Hauptseminar/Master Seminar:
Image-based tool tracking for computer aided biopsy procedures

Prof. Nassir Navab, Dr. Christoph Hennersperger, Rüdiger Göbl, Julia Rackerseder

Type: Master Seminar Module IN2107
SWS: 2
ECTS: 4 Credits
Course Language: English

Content

In traditional surgery, the outcome of the procedure depends entirely on the skills of the physicians and nurses. Today, interventional imaging and new solutions support the physicians during the intervention, with the main goal of improving patient safety. We need to overcome many challenges, including spatial constraints in the OR as well as the desire for minimally invasive procedures. With respect to the diagnosis in various medical disciplines (e.g. neurosurgery, breast care, general oncology, etc.), a biopsy is the main source of information for the appropriate treatment strategy.

Most of today's biopsy procedures are still performed without additional guidance and support by imaging, causing unnecessary complications and partially low success rates. Interventional and general imaging could potentially provide support during biopsy in interventional settings, and researchers have focused on this area over the last years.

This seminar course focuses on current research topics in the field of images-based tracking for biopsy applications, covering a variety of interventional settings and applications.

The seminar will cover:

• Interventional imaging (mainly ultrasound, but also MRI, CT)
• Image-based tracking methods (e.g. needle tracking)
• Applications to different medical areas (e.g. Neurosurgery, breast tumor care)
• Etc.

Announcements

• [01.06.2016] Initial seminar information page created.
• [28.09.2016] The date of the introductory meeting changed: it is now Tuesday, 25th of October at 13:00, instead of 27th as initially announced.
• [21.10.2016] The dates of the presentations are fixed.
• [15.12.2016] The presentation time-slots have been assigned.

Registration

• TUM students: Register in the matching system for the course registration between 01.07.2016 and 06.07.2016 (link). Keep in mind that your chances to be assigned to the course increase if you give it a higher rank in your choices.
• Exchange students without TUMonline account: Please send a nice mail to Christoph Hennersperger to indicate that you want to participate, including your name, your birthday, program of study and Matrikelnummer (if you already have one). We will then enroll you in the course, given you match the requirements (Master's student).
• Maximum number of participants: 12

Regulations

In this Master Seminar (formerly Hauptseminar), each student is asked to select one paper from a list. In order to successfully complete the seminar, participants have to fulfill these requirements - all three will influence the final grade:

• Presentation: The selected paper is presented to the other participants (15 minutes presentation, 10 minutes questions). Use the CAMP templates for PowerPoint  camp-tum-jhu-slides.potx, or Latex:  CAMP-latex-template.zip.
• Written Report: A document of maximum 8 pages (i.e. a PDF with 8 pages) is written and submitted one week after the presentation, 23:59. Please download and use the  CAMP Seminar Latex template. Alternatively, you can also use the LNCS Latex template llncs2e.zip directly from the Springer website.
• Attendance: Participants have to participate actively in all seminar sessions.

Each presentation is followed by a discussion and everyone is encouraged to actively participate. The report must include all references used and must be written completely in your own words. Copy and paste will not be tolerated. Both report and presentation have to be done in English.

Schedule

The seminar consists of a preliminary meeting, an introductory meeting and seminar sessions. Each of the sessions will consist of several student presentations. All seminar participants are expected to be present at every session and to actively participate in the discussion.

Date	Time	Room	Topic	By	Material
30.06.2016	14:00-14:30	03.13.010	Preliminary Meeting	Tutors
25.10.2016	13:00-14:00	03.13.010	Introductory Meeting	Tutors	Papers
27.10.2016	12:00 (AM)	email	Paper selection: e-Mail to Rüdiger Göbl	Students
from 27th of October		Tutor offices	You may contact your tutor and arrange an appointment to discuss outline of your presentation and ask targeted questions
15.12.2016	13:00-17:00	03.13.010	Presentation Training	Tutors
10.01.2017	10:00-12:00	00.12.019	Paper Presentations I	Students
11.01.2017	14:00-16:00	01.11.018	Paper Presentations II	Students
18.01.2017	23:59	email	Written reports due: e-Mail to Rüdiger Göbl	Students

Paper Presentations

Presentation duration: 15 minutes presentation, 10 minutes questions

First Name	Name	Date	Time
Sebastian	Requena Witzig	10.01.2017	10:30
Ramona	Schneider	10.01.2017	11:00
Philipp	Jutzi	10.01.2017	11:30
Maximilian	Geißler	10.01.2017	10:00
Irving	Cabrera	11.01.2017	14:00
Benito	Diaz Nava	11.01.2017	15:00
Alexander	Binsmaier	11.01.2017	14:30

Paper Assignments

First Name	Name	Paper Assigned	Tutor
Maximilian	Geißler	[5]	Rüdiger Göbl
Sebastian	Requena Witzig	[2]	Rüdiger Göbl
Ramona	Schneider	[13]	Julia Rackerseder
Philipp	Jutzi	[10]	Julia Rackerseder
Irving	Cabrera	[11]	Dr. Christoph Hennersperger
Alexander	Binsmaier	[4]	Dr. Christoph Hennersperger
Benito	Diaz Nava	[1]	Rüdiger Göbl

List of Papers

[1] N. Shahriari, R. J. Roesthuis, N. J. Van De Berg, J. J. Van Den Dobbelsteen, and S. Misra, “Steering an actuated-tip needle in biological tissue: Fusing FBG-sensor data and ultrasound images,” in Proceedings - IEEE International Conference on Robotics and Automation, 2016, vol. 2016–June, pp. 4443–4449.

