TubeTK/Data

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Data

100 Healthy Normal MRIs and MRAs from UNC

Intracranial-Teaser.jpg This dataset contains 100 (T1, MRA) image pairs from healthy patients, acquired by a Siemens Allegra head-only 3T MR system. The voxel spacing for the MRA images is (0.5x0.5x0.8mm) with a volume size of (448x448x128voxel); The voxel spacing for the T1 images is 1mm isotropic with a volume size of (176x256x176voxel).

The full dataset can be downloaded here. A subset of this dataset which also includes intra-cranial vasculature (centerline + radius), extracted from the MRA images, can be downloaded from here.



Recognition in Ultrasound (REUS) Database

REUS-Teaser.jpg This dataset contains Ultrasound videos, acquired on a (hand-made) noodle phantom. The database is split into template videos and search path videos and is designed to evaluate recognition algorithms. It can be downloaded from here.

TubeTK Testing data

A good resource for data to experiment with TubeTK is the testing data, available from here.

Patents

  • 6,690,816 : "Systems and methods for tubular object processing" Stephen R. Aylward, Elizabeth Bullitt, Daniel Fritsch, Stephen M. Pizer, February 2004
    • Patent is held by UNC. A world-wide, unrestricted, free license has been granted.

Books

S. Aylward and E. Bullitt, Chapter 11: Clinical Applications Involving Vascular Image Segmentation and Registration. Angiography and Plaque Imaging: Advanced Segmentation Tequniques, Academic Press, 2002 pp. 529-579

Journal Articles

  • R. C. Gessner, S. R. Aylward, and P. A. Dayton: Mapping Microvasculature with Acoustic Angiography Yields Quantifiable Differences between Healthy and Tumor-bearing Tissue Volumes in a Rodent Model, Radiology, vol. 264, no. 3, pp. 733–740, 2012.
  • E. Bullitt, D. Zeng, B. Mortamet, A. Ghosh, S. Aylward, W. Lin, B. L. Marks, and K. Smith: The effects of healthy aging on intracerebral blood vessels visualized by magnetic resonance angiography. Neurobiology of Aging, vol. 31, no. 2, pp. 290–300, 2010.
  • E. Bullitt, M. Ewend, J. Vredenburgh, A. Friedman, W. Lin, K. Wilber, D. Zeng, S. Aylward, and D. Reardon: Computerized assessment of vessel morphological changes during treatment of glioblastoma multiforme: Report of a case imaged serially by MRA over four years. NeuroImage, vol. 47, pp. T143–T151, 2009.
  • G. Piliere, M. H. Van Horn, R. Dixon, J. Stavas, S. Aylward, and E. Bullitt: Vessel target location estimation during the TIPS procedure. Medical Image Analysis, vol. 13, no. 3, pp. 519–529, 2009.
  • E. Bullitt, S. R. Aylward, T. Van Dyke, and W. Lin: Computer-assisted measurement of vessel shape from 3T magnetic resonance angiography of mouse brain, Methods, vol. 43, no. 1, pp. 29–34, 2007.
  • S. Aylward, K. Cleary, and D. Hawkes: Intraoperative image processing for surgical guidance. IEEE Transactions on Medical Imaging, vol. 24, no. 11, pp. 1401–1404, 2005.
  • E. Bullitt, D. Zeng, G. Gerig, S. Aylward, S. Joshi, J. Smith, W. Lin, and M. Ewend: Vessel tortuosity and brain tumor malignancy: A blinded study. Academic Radiology, vol. 12, no. 10, pp. 1232–1240, 2005 (Winner 2006 Herbert M. Stauffer Award by the Association of University Radiologists PMID: 16179200)
  • E. Bullitt, K. Muller, I. Jung, W. Lin, and S. Aylward: Analyzing attributes of vessel populations. Medical Image Analysis, vol. 9, no. 1, pp. 39–49, 2005.
  • E. Bullitt, M. Ewend, S. Aylward, W. Lin, G. Gerig, S. Joshi, I. Jung, K. Muller, and J. Smith: Abnormal vessel tortuosity as a marker of treatment response of malignant gliomas: Preliminary report. Technology in Cancer Research & Treatment, vol. 3, no. 6, pp. 577–584, 2004.
  • Y. Fridman, S. Pizer, S. Aylward, and E. Bullitt: Extracting branching tubular object geometry via cores. Medical Image Analysis, vol. 8, no. 3, pp. 169–176, 2004.
  • J. Jomier, S. Weeks, and S. R. Aylward: Vascular image registration for intra-operative 3D ultrasound annotation. International Congress Series, vol. 1268, pp. 1308–1308, 2004.
  • S. Aylward, J. Jomier, S. Weeks, and E. Bullitt: Registration and analysis of vascular images. International Journal of Computer Vision, vol. 55, no. 2–3, pp. 123–138, 2003.
  • E. Bullitt, G. Gerig, S. Pizer, W. Lin, and S. Aylward: Measuring tortuosity of the intracerebral vasculature from MRA images. IEEE Transactions on Medical Imaging, vol. 22, no. 9, pp. 1163–1171, 2003.
  • D. Wallace, A. Capone, J. Jomier, S. Aylward, M. Landers, M. Trese, and P.-R. S. Grp: Computer automated quantification of plus disease in RetCam images of retinopathy of prematurity. Investigative Ophthamology & Visual Science, vol. 44, no. 1, p. U116, 2003.
  • D. Wallace, J. Jomier, S. Aylward, and M. Landers: Computer-automated quantification of plus disease in retinopathy of prematurity. Journal of AAPOS, vol. 7, no. 2, pp. 126–130, 2003.
  • E. Bullitt and S. Aylward: Patient-specific vascular models for endovascular and open operative procedures. International Congress Series, vol. 1247, pp. 129–138, 2002.
  • S. R. Aylward and E. Bullitt: Initialization, noise, singularities, and scale in height ridge traversal for tubular object centerline extraction. IEEE Transactions on Medical Imaging, vol. 21, no. 2, pp. 61–75, 2002.
  • E. Bullitt, S. Aylward, K. Smith, S. Mukherji, M. Jiroutek, and K. Muller: Symbolic description of intracerebral vessels segmented from magnetic resonance angiograms and evaluation by comparison with X-ray angiograms. Medical Image Analysis, vol. 5, no. 2, pp. 157–169, 2001.
  • E. Bullitt, S. Aylward, E. Bernard, and G. Gerig: Computer-assisted visualization of arteriovenous malformations on the home personal computer. Neurosurgery, vol. 48, no. 3, pp. 576–582, 2001.
  • E. Bullitt, A. Liu, S. Aylward, C. Coffey, J. Stone, S. Mukherji, K. Muller, and S. Pizer: Registration of 3D cerebral vessels with 2D digital angiograms: Clinical evaluation. Academic Radiology, vol. 6, no. 9, pp. 539–546, 1999.
  • S. Aylward, E. Bullitt, and P. Stephen: VTree3D: Fast and effective vessel, bronchial tube, duct, and bone display. Radiology, vol. 209P, no. S, p. 394, 1998.
  • E. Bullitt, A. Liu, S. Aylward, M. Soltys, J. Rosenman, and S. Pizer: Methods for displaying intracerebral vascular anatomy. Americal Journal of Neuroradiology, vol. 18, no. 3, pp. 417–420, Mar. 1997.

IPMI and MICCAI Publications

  • R. Kwitt, D. Pace, M. Niethammer and S. Aylward: Studying Cerebral Vasculature Using Structure Proximity and