Its Been Fun...

Hello everyone!
This is going to be my last post before tomorrow's presentations. 

My project has definitely been a learning experience. I went from knowing nothing about computer-aided design software to using it every week. I was able to work with laser scanners and other technology that I hadn't even heard of until this year. 

The link below will take you to my final presentation:
https://docs.google.com/presentation/d/1x-SOn5GfE5_2KSygokR5jdGvltnReNt1c0Dt344mdZI/edit?usp=sharing

Thank you for following along on this journey!

Week 11: Quantifying Wound Volume

This week I finally had a breakthrough in how to quantify my data so that it's more accurate. MeshLab has a lot of features, including a way to assign number values to a model's geometry.

My first step was to go through the process that I had discussed in my post from week 9 to scale the model to real life measurements. I used an electronic ruler to find the length of the wound in millimeters then adjusted the models dimensions.

One challenge I faced was trying to find the area of the base. Since these are triangulated models, most of the selection tools captured a rectangular area. 

However, by using the paint tool, I was able to customize the face I wanted to select. I had to be incredibly careful not to color areas that were not in the base.

The computation tool was able to give me a good approximation of the area of the base, as well as the perimeter of the wound. The picture below shows the area used to calculate the base.

Next I used the measuring tape tool to calculate the depth of the wound. This step is shown in the image below.

My volume calculation came from multiplying the area of the base times the height. For this particular model, my approximation was 14,493.875 millimeters cubed. 

Week 10: The Final Product

Early on, I decided a paper was the best way to compile all the information I have learned throughout this project. I began work on the paper entitled "Development of phantom wound for laser scanning assessment in order to augment wound tracking" this week.

This gave me time to reflect on the results that I have currently.

The scans are clearly very good representations of the phantom wound models. They are similar in color and texture. Even small indentations caused by the silicon can be seen on the computer model.

It also presents the possibility of quantifying wound volume, which could lead to incredible advances in how doctors look at wounds.

However, I did notice one source of error on my results. Unfortunately, I was never able to tackle the glare that appeared on the scans. This causes a small amount of interference on the images as shown below. Exploring new sources of light could probably resolve the issue.

Other than that, I am pretty happy with the results I have and will start to brainstorm ways to present the findings to an audience. 

Qualitative Data in Science

As we near the end of senior project, I have been giving some thought into what I would like to present as the results of this research study. 

Due to time constraints, I was not able to scan wounds on actual patients. Instead of presenting the data on a large cluster of wounds, I have decided to take a qualitative approach to discussing the wound models and their digitization. 

Qualitative data includes anything that is not numerical in nature. There are three general types of qualitative data in science. 

In-depth interviews involve talking to a person or group. As is expected, their responses usually cannot be converted into numbers. Even setting a scale which appropriates a number to each response may not be feasible, since responses may vary and cause over-generalizations. 

Another type are written documents. While the content of the documents can be analyzed, they are similar to in-depth interviews. The results depend on the words in the document rather than any numerical values. 

The last type I'm going to talk about is direct observation. This depends on the experience of the experimenter through any of their senses. As such, the results that come out of this type of study can be very different. The data can range as anything from audio recordings to drawings.

The results for my project will be the wound models as well as pictures of their scans. This will allow me to compare the phantoms to the scans to judge how well they are represented. I can look at color, size, depth, and texture in order to address the viability of laser scanning to digitize a wound's morphology. 

Other Medical Applications of Laser Scanning

In an earlier post, I talked about the different types of laser scanners used in medical studies. This week, I looked into the multitude of ways laser scanners are being used to advance medical care.

Laser scanning has become an increasingly popular diagnostic tool. This is because it allows for noninvasive imaging of what is occurring in the body. 

One example is using laser-doppler vibrometery in the human ear. A laser-doppler vibrometer measures the vibration of a surface without contact. It can track the movement of the tympanic membrane of the ear in order to make sure that a person's hearing is fine, after an implant for example. An article about this can be found here. 

Other scientists have used a laser scanner with a camera and inserted it into blood vessels. This technique allows them to assess any cardiovascular risks such as strokes and heart attacks caused by plaque build-up in the veins or arteries. The design of the laser scanner is shown in the model below and the details of the experiment can be found here.

There are also specific laser scanners made solely for the purpose of fitting prosthetics. These can be used to design prosthetic and orthotic devices without putting a patient through the process of a plaster fitting, leading to increased convenience and comfort. 

Week 9: Scaling the Digital Representation of the Model

Last week, I pointed out the numbers MeshLab puts out with its measuring tool are purely arbitrary. This is because the file has no information on the original size of the object. 

After doing some research, I have discovered that there is a way to reorient the MeshLab scale to match real life. Essentially the numbers in the corner are meaningless until they are compared to real life units. 

Since I have been working with models this should be relatively easy to do. I will take measurements on the length and the width of the wound area. 

After I have these, I can divide the numbers by the computers arbitrary scale. This will produce a scale factor I can apply to the model. 

To put this into the program, I will go under filters --> normals, curvatures, and orientation --> transform: scale. By enabling uniform scaling, I will not have to worry about separating the scale into the three axes. 

The next problem I will tackle is trying to find a way to measure depth since it is hard to draw a line from the surface skin to the bottom of the wound. With all this information, I can calculate an approximation of the wound volume. 

Week 8: First Impressions of MeshLab

This week, I finally started to take a look at the MeshLab program. This blog post is going to catalog some of the first things I noticed.

One of the most striking things, that make it different from Artec Studio 11, is the fact that the files don't carry color information. This is how one of the wound models looked when I first uploaded it. 

 

The ring around the model allows me to rotate it in all directions. It is actually more versatile than the model on Artec Studio 11. 

