Week 7: What Exactly is a STL File?

Since 3D image processing is relatively new territory for me, it has been a pretty steep learning curve over the past few weeks. 

I have been using Artec Studio 11 to construct the 3D models. However, this program is limited in its ability to take measurements. 

This means that I will have to use a different software to account for exact wound dimensions and volume. 

Dr. Ryan suggested MeshLab as an alternative. However, this program takes STL (Stereolithography) files as input rather than the scan format used by Artec Studio 11. 

As someone who is new to these programs, I had no idea what the difference between a STL and other computer-aided design (CAD) files was. 

After a little bit of research I discovered that STL files only account for the surface geometry of 3D objects. They do not have data on things like texture and color.

An STL file can also be referred to as Standard Triangle/Tessellation Language. This is because STL files are created from raw data of triangulated surfaces. The diagram below gives a better idea of what this means. 

http://www.wingchunland.com/wiki.php?s=STL_(file_format)

For the purpose of measuring wound volume, data on color and texture would not be relevant. This is why a STL file could work perfectly for this part of my project. 

I hope this gave you a better idea on the differences between 3D image file types. Feel free to ask any questions! 

Week 6: Assessing the Value of the Scans

Over the past few weeks, I have been experimenting with and perfecting the scans of my models. Finally, I have decided that manual alignment and sharp fusion produce the best resulting image. 

Today, I met with Dr. Kate Davenport, a pediatric surgeon at Phoenix Children's Hospital. She took a look at the scans to see how valuable they could be for physicians. 

One thing we both observed is that laser scanning gives a pretty accurate view of the depth and volume of a wound. This sets a good focus for the rest of my project. 

From here on out, I will spend time trying to find ways to quantify the wound volume. The hope is to use it for monitoring wounds. A comparison of wound size over time can indicate whether healing is occurring. 

Laser scanning offers an noninvasive way to look at wound dimensions. Rather than taking a ruler and judging a rough estimate, the laser scanner creates an image that physicians can interact with, without harming the patient.

Another task I must complete is getting the appropriate training and papers filed to begin scanning wounds on actual patients. This requires regulatory and hospital approval. 

Different Types of Laser Scanners

Welcome back!

I hope everyone had a fantastic spring break and is ready to get back to work. 

One aspect of my project is becoming familiar with the research that is already out there. Over the last few weeks, I have looked at journal articles about laser scanners and how they have been applied for medical purposes. 

I noticed that researchers were actually using different types of laser scanners. While all of them are noninvasive, they give different information about a patient.

The most basic of these is confocal laser scanning microscopy (CLSM). CLSM uses a lens with a pinhole to eliminate unfocused light. This creates beams that are able to assess different depths on the object. This picture shows how the process works. https://en.wikipedia.org/wiki/Confocal_microscopy#/media/File:Confocalprinciple_in_English.svg

Laser Doppler Imaging (LDI) is used to measure blood flow under the skin. An infrared laser is emitted and hits blood cells. This causes a change in wavelength based on how fast the blood is moving. This information is converted into electrical signals that produce a quantitative measurement of blood flow. 

LDI is useful when comparing normal blood flow to the abnormal blood flow around any wound, especially for burns. 

For my project, I will be utilizing a scanner that is a more similar to CLSM. The Artec Spider produces its own light source and uses depth measurements to reconstruct an object. Rather than looking at blood flow and other internal features, I will be looking at outer components such as depth and perimeter. 

Week 5: Manual Alignment

This week, I took a closer look into the manual alignment process. 

The autopilot feature works great when there is just one scan to process. In the beginning, I used a turntable to scan the whole view of an object at once. However, when I potentially scan actual wounds, I cannot place the patient on a turntable to spin them around. Instead, I would take multiple scans from different angles. 

This is where manual alignment becomes useful. The computer will often struggle with stacking the scans the right way. However, I can pick three matching points myself in order to match up the scans. The picture below shows just that.

The resulting scan looks like this. This is a clear improvement from the one under it, which is the image I got using the autopilot feature. 

The second wound model has less distinguishing features, which would make manual alignment more challenging. To remedy this, I used an expo marker to create markings on the edges of the model.

                               

Catch you next week! 

Why Angle Matters

One of the important parts of 3D image processing is making sure there is a full, rounded view of the object. 

Artec Studio 11 allows you to drag around the scan to make sure everything appears as it does in real life. This important function is essential for the proper visualization of any wounds I will potentially scan. 

One way 3D visualization is useful is when I am performing the base removal. In the picture below, I scanned my wound model while it was set on the table. Using the program, I was able to move it in a way that let me remove the table without erasing parts of the model.

A three dimensional view can also be useful in seeing discrepancies in the scan. The two images below show why this is essential for image processing.

This first image is the front view I would get if I did not turn the model at all.

However, a change in the angle reveals some interference, which may seem harmless at first but could ruin the integrity of the scan. I am not exactly sure what caused the issue on top of my scan. I will look into what those floating objects are this week.

As these images show, it is important to take a complete view of a situation, not only in 3D image processing, but also in life. 

See you on my next post! 

Week 4: 3D Image Processing

This week, I spent time scanning my wound models and processing them on the computer. For now, we have been using Artec Studio 11 to finish up and improve the elements of any scans we take. 

There are several ways to process 3D images. 

The most simple approach is to the use autopilot feature built into the program. This setting edits the scans in the most basic ways.

However, there are also manual options to process the 3D scans.

Sometimes the computer is unable to align multiple scans properly. When this happens, you can use manual alignment to make sure the images line up. Next week, I will be spending some time learning how to use this tool. 

Another useful tool is fusion. This blends all the images together. There are three types of fusion: fast, smooth, and sharp. 

Each is better suited for different types of scans. Fast is used for a quick image with minimal hole filling. Smooth fusion fills in gaps in the model, which is essential in printing 3D objects. Sharp fusion has the best image quality, especially for the Artec Spider scanner.

Mesh simplification optimizes the number of polygons to make the sharpest model possible. 

The eraser tool allows the user to take out objects that were accidentally included in the scan, like the base the model is placed on, for example. 

Other more advanced processing tools can be used to fix the texture and coloring of an object. 

As I continue working on this project, I hope to become more skilled at using this program. Eventually, I would like to be able to process 3D scans more quickly with higher quality. 

Week 3: Scanning the Models

Last week, I finally was able to use the laser scanner to create images of the wound models. 

The Artec Space Spider 3D Scanner is a handheld device that captures the details and colors of objects with amazing accuracy. It uses blue light technology to create geometrically sound models in the computer program, Artec Studio 11. 

To capture the full object, I had to rotate the scanner around the whole object. This is how it looked in the computer program. 

The front view shows a model with smooth fusion and increased brightness. 

As you can see, the sideview has a few discrepancies. This is because of the glare that results from scanning a reflective object. 

One of the problems that I will tackle this week is finding ways to improve the lighting for the scan. Usually, engineers use powder to reduce the shine of an object. However, since I will potentially be using the scanner on real wounds (following regulatory/hospital approval), powders/chemicals are not a strong option to reduce the glare off blood. 

See you on my next post!