Sample Thesis Projects

A Master’s Thesis…

Original investigation with expository illustrations (includes 3-D instructional model, computer visualized images, animated sequence, or video) completed under a University approved faculty preceptor and department faculty advisor. All work complies with University research, publication, copyright, and patent policy.

Pancreatic Cancer Genome Sequencing Research at Johns Hopkins: An Online Multimedia Patient Education Program :: WENJING “BETTY” WU

Pancreatic cancer is among the most lethal forms of cancer because it is difficult to detect and treat. Just like other cancers, pancreatic cancer is, in essence, a genetic disease. Studies of cancer genomes with new high throughput sequencing technologies, alternatively called second-generation or next-generation sequencing, have shed new light on personalized pancreatic cancer research and novel patient-specific clinical interventions. The Sol Goldman Pancreatic Cancer Research Center at Johns Hopkins recently completed a large pancreatic cancer genome sequencing project. The team established the National Familial Pancreas Tumor Registry (, discovered many of the genes involved in the development of pancreatic cancer, and helped identify the pre-cursor lesions that give rise to invasive pancreatic cancer. It is crucial that patients and their families are able to learn about this ongoing research and understand how the cutting-edge cancer sequencing technology can help them. No current online resource addressing cancer genome sequencing is easily accessible, or appears in a comprehensive and organized visual format. Due to the rapidly evolving nature of second-generation sequencing techniques, teaching materials on related biological topics can become obsolete quickly. A comprehensive and up-to-date online educational program with multimedia components and interactive modules will fill this void. The primary goal of this project was to educate pancreatic cancer patients and their families about second-generation DNA sequencing technologies and ongoing pancreatic cancer genome research at Johns Hopkins, utilizing clear and engaging visuals. The goal has been achieved by a combination of engaging infographic animation, informative interview videos, and interactive review quizzes. All components were reviewed by content experts and integrated into a dynamic webpage on the website of the Sol Goldman Pancreatic Cancer Research Cencer ( This cross-platform design creates a dynamic and efficient learning experience for users and may also contribute to the development of future web-delivered instructional design projects. To view this project, visit

A Visual Resource for Liver Transplant: Anatomic Implications for Postoperative Care :: ELYSSA SIEGEL
Liver BiopsyOver 6,300 liver transplants were performed in the US in 2011. A caval preservation “piggyback” technique is commonly used; the donor inferior vena cava (IVC) is fashioned into a pouch that is anastomosed, side-to-side, to the intact recipient IVC. This technique creates a significantly altered postoperative caval configuration that is confusing to visualize and is not well understood by healthcare practitioners. Following liver transplant, patients are lifelong recipients of specialized healthcare, monitored carefully by their transplant surgeons and other specialists when complications arise. Clinical specialists, such as interventional radiologists and endoscopists, must be aware of the significantly altered postoperative anatomy to avoid iatrogenic injury. This project was undertaken to address a lack of resources in which the postoperative configuration is depicted. Visuals are essential to depict this complex anatomy and other postoperative issues and to facilitate communication between transplant surgeons and other healthcare professionals. The “Visual Resource for Liver Transplant” website ( was created to communicate this visually rich information to a widespread audience. Four interactive modules depicting altered anatomy and segmental liver anatomy were produced. These modules allow the user to show and hide eight different anatomical structures and the segments of the liver as well as to compare two postoperative anatomies side-by-side on the same screen. Four full-color 2D animations were created describing common postoperative complications and methods of treatment: Liver Biopsy, Hepatic Artery Stenosis/Thrombosis, Bile Duct Stricture (ERCP), and Bile Duct Leak (ERCP). Liver transplant patients are often particularly invested in understanding the specialized healthcare they require following a transplant. The clear and accurate visual elements (animations and interactive illustrations) combined with a glossary of medical terms were designed to help a sophisticated lay audience utilize this resource. All content was iii embedded within a website, offering a non-linear approach to understand and visualize the postoperative altered anatomy. The site has broad applications to facilitate communication among healthcare professionals and to enhance outcomes for transplant patients.