Another nice thing about this program is the many options it offers. For example, I am able to add a 3D coordinate axis to the model, as shown below.

 

 Once I get more familiar with how to take measurements, I'm sure the axes will come in handy. 

I can also use the measuring tape tool to take an approximation of the wound length and width. However, this is not very useful when trying to assess depth since I can't draw an accurate line from the surface of the wound to the bottom. 

The two numbers in the left corner gave numerical values to the length of the yellow lines. However, these are arbitrary units used by the program. A scan of a door would be reduced to the same size as that of a mouse. One of the next things I have to do is convert these arbitrary units to real measurements. 

It has definitely been a challenge to navigate another new program. Next week, I'll look up some tutorials to figure out all the features MeshLab has to offer. 

HIPAA: A Guide to Patient Privacy

Privacy is an important right, especially for patients who don't need another thing to worry about. 

HIPAA (The Health Insurance Portability and Accountability Act) was passed by Congress in 1996 to protect health insurance coverage for workers as well as ensure patient privacy. 

https://ora.georgetown.edu/irb/HIPAA

Anything on a patient's medical record or related to their insurance coverage cannot be disclosed. This includes any medical bills or descriptions of their condition. 

The protection is very inclusive. Healthcare providers are not even allowed to discuss any conversations about a patient's health or treatment. 

There is also some information secured by HIPAA that may not directly have to do with a patient's stay at the hospital. Addresses, phone numbers, email addresses, and license plate numbers are all protected by HIPAA. A hospital may not give out any of these details. 

HIPAA also ensures that patients are able to access all the information they need. They may request copies of their health records as well as any notices explaining how they have been used and shared. 

When any information is needed by healthcare professionals for research, they must file papers to the IRB (Institutional Review Board). This makes sure that the rights and welfare of human subjects are safeguarded. 

Personalized Medicine is the Future

It is officially the final month of our senior projects.
To all the seniors out there, I hope you are happy with all the college acceptances that came out this week! 

For this post, I am going to be talking about the emerging field of personalized medicine. Also called precision and stratified medicine, this procedure tailors diagnosis and treatment to specific patients. 

Every person is different. Each patient has a unique set of genes and their expressions. Thus, it only makes sense that some diagnoses and treatments would vary. Personalized medicine takes into account takes the individuality of every patient.

In the words of former president Barack Obama, precision medicine promises "the right treatments at the right time, every time, to the right person." 

An example of this are the new advances in genomics. New technology allows us to sequence people's genes. This not only gives insight into human DNA, but also allows for diagnosis of hereditary diseases. For instance, a mutated BRCA1 gene usually leads to the develop of breast cancer in a patient. 

However, the genetic information itself is not what makes the difference, but the behavior following. If genetics predisposes someone to diabetes, they have to take action to avoid the disease early-on. 

This movement toward individualized medicine makes sense. Patients want to know they are getting the best care possible. This new treatment system ensures each patient is given the time and attention they need. 

Now to relate this to my project, I would argue that laser scanning a patient's wound is a form of personalized medicine.

Potentially, the physician would be given information on the wound dimensions and volume of each patient. Instead of applying the same treatment plan for every wound, doctor's would be able to make specific observations about what the best course of action is for each patient. 

See you next week!

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! 

The Basics of Laser Scanners

During the end of this week and the beginning of the next, I will be spending time learning how to use the laser scanner and becoming acquainted with the programs used to produce 3D images. 

Let's first discuss how a laser scanner works.
Laser scanners let out beams of controlled lasers that take a distance measurement to an object. This means that they can create an accurate rendering of the outer surface of any model. 

Laser scanners are found everywhere, from police laser speed guns, to the cashier scanners in grocery stores.
For the purpose of my project, I will be looking at how they can be applied in the medical field.
 

https://virulentwordofmouse.wordpress
.com/2011/07/04/the-grocery-scanner-and-
barcode-economy/

http://www.stealthveil.com/guides/police-laser

This week I read some journal articles on how researchers have used laser scanners in relation to wounds in the past. 

One study focused on the use of digital image analysis to assess wound area and volume. In this paper, physicians reported a 95% confidence interval and there was no statistical significance difference between their measurement of the wounds. The full article can be found here. 

Another used Laser Doppler Imaging to assess the severity of pediatric burns. Burn outcomes are predicted accurately by physical examination of a physician 50 to 65% of the time. However, the Laser Doppler Imaging showed an overall accuracy of 96%. The full article can be found here. 

I'm really excited to finally start using the equipment.
I'll let you know how it goes next week!

Types of Wounds

There are several ways wounds can be classified. 

Acute and chronic describes the amount of time it takes for a wound to heal. Acute wounds go through the normal healing process and show signs of repair within four weeks. Chronic wounds take much longer to heal because of complications such as infection or diabetes. 

There are six basic types of wounds: 

1. Abrasions occur when skin is rubbed or scraped off by friction.

2. Incisions are made by cutting with a sharp object. This includes wounds created during surgery. Incisions are not likely to become infected since the free flow of blood washes out most microorganisms. 

3. Lacerations are wounds that were torn by blunt objects. 

4. An injury to the skin due to heat, cold, electricity, chemicals, or radiation is called a burn. 

5. Puncture wounds leave a small hole while penetrating into the tissue. 

6. Avulsions, a tearing away of tissue from a body part, always involve heavy bleeding. 

All wounds either fall under these categories or are a mixture of these types. 

I will be focusing on wounds that have an outer manifestation. This is because laser scanners are used to create models of the outside surface of an object.
The first four in the list have the greatest applicability for this project. 

For my next post, I will go into greater detail about the basics of laser scanners and how they have been used in the past for medical purposes.