[2] M. Mura, S. Parrini, G. Ciuti, V. Ferrari, C. Freschi, M. Ferrari, P. Dario, and A. Menciassi, “A computer-assisted robotic platform for vascular procedures exploiting 3D US-based tracking,” Comput. Assist. Surg., vol. 21, no. 1, pp. 63–79, 2016.

[3] A. Pourtaherian, S. Zinger, P. H. N. de With, H. H. M. Korsten, and N. Mihajlovic, “Benchmarking of state-of-the-art needle detection algorithms in 3D ultrasound data volumes,” Prog. Biomed. Opt. Imaging - Proc. SPIE, vol. 9415, p. 94152B, 2015.

[4] P. Chatelain, A. Krupa, and M. Marchal, “Real-time needle detection and tracking using a visually servoed 3D ultrasound probe,” Proc. - IEEE Int. Conf. Robot. Autom., pp. 1679–1681, 2013.

[5] H. R. S. Neshat and R. V. Patel, “Real-time parametric curved needle segmentation in 3D ultrasound images,” Proc. 2nd Bienn. IEEE/RAS-EMBS Int. Conf. Biomed. Robot. Biomechatronics, BioRob^? 2008, pp. 670–675, 2008.

[6] S. Cheung and R. Rohling, “Enhancement of needle visibility in ultrasound-guided percutaneous procedures,” Ultrasound Med. Biol., vol. 30, no. 5, pp. 617–624, 2004.

[7] N. I. Sainani, R. S. Arellano, P. B. Shyn, D. A. Gervais, P. R. Mueller, and S. G. Silverman, “The challenging image-guided abdominal mass biopsy: Established and emerging techniques ‘if you can see it, you can biopsy it,’” Abdom. Imaging, vol. 38, no. 4, pp. 672–696, 2013.

[8] O. Zettinig, A. Shah, C. Hennersperger, M. Eiber, C. Kroll, H. K??bler, T. Maurer, F. Milletari, J. Rackerseder, C. Schulte zu Berge, E. Storz, B. Frisch, and N. Navab, “Multimodal image-guided prostate fusion biopsy based on automatic deformable registration,” Int. J. Comput. Assist. Radiol. Surg., vol. 10, no. 12, pp. 1997–2007, 2015.

[9] A. M. Franz, T. Haidegger, W. Birkfellner, K. Cleary, T. M. Peters, and L. Maier-Hein, “Electromagnetic tracking in medicine -A review of technology, validation, and applications,” IEEE Trans. Med. Imaging, vol. 33, no. 8, pp. 1702–1725, 2014.

[10] C. R. Weiss, S. G. Nour, and J. S. Lewin, “MR-guided biopsy: A review of current techniques and applications,” J. Magn. Reson. Imaging, vol. 27, no. 2, pp. 311–325, Feb. 2008.

[11] D. R. Elgort, E. Y. Wong, C. M. Hillenbrand, F. K. Wacker, J. S. Lewin, and J. L. Duerk, “Real-time catheter tracking and adaptive imaging,” J. Magn. Reson. Imaging, vol. 18, no. 5, pp. 621–626, Nov. 2003.

[12] C. Baur, S. Albarqouni, S. Demirci, N. Navab, and P. Fallavollita, “CathNets: Detection and Single-View Depth Prediction of Catheter Electrodes,” in Medical Imaging and Augmented Reality: 7th International Conference, MIAR 2016, Bern, Switzerland, August 24-26, 2016, Proceedings, G. Zheng, H. Liao, P. Jannin, P. Cattin, and S.-L. Lee, Eds. Cham: Springer International Publishing, 2016, pp. 38–49.

[13] L. C. Garcia-Peraza-Herrera, W. Li, C. Gruijthuijsen, A. Devreker, G. Attilakos, J. Deprest, E. Vander Poorten, D. Stoyanov, T. Vercauteren, and S. Ourselin, “Real-Time Segmentation of Non-Rigid Surgical Tools based on Deep Learning and Tracking,” pp. 1–12, 2016.

Literature and Helpful Links

A lot of scientific publications can be found online.

The following list may help you to find some further information on your particular topic:

• Microsoft Academic Search
• Google Scholar
• CiteSeer
• CiteULike
• Collection of Computer Science Bibliographies

Some publishers:

• ScienceDirect (Elsevier Journals)
• IEEE Journals
• ACM Digital Library

Libraries (online and offline):

• http://rzblx1.uni-regensburg.de/ezeit/ (Elektronische Zeitschriften Bibliothek)
• Verbundkatalog des Bibliotheksverbundes Bayern (BVB)
• Computer ORG
• http://www.ub.tum.de/ (TUM Library)
  • To get access onto the electronic library, see http://www.ub.tum.de/medien/ejournals/readme.html
  • "proxy.biblio.tu-muenchen.de" mit Port 8080 (nur fuer http). Damit klappen zumindest portal.acm.org und computer.org meistens
• Various proceedings of conferences in our AR-Lab, 03.13.036 (These proceedings are not for lending!)

Some further hints for working with references:

• JabRef is a Java program for comfortable working with Bibtex literature databases. Handy feature: if you know the PubMed ID for an article, JabRef can import data from there (via "Web Search/Medline").
• Mendeley is a cross-platform program for organising your references.

If you find useful resources that are not already listed here, please tell us, so we can add them for others. Thanks.