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HCI Research: 3D Data Segmentation – Old Page

HCI Research: 3D Data Segmentation – Old Page

CT 3D imaging

Ambiguity is present in all types of images. How do experts resolve ambiguities in interpretation of 3D imaging?

Prof. Ruth West (University of North Texas), is engaged in collaborative research with Prof. Cindy Grimm (Oregon State Univserity) and Prof. Tao Ju (Washington University St. Louis) to study the cognitive and perceptual basis of how experts extract 3D shapes from volumetric data, such as electron tomography, MRI or CT imaging. This process, known as “segmentation” plays an essential role in the interpretation and analysis of volume data in a variety of application domains.

Understanding what a segmenter sees, thinks, and does while interacting with a data set will help to make future tools more efficient, alleviating the major scientific bottleneck posed by the time-intensive nature of segmentation. It will also help in developing better tools to improve the accuracy and repeatability of the segmentation process, positively enhancing the quality of the resulting data for use in a variety of  applications, including biomedicine, clinical practice and environmental engineering.

This work is supported by NSF Collaborative: Developing Conceptual Models for Navigation, Marking and Inspection in the Context of 3D Image Segmentation, IIS-1302248, IIS-1302142, IIS-1302200.


IRB Information

Other documents:

  1. Approval Notice

  2. Research Protocol

  3. Verbal Consent Form

  4. Phone Consent

  5. Recruitment Email

  6. Interview Questions

Information about the 3D image segmentation study

Project Title: Developing conceptual models for navigation, marking, and inspection in the context of 3D image segmentation

Principal Investigators: Ruth West (University of North Texas), Cindy Grimm (Oregon State University), Tao Ju (Washington University in St. Louis)

Student Researcher: Michelle Vaughan (Washington University in St. Louis), Anne Carlew (University of North Texas), Jeremy Deutsch (University of North Texas), Meghan Kajihara (University of North Texas), Max Parola (University of North Texas), Anahita Sanandaji (Oregon State University)


Co-Investigator(s): Ruth West (University of North Texas)


Sponsor: National Science Foundation

Version Date: 4/24/2013


This form contains information you will need to help you decide whether to be in this research study or not.  Please read the form carefully and ask the study team member(s) questions about anything that is not clear.


The purpose of this research study is to investigate 3D image segmentation as a human-computer interaction paradigm and to understand human factors that are involved in the current segmentation process, with the goal of making the process more efficient, accurate and repeatable. The investigation is motivated by our experience with a range of domain experts who have all highlighted similar areas of inadequacies in current tools, such as navigation, marking and inspection. Our hypotheses are that the segmentation process could be significantly improved with a better understanding of how humans perform low-level perception and cognition tasks in the context of 3D segmentation (e.g., visual cues, delineation of structures by marks, and local accuracy or quality criteria) and how domain experts wish to specify high-level segmentation constraints (e.g., connectivity, topology, and shape).

We expect 30 people (maximum 50) to be invited to take part in this study.


You are being invited to take part in this study because you have experience with segmenting 3D images.


You will first be asked to create a 3D image segmentation of a data set you are familiar with using the segmentation tool(s) you currently used. During this process you will be asked to “think aloud”, explaining what you are doing and why to the best of your ability. During and after this interview process we may ask specific questions to clarify what you are doing and why. We expect this to take approximately 2-3 hours. We will video tape your monitor and record the questions and answers. The video tape will be stored without any personal information to identify you (other than the content of the video itself).

Codify discussions: After the interview we will codify the segmentation process, characterizing low-level sub-tasks, constrains, visual cues, and global segmentation constraints. We will ask for your input on this characterization to ensure that it accurately reflects your view of the segmentation process. This conversation will take place via a combination of shared documents (eg Google docs), email, and follow-up phone or Skype conversations. We expect this process to continue for approximately 3-6 months after the initial study; our estimated amount of time spent in this conversation is 1-2 hours per 3-4 weeks.

Approximately 6-9 months after the initial interview we will return for a second interview. Procedures for this interview will be similar to the first, except that you will be asked to work with a customized segmentation tool developed by the study authors. We will work with you in the week prior to the visit to ensure that the tool will work with your data, and we will provide a brief training session as part of the interview process.

In the following year we will repeat the entire interview and codify process, only this time the goal is to capture the higher-level goals of your segmentation task.

Software discussions: You may also participate in on-going discussions about algorithm and interface development. These discussions will take place through shared documents, email, and phone or Skype conversations.

The interviews require recording. If you do not wish to be recorded you may still participate in the discussion stages.

