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Displaying Medical Imagery in Voxler 3

Though many users of Golden Software products display data used in geology, oil and gas, and other geoscience-based industries, many other types of data can be modelled in our software! This week, I'll show you an example by displaying MRI and CT scan imagery in Voxler. I'll be using data in the form of DICOM files and Voxler VDAT files. Please note that DICOM is a container format, so the data may be formatted differently in different DICOM files. This means it is possible that some files may be formatted in a manner that Voxler cannot understand.

MRISlice.png

Single DICOM file displayed with an ObliqueImage module

Many DICOM files can be imported directly into Voxler as a lattice or as a bitmap. The DICOM files I use in this example are imported as lattices. You can import a single DICOM file, or you can select multiple files from the same data set, and import them into the same data module. Importing more than one file will give you more graphics output modules to choose from when displaying the data. The image above is an example of a single DICOM file imported and displayed with an ObliqueImage module.

wholeFootBlackBG.png

CT scan image saved as VDAT file, displayed with a VolRender module

Voxler 3 also comes with several examples of medical imagery that have been saved in the Voxler VDAT file format. By default, these files are located at C:\Program Files\Golden Software\Voxler 3\Samples. The image above was created using the CT_foot.VDAT file.

Medical imagery from MRI and CT scans is traditionally displayed in grayscale. However, the colormap is a useful tool for highlighting areas of interest! For example, I adjusted the colormap for the VolRender module displaying the data for the foot to reveal a closer look of the bone in the image at the top of the post. One more example is below. In this example, multiple DICOM files were imported into a single data module and displayed using a VolRender module. Below is a comparison of displaying the VolRender in grayscale versus adjusting the colormap to add color and to understate areas that are not of interest by adjusting the opacity.

MRIs.png

MRI scan image presented using a VolRender module, displayed in grayscale and colored with a custom colormap

Additionally, DICOM files that import as a lattice into Voxler can be used as grids in Surfer and Grapher! DICOM files that import as a bitmap can be used in Surfer, Grapher, MapViewer, and Strater! Do you have unique or interesting data visualized with Golden Software products? We'd love to see how you display it! Send your images directly This email address is being protected from spambots. You need JavaScript enabled to view it., post them on our Facebook page, or tweet them to us!

Do you have any questions about this post? Do you have an idea for a blog post or have a topic you'd like to see featured? Let me know! Leave a comment, or send an email to This email address is being protected from spambots. You need JavaScript enabled to view it..

 

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10 February 2016
Real Life Applications

Ski season is officially underway! We’ve been getting a lot of snow in Colorado and powder fever is setting in. As a result, the LiDAR Magazine article introducing FATMAP’s interactive 3D Ski Maps caught my attention. When I first moved to Colorado, I spent an entire season learning how to navigate my favorite ski resorts and find the best ski runs for me. The trail maps kept me from getting lost, but they don’t provide much information about terrain. As a result, I occasionally found myself on a run that was beyond my skill level.  My first time skiing a Colorado mountain, I ended up facing a section of steep moguls and riding down them on my backside!  Of course, I can’t even count the number of times I accidentally slowed down just before a flat section of trail when I learned to snowboard. An interactive 3D ski map in my pocket would have saved me lots of bumps, bruises, and frustration.

The new FATMAP Ski app combines high resolution imagery with 3D terrain information to provide more true-to-life trail maps for users. Maps of many US and European ski resorts are available as free downloads, and advanced features such as live location tracking and gradient information can be purchased for each location. While I was exploring the maps in this new app, I began to wonder if I could create a similar map using Surfer and Voxler.

I’ve always wanted to ski the Alps, so I decided to map a ski resort in Chamonix, France. I downloaded DEM data for the area from the Marine Geoscience Data System, calibrated a Google Maps image of the area, and digitized some trail maps. I then imported my grid, image, and ski trail vectors into Voxler and used a HeightField module with an image overlay and vector overlay to display my map. The resulting Voxler 3D map can be navigated in a similar fashion to the FATMAP trail maps, and now I can virtually explore any area I’m interested in visiting using Voxler and online data resources. 

Voxler: interactive 3D ski map using image and vector overlays

Voxler: 3D Ski Map of Chamonix

I must say that after exploring the Chamonix ski resorts in 3D, I’ve decided a hiking trip to the Alps may be more my speed. 

