Monthly Archives: December 2014

Set Up Apache Web Server Mavericks



Hemlock Inventory / Analysis Data?


We’ve met at SAMAB and I remembered the FIA office is here in Knoxville.

I have a question and thought you’d be a likely person to ask – I’m wondering if you happen to have access to or be aware of a high-resolution dataset depicting hemlock point locations or polygons in Great Smoky Mountains National Park? I realize hemlocks are the subject of scrutiny given their decline due to the HWA.

I’m interested in using high accuracy data models of hemlock distribution to test the accuracy of a statistically derived distribution model that pairs point occurrence records for hemlock collected by volunteers with constraining environmental variables to explore the maximum distribution subject to the environmental constraints (maximum entropy).

Because the point location data I have is collected by humans on the ground, there’s a risk for bias in the records (e.g., we may have an abundance of "trees that grow near trails").

I was thinking I could use a hemlock declines dataset from the Forest Service to come up with an objective way of establishing the actual distribution of Hemlocks (or rather, the "preferred" distribution, pre-adelgid).

The highest resolution dataset the Park Service has online delineating hemlock distribution seems to be polygons created by photo interpreters working with 1:12,000 scale color infrared images.

If the kind of dataset I’m hoping for does not already exist, I’m thinking to use OpenForis Collect Earth to visually examine the 15 x 15 m satellite imagery in Google Earth to record the location of denuded hemlock skeletons in the Park.

I don’t know what the exact mortality of hemlock in the Park is, but it seems to be pretty comprehensive. I’m hoping point coordinates for hemlock skeletons will inform a "ground truthed" distribution of hemlocks in comparison to the statistical model’s predicted distribution.

At any rate, Paul Super with the Park Service suggested I should inquire with the Forest Service first.

Thanks for any thoughts on this,


Tanner M. Jessel
Information Technology Specialist
Center for Renewable Carbon

The University of Tennessee
Institute of Agriculture
Center for Renewable Carbon
Mail: 2506 Jacob Drive
865-946-1162 (o)
865-946-1109 (f)

“Ground Truthing” maxent model


I have not seen the new 32 datasets and have been meaning to ask Tom Colson if they are in IRMA yet.

"Accuracy" in the case of the vegetation overstory dataset depends on the knowledge, experience, and intuition of whomever is interpreting the color infrared aerial photos and digitizing the polygons – the 80% accuracy is a measure of how well the photo interpreter’s data model matches the actual conditions on the ground (which again is only an estimate of accuracy since you can’t realistically visit every digitized polygon to assess reality).

Tom would have to correct me where I’m wrong, but I think the new 32 datasets have higher "accuracy" in the sense that the newer data models better reflect the true conditions on the ground – either from better quality digitizing, or from additional refinement of the prior data models based on subsequent site visits.

I don’t know if the new 32 datasets have higher resolution – but I doubt it: higher resolution data is expensive to collect – and as you point out, all the datasets would need to be the same resolution to combine in a spatial analysis, and it seems unlikely anyone has money for higher resolution than 30 by 30 meters (Outside Google and the NSA).

I do think that we can realistically (and affordably) get higher resolution data for hemlock locations (lat/long, not polygons) – meaning we use OpenForis Collect Earth to pinpoint dead hemlocks with Google Earth’s 15 x 15 m aerial images (1:2,400 scale, I presume).

This is in contrast to relying on spectral characteristics to create polygons from the 1:12,000 scale color infrared aerial images collected for the vegetation overstory layer back in the 90s.

I’ll ask the Forest Service if they already did the work of gathering point locations for hemlocks in the Smokies using remote sensing data.

If they haven’t, what I’m proposing would really come down to someone very patiently sitting down with OpenForis and systematically collecting spatial coordinates for hemlock skeletons preserved in Google Earth’s 15 x 15 m satellite images.

I have no clue how long that would take, but I’d be willing to try it out and provide an estimate.


“Ground Truthing” maxent model

Hi Keith, Todd, and fellow DLIA Science Advisors,

I did a GIS project using Maxent in the spring 2014 semester using the ten environmental layers and ATBI data I had access to.

I looked at hemlock forest decline as a function of community association, using Maxent models to delineate typical hemlock forest communities (e.g., hemlock-silverbell, hemlock-pine, etc.) and an ancillary dataset to quantify "decline" objectively.

The work is described here (you’ll notice I "borrowed" slides for class from my 2013 DLIA conference presentation):

My interest in this class project was partly motivated by a desire to "ground reference" hemlock distribution models.

For example, the maxent model can "ground truth" models based on remotely sensed photo interpretations, and vice versa.

I am unaware of how either UT, NPS or DLIA would go about "ground truthing" new predictive models produced with the new collection of 32 environmental layers.

However, the precipitous decline of Hemlock in the past decade in GRSMNP offers a macabre opportunity:

"Discover Death."