To view this project, visit

Pudendal Nerve Entrapment: An Anatomical Study And Three-Dimensional Visualization Of Nerve Variations And Branching Patterns :: COURTNEY McKENNA
Entrapment of the pudendal nerve can lead to chronic debilitating pain. The complex course and anatomical variations of the pudendal nerve and its branches provide opportunities for injury and entrapment. This anatomy is poorly understood and inadequately illustrated. Originating from the sacral plexus, the pudendal nerve leaves the pelvis through the greater sciatic notch and travels between the sacrospinous ligament and sacrotuberous ligament, into the ischiorectal fossa where it enters Alcock’s canal and exits anteriorly traveling through the pubic ramus canal as the dorsal nerve of the clitoris or the penis. The rectal and perineal nerve branches arise at varying sites along this pathway. Limitations in existing anatomic understanding, ineffective surgical outcomes, and the high incidence of chronic pelvic pain create a need for an innovative visualization. Cadaveric dissections of 10 hemipelvises were completed to study the multiple branching patterns and varied course of the pudendal nerve. A detailed Illustration and diagrammatic insert documenting measurements was created of each hemipelvis. High density MR Neurography and CT scans were taken of one male and one female pelvis block pre and post surgical dissection in which pudendal nerve branches were identified and marked. A 3D computer model showing the most common branching pattern and pathway variations of the pudendal nerve seen in the above research was created. Each hemipelvis demonstrated considerable variation in branching patterns adjacent to the sacrospinous ligament: 50% had 2 trunks present, 40% had 3 trunks present, 1 had 1 trunk present, and 60% had a separate rectal branch. A common perineal/dorsal trunk and common rectal/perineal trunk was seen most often. Each pudendal nerve branch coursed as a separate nerve 100% of the time after crossing the sacrospinous ligament. Variation of the level at which the dorsal nerve to the clitoris/penis exited Alcock’s canal in relation to the ischial tuberosity ranged from 25mm to 45mm in the 10 hemipelvises. Detailed anatomical illustrations and a 3D pelvis model will provide clinicians, radiologists, surgeons and patients a innovative visualization, thus aiding in better understanding of the complexity of pudendal nerve anatomy and its zones of entrapment, increasing successful diagnosis and treatment for those suffering with chronic pelvic pain due to pudendal neuralgia.

Revealing the Face of an Ancient Egyptian: Synthesis of Current and Traditional Approaches to Evidence-Based Facial Approximation :: KAITLIN LINDSAY
Forensic facial approximation plays a unique role in archaeology and mummy studies by visualizing the appearance of people from the past. This thesis consists of a case report of the study and 3D facial approximation of an ancient Egyptian mummy head using medical imaging data and the digital sculpting program, ZBrush. The goals of the project included a description of the physical state of the head as revealed by CT and MRI scans, a biological profile of the deceased, and an attempt to gain knowledge regarding this individuals pre- and post-mortem history.
The project revealed the mummy to be an adult woman from the 20th, 21st, or 22nd Dynasty. Areas of damage caused by looting and possible trephination or skull fracture were observed. After a thorough literature review of facial approximation techniques, the mummys face was approximated using only those methods based on the most solid anatomical or statistical evidence. The results of the project made it clear that although certain improvements have been made in devising repeatable and evidence-based guidelines for facial approximation, there are many proposed methods still awaiting confirmation from comprehensive studies. It is hoped this work will assist artists, investigators, and anthropologists in visualizing the faces of unidentified or ancient remains by documenting the process of facial approximation in 2012 using modern software and a synthesis of the latest published evidence-based techniques.

Didactic Magnetic Resonance Neurography: Illustrating a Web-Based Anatomical Atlas of the Lumbosacral Plexus :: EO TRUEBLOOD

Within the past twenty years, there have been great strides in Magnetic Resonance Neurography (MRN) making it possible to see smaller nerves, including those of the lumbosacral plexus. By contrast, what has been lagging is the ability of radiologists to identify these nerves and their pathologies. This gap has created a need for new and specific learning tools. In the rapidly changing landscape of educational materials and quickly advancing medical technology and implementation of MRN, there is an ever growing need to find better ways to educate students and medical professionals alike. This thesis creates the foundation for a powerful teaching tool by combining the interactivity of digital media, cutting-edge 3Tesla MRN, and customized 2D MRN illustrations and 3D digital models with expert knowledge from specialists in the field. This teaching platform allows the user to work intuitively with MRN images, using similar tools as they would on a radiology work station while cross referencing a 3D digital model. The 3D interactive model allows for better understanding of the nerve paths of the lumbosacral plexus, and surrounding anatomical structures. This thesis not only helps combine the above mentioned tools and educational elements, it also is the product of an exploration as to how best represent those specific elements. The 2D MRN color overlay illustrations were created using OsiriX DICOM imaging software and Adobe® Photoshop® in tandem. OsiriX allowed for the MRN images to be exported as usable Tiff files in Photoshop®. Photoshop® was further used to create the layers of instructional color, and labels. OsiriX and the Pixologic. 3D sculpting software ZBrush® were used to create the 3D digital sculpture of the peripheral nerves of the lumbosacral plexus, muscles, and the bony anatomy. In OsiriX, CT data was rendered as a skeletal surface model and exported as an Obj file. ZBrush® was used to augment a preexisting 3D muscle model into all the needed muscles and ligaments. The peripheral nerves of the lumbosacral plexus were also created in ZBrush® using a tool called “Zspheres”. Flow charts were created to visually understand the interactivity paths within the website. Storyboards were created from the flowcharts, setting the visual foundation for the website. Both the flowcharts and storyboards were created in Adobe® Illustrator®, as well as the final website interface. The interface is the union of all the different teaching tools and interactive elements, with a cohesive style, color scheme, and logical flow of information. This thesis sets the groundwork for creating a system, which can increase the ability of professionals using MRN to accurately diagnose and treat disorders of the peripheral nerves. The combination of good MRN visuals, proper instruction in identification of anatomy, didactic illustrations, and an interactive interface is what gives its users an opportunity to build a better understanding of the lumbosacral plexus.

