ed by satellite technology and how can it help stakeholders across the timber suply chain?'.

Starting in a few hours... join @CH_Logging's livestream on tackling illegal logging with satellite technology. @WILDLABSNET https://t.co/eeqwiVOf38

— GlobalTreesCampaign (@globaltrees) June 20, 2017

WATCH HERE: https://www.chathamhouse.org/livestream

@ Jan Kees are you working in th Netherlands by any chance?

Hi Anthony, Isla's list is very comprehensive.  The Vulcan Domain Awareness System (DAS) started at LEWA in Kenya where our own JIGZAW web based intelligence database and analysis network has been operational for 6 years.  DAS is about current operations, JIGZAW is about sharing information from sources (open or covert) and creating intelligence on modus operandi and the players involved in poaching, supply chain, organised crime and corrupt officials.  IT does similar things to I2 or Palantir (not automatic data linking) but its free.  DAS and JIGZAW can share data.   In Kruger there are examples of serioously joined up data sharing from sensors and Ten Boma in Tsavo is doing similar things with some success I believe.  Our approach is more strategic, which is to enable information sharing between NGOs and protected parks and trusted national agencies.  The key word is trust.  There is a lack of analytical capacity at the tactical level and at present Big Data is not yet the best way to capture what the local people are saying, thinking and concerned about.  It is sheer old fashioned HUMINT and that takes training and resources.  JIGZAW helps people who know how to do that, to do it securely and more efficiently.  JIGZAW is also license free software only to those in the wildlife conservancy business.  Brief presentation attached.  Good luck

Hi Arik

Did you already test it with wolves?? I would be very interested in learning your results as I am preparing some accustic monitoring of wolves for my PhD.

keeping in touch

Nuno

Hi guys, interesting discussion. As you may have read, we are developing an elephant-detector (to avoid HWC's). The technology we are using (neural networks)  can also be used to learn to recognize wolves automatically. If you have wolf-sound samples for us, we can create a classifier to automatically process your recordings. Alternatively we may be able to run the classifier in real-time on a RPi. But like you mentioned above, power consumption is an issue. Maybe less so if we can mount the sensor on a street light with car battery or something. What do you think?

This is a great blog, it's really interesting!

For those of you who work with large datasets and/or have a high turn over in temp files, the below list of software packages just makes life easier when managing laptop space, cleaning up cached files and zipping/unzipping compressed documents. Enjoy:

- For extended displays etc. Display Fusion. Free for the first month or so for the advanced version and then basic but still free after that. Most importantly allows you to have multiple display profiles so when you remove your laptop from a dock you can switch to a different profile and visa versa.  

- For cleaning up a computer with a bunch of rubbish in cache folders etc. (taking up memory and slowing things down) which are difficult to find- CCleader.

- For playing all media and audio types while circumventing the frequent codec problem encountered with windows media player: VLC Media Player.

- For zipping and unzipping a variety of files and a generally superior compression ratio: 7-Zip. This also works for extracting pictures etc. from word documents without opening them- allows you to cut down on word document size without the palaver of opening and scrolling through it.

- Google Earth has now unlocked it’s PRO version with increased functionality for general use (used to cost $400 per year). You can download Google Earth PRO here.

- For programmers or those wishing to view script or large logs in a simple note pad layout but with proper coded colours, indents, file tabs etc. Notepad++.

- Finally for understanding how much space is available and what is taking up the room on any driver: SpaceSniffer.exe. Spacesniffer gives you a graphical representation of whatever driver you point it at (e.g. C Drive) which will allow you to identify possible areas of wasted space and/or bad sectors on external harddrives.

All of the software here was either introduced to me during my time with the Environment Agency or working with the Canadian government so they’ve all been vetted. The only one which is a new download mirror is the CCleaner link but it looks like the software I use on my machine currently. I usually download if from CNET but that comes up with a large number of popups…