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21 January 2016
Voxler

Golden Software customers possess a broad assortment of backgrounds from earth science and engineering to education and politics. This vast background results in a variety of uses for Golden Software’s products. Each customer uses the software in a unique way, and we are pleased to share these stories. This newsletter features Philippe Lemoyne, Professional Engineer, and Martin Page, Professional Chemist, of Services Enviro-Mart, Inc. and their use of Voxler.

Services Enviro-Mart, Inc. is a soil and underground water decontamination service company located in Quebec, Canada. Their services include the elimination of organic contaminants and odors. Enviro-Mart utilizes a revolutionary technology, Cool-Ox™, to treat the contaminants. The technology is typically less expensive and invasive than remediation via excavation.

Part of Enviro-Mart’s remediation process is mapping the contamination site. This is accomplished by using Voxler’s modeling capabilities. The below image is of a soil remediation project for oil leaking beneath an apartment building’s heating room displayed in Voxler. The contamination plume was computed by interpolating analyzed soil samples. The red isosurface, shown in the center of the below model, represents a C (3500ppm) level of C10-C50 petroleum hydrocarbon contamination. The acceptable level for residential locations, as specified by the MDDEP, is A (300ppm) or B (700ppm) levels.

OilLeakRemediation 01
An orthographic view of the project. The leaking underground storage tank was removed
from the PE3 and PE5 section and the contaminated bedrock was excavated. Thereafter, boring
samples were taken from the surrounding area to determine the contamination plume.
PE3 and PE5 were extracted from new soil which replaced the underground storage tank.
OilLeakRemediation 02
This OrthoImage module displays a 2D planar profile of
contamination at a depth between PE6-3 and PE7-2.
OilLeakRemediation 05
A grid file was generated in Surfer and imported into Voxler to
represent the bedrock top detected at each boring location.
OilLeakRemediation 07
The bottom view of the project displays the effect of removing the bedrock beneath the
storage tank’s former location. As previously mentioned, the red isosurface represents a
(3500ppm) level of C10-C50 petroleum hydrocarbon contamination.

Once the contamination plume was modeled, Enviro-Mart injected Cool-Ox into the polluted soil. The injections occurred over a 20 week period with the majority of the injections occurring in the first 10 weeks. The final 10 weeks were spent battling troublesome pockets of contaminated soil. These “pockets of resistance” were caused by the uneven bedrock and poor oxide mobility in soil. These two factors made it difficult for the Cool-Ox to flow into all points of contamination.

At the end of the 20 week injection timeframe, the total level of petroleum hydrocarbons was reduced from greater than C levels (3500ppm) to A-B levels (500ppm). The total level of polycyclic aromatic hydrocarbons was reduced from greater than B levels (1.7ppm) to undetectable amounts (<0.1ppm).

See more information on Voxler and Surfer 3DE mapping software. 

Further information can be found on the Services Enviro-Mart, Inc. website: http://servicesenviromart.com/index.php.

Download the PDF version of this article.

14 January 2016
Voxler

Cornell David, Manager and Senior Geophysicist at GeoMathics One, a geological and geophysical service company located in Bucharest Romania, first encountered Golden Software products in 1990.

GeoMathics One uses Voxler to display an assortment of geophysical data including 3D chemical distribution and 3D geophysical data acquired with Electrical Resistivity Tomography systems. David states, “I’ve appreciated Voxler from the beginning. Voxler gives you the ability to plan a 3D geophysical investigation.”

Coal Layers: Six hectares of surface were investigated using ERT (Electrical Resistivity Tomography) method to reveal stratified Pliocene lacustrine facies coal layers, interbedded in clayey deposits. Both Wenner and Schlumberger arrays were used to acquire data along 8 profiles, 40 m distance between them, 40 electrodes, 5 m spacing. The structure was confirmed by later drillings.
Rhyolite Body: The image represents results of an ERT performed to relieve a micro-granitic
body inside an elongated hill. 2D sections, at 50 m distance, crossed the hill from one side to the other.
Electrodes spacing was 5 m. The intrusive body is faulted by an important transversal
fault in the middle part of the hill.
Medieval Catacomb: Detailed 3D resistivity tomography was performed to confirm the existence of a
buried catacomb, in the vicinity of a medieval domain. Dipol-Dipol array and layout with 2 m
electrodes spacing were used to produce the image of underground resistivity.

Over the years, David has witnessed the growth of Golden Software’s products and has evolved into a confident user. When asked, “Why use Golden Software products?” David replied, “Because the ratio between price and efficiency is the best for a small company [such as ours].”

To learn more about GeoMathics One’s investigations, visit www.geomathics-one.ro.

Download the PDF version of this article.

 

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