Visualizing Protein Databases: Cardiomyocyte of a Rabbit (Oryctolagus cuniculas) as a Prototype ::ELIZABETH COOK
The study of DNA and proteins is a frontier that holds enormous potential for better understanding of diseases and aging. Though cells are tremendously complex environments, we are constantly learning more about their composition, compartments, and the myriad of proteins that drive cellular function. Techniques for identifying and studying these proteins (proteomics) have generated enormous quantities of data. While there has been rapid evolution in the field of bioinformatics where information is processed and curated, a critical failure lies in the communication of this data through impactful means to other scientists, students, and curious lay people. Upon collaboration with bioinformaticians and researchers, a conceptual prototype was developed that proposes a unique solution for visually organizing and indexing complex biomedical subject matter for easy search and retrieval. Using code to link our prototype with existing databases, we can harness their power on the back end of this new model. The development of an appropriate and intuitive interface will preserve the functionality of a comprehensive protein database. The cardiomyocyte of a rabbit was chosen as a model, and original artwork was created to demonstrate how a user would visually navigate through the cell and through different levels of scale to retrieve data. This new model will place biomedical data firmly within the context of cell anatomy. This will allow the user to appreciate relationships between form and function, make new connections between data, visualize physiological concepts, and better communicate ideas to peers and students.

Virtual Resurrection of a New Species of Hadrosauroid Dinosaur Provides Novel Insight into Chewing Biomechanics :: DAVID CHENEY

Virtual Resurrection of a New Species of Hadrosauroid Dinosaur Provides Novel Insight into Chewing BiomechanicsThe Hadrosaurid dinosaurs were among the most diverse and successful of all herbivores dinosaurs known. Understanding their highly adaptive masticatory pattern may have contributed to their success. This virtual reconstruction of a dinosaur skull created by David Cheney from surface laser scans of all 23 bones of the skull and the resulting animation offers the most definitive evidence to demonstrate the pleurokinetic mastication cycle first theorized by Dr. David Weishampel in the Center for Functional Anatomy and Evolution here at Hopkins back to the 1990s. Additionally, te model will allow researchers to investigate the plausibility of many long-standing hypotheses with unpresendedted efficacy and accuracy.

A Qualitative Analysis of Infant Suckling in Four Species using Digital Animation :: DEVON (NYKAZA) STUART

Using Adobe Flash Devon Nykaza (JHU 07) was able to created scientific digital animations that revealed differences and new similarities in suckling among four species (miniature pigs, long tailed macaques, domestic cats, and opossums). The visual success of the graphic solution highlights differences in the suckling mechanism among species and confirms the differences in the suckling mechanism correlated with differences in adult behavior and head morphology.

The Anatomy of the Grey-headed Flying Fox, Pteropus policephalus :: CATHERINE DELPHIA
This thesis provides a comprehensive source of the gross anatomy of bats including essential information for treating and caring for the captive animals. Catherine Delphia (JHU 06) under the preceptor ship of Dr. Brent Whitaker Deputy Director at the National Aquarium in Baltimore, and Dr. Kerryn Parry Jones, University of Sydney Australia, studied and examined, through dissection, the anatomy of the grey-headed flying fox, a fruit bat recently listed as endangered in Australia. It establishes a cohesive series of illustrations that visually describe the gross anatomy of the fruit bat. Surgical approaches, medical treatments, and clinical recognition of disease or injury can only be facilitated by understanding this information.