The discussion stages require an email address and/or phone or skype conversations. If you wish to remain anonymous for these stages you may do so through an anonymous account supplied to you by PI Grimm. She will be the only study team member who will know your identity.

The entire study duration is approximately three years. You may participate for some or all of that time, and may withdraw at any time.

Approximate study length and time commitments:

Participation questions. You may consent to participate in just the interviews, the interviews and the discussion phases, or just the discussion phases. If you wish, we will create an anonymous login for the discussion phase. We will destroy the video tapes after they are transcribed, unless you give us permission not to.

Future contact: We may contact you in the future for another similar study.  You may ask us to stop contacting you at any time, and withdraw from the study at any time.

Study results: The results of the study will be available to you in the following three forms:

1)Whether or not you choose to participate in the discussion sessions you may request a copy of the on-going findings as they are developed in the shared documents.

2)The study findings will be published in a scholarly journal. You may request to have a copy of any and all papers written based on the study.

3)The software under development will be open-source and available for your use.


The possible risks and/or discomforts associated with the being in the study include:  Boredom, fatigue, and frustration while using software under development. If you are participating in the discussions there is some risk of embarrassment and conflict because of differences of opinion amongst participants and study personnel. The PI will moderate the discussions to reduce conflict where possible, and in extreme cases will exclude participants who are overly disruptive or abusive.

There is some small risk that the overall quality of the segmentations you (and possibly your colleagues) produce will be called into question because of the results of this study, or that you may find that you need to change your segmentation approach. One of the goals of this study is to identify the source of errors in segmentation, and to find ways to mitigate sources of these errors.

In the discussion stage the data collected will be in the form of shared Google documents. There is some risk of breach of confidentiality if study participants share data from these links beyond the designated study personnel and participants. There is also a very minimal risk of this data being lost or corrupted because of changes at Google or web-based attacks.


The benefits to you are a better self-understanding of the segmentation process, and (potentially) development of better segmentation tools by both the authors of this study and other groups working on novel segmentation approaches.

The community of people using segmentation tools (you) is largely divorced from the people building segmentation tools. By formulating and studying segmentation as a human perception and cognitive task, we aim to bridge the gap between the two communities, leading both to better designs for current and future segmentation tools and the framing of new problems for segmentation algorithms. For end users, our working prototype will support a more effective segmentation experience that is powered by the underlying conceptual framework. Furthermore, formalizing the kinds of perceptual cues and conceptual models users have when approaching the segmentation problem can serve as a useful test-case for understanding the more general domain of how perception and cognition interact when they are re-mapped to solve a problem they were never designed for.


You will not be paid for being in this research study. However, your lab director has agreed to let us conduct these interviews during work hours, and for you to participate in the discussions during work hours as well.


This study is part of a National Science Foundation grant.


The information you provide during this research study will be kept confidential to the extent permitted by law.   Research records will be stored securely and only researchers will have access to the records. Federal regulatory agencies and the Oregon State University Institutional Review Board (a committee that reviews and approves research studies) may inspect and copy records pertaining to this research.  Some of these records could contain information that personally identifies you.

If the results of this project are published your identity will not be made public unless you specifically ask to be included in the acknowledgements section.

The National Science Foundation, as the sponsor of this study, may request to see the information obtained in this study.

Only study members will have access to the video and audio recordings. These recordings will be destroyed after they have been analyzed if you requested them to be. You may ask for the recordings to be destroyed at any time.

To help ensure confidentiality, we will use an identification code to link video recordings with your personal information and to link you with any anonymous email/contact information. Only the PI will have access to the link between the identification codes/anonymous emails and your personal identification. If you have agreed to use your own email for discussions, both the study members and other participants will have access to that information; all data will be anonymized before being published, however. The video recordings will be stored on secured laptops (one at each site) and the identification codes on a single piece of paper kept in a locked drawer in PI Grimm’s office.


Participation in this study is voluntary.  If you decide to participate, you are free to withdraw at any time without penalty. You will not be treated differently if you decide to stop taking part in the study. If you choose to withdraw from this project before it ends, the researchers may keep information collected about you and this information may be included in study reports.

The new segmentation tools we are working on, along with papers published, will all be available on-line at http://volumeviewer.cse.wustl.edu/. You may use the software or the results of the study whether or not you participate in the study. You may also contribute to discussions of the software through either personal communication with the authors or through an on-line wiki available from that site.


If you have any questions about this research project, please contact: PI Grimm, cindy.grimm@oregonstate.edu (541) 737-4914.

If you have questions about your rights or welfare as a participant, please contact the Oregon State University Institutional Review Board (IRB) Office, at (541) 737-8008 or by email at IRB@oregonstate.edu

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