I propose that "discovering death" of hemlock is possible given the availability of high resolution satellite imagery captured by vendors supplying data to Google Earth. This imagery preserves the distinctive visual properties of hemlock skeletons that can be georeferenced.

The high mortality of hemlock in the Park may offer a unique opportunity reveal exact geographic coordinates for hemlock, revealed by their denuded skeletons. In contrast with the surrounding forest, I surmise hemlock are easily discernable – either manually or via automation – from high resolution satellite imagery available from Google Earth. I also am optimistic that the relatively small geographic area of the Park would pose a reasonable burden for manually georeferencing hemlock trees.

To collect this data, I would suggest we can use a free software package from the UN Food and Agriculture Organization called OpenForis Collect Earth <> to pinpoint locations of denuded hemlock from hi-res, 15m x 15m satellite imagery supplied by Google

This is the next best thing to "complete physical inventory," lying somewhere between exact locations provided by DLIA volunteers’ boots-on-the-ground collecting point coordinates for hemlock trees and the other side of the inventory spectrum: generalized locations extracted from 30 x 30 m remotely sensed imagery.

It is interesting to contrast point location data from the ATBI database against the Park’s official "Hemlock distribution" dataset – a point I made in my slide set for my class presentation on slide 24. This slide shows ATBI point locations for hemlock far afield from the "official" NPS hemlock polygons derived from remotely sensed photo interpretation.

Given hemlock’s unique situation in the Park, we might be able to construct a highly accurate, nearly comprehensive inventory of the locations of hemlock trees.

I believe we could then use this high-accuracy point inventory as a reference for comparison to gauge the strength of the maxent model’s ability to match the "truth on the ground" using its 32 environmental layers – with respect to hemlock as a model species, at least.

This approach would eliminate any sampling bias inherent in DLIA-supplied point locations used to inform the Maxent predictive model.

We could also compare and contrast predictive models using different datasets – a "comprehensive inventory" produced dataset, versus a "citizen science" produced dataset, and determine what, if any effect inherent "sampling bias" might have on the final product (again, with respect to hemlock trees).

Anyway, something to think about as we move forward thinking about ground-referencing the models produced from DLIA point locations and the new environmental layers.


Tanner M. Jessel
Information Technology Specialist
Center for Renewable Carbon

The University of Tennessee
Institute of Agriculture
Center for Renewable Carbon
Mail: 2506 Jacob Drive
865-946-1162 (o)
865-946-1109 (f)

Collection Digitization Funding Opportunity / Hi-Res MicroCT concept


Todd likes it too, although he’s super busy, he asked me to look in to it.

​Well, I think having a 3D model of any organism is valuable at face value, particularly because we can share the 3D models for research and education via services like Morphbank or via the DLIA Website, or perhaps even via DVD of data for sale.

The first step is obtaining the technical equipment to do the digitization, i.e., the 3D scanner and associated computer equipment.

I have no thoughts on which particular organisms should be done for science – although I have a few ideas on which ones should be done for commerce.

The way Kickstarter normally works is that the donor is promised something in return for their contribution.

You can have different compensation for different levels of contribution.

For example, if you donate $1,000, then perhaps you get a 3D printed gold-plated brass cicada in return:

For $20.00, perhaps you get one 3D printed in plastic polymer:

674x501_738971_608207_1350353664.jpg dragonfly 1 2 by ocb on Shapeways
Shapeways is the world’s leading 3D printing service and marketplace. Design, Prototype, Buy and Sell products with 3D Printing.
Read more…

I would suggest the way it works for us is we choose the most easily digitized and most palatable creatures to digitize and sell.

I imagine that a "lightning bug pendant" would be a hot seller. Who knows how it would turn out digitized – maybe something like this:

674x501_280671_132612_1338413387.jpg Spider in "Amber" by lensman on Shapeways
A spider trapped in amber is the sort of look I was aiming to achieve with this piece and, thanks to the way Frosted Ultra Detail is used, and 3D printing
Read more…


3D Printing Connection

Hi Todd,

Here is a 3D model of a comet provided by the European Space Agency:

I heard about this application on today’s Stardate on NPR:

The piece explained the science applications well:

"It offers advantages for science as well. Astronomers can build 3D models of comets, dying stars, magnetic fields, and other things that are normally seen only in two dimensions. That helps them understand how such objects form and evolve."

Also, at First Friday, I met Issac Merkle, creative director at

They were demonstrating their 3D printing tech.

I asked if they had experience with 3D scanning.

Issac in particular does.

I asked if they might be interested in a demonstration project / collaboration.

They do not have the highest resolution 3D scanner (or printer, for that matter), but it might be a worthwhile demonstration / pool of labor to get some 3D digitization to provide a "proof of concept" for a potential "Kickstarter" or other crowd-funded acquisition of a hi-res 3D scanner.

Perhaps this is something to talk about on the Dec 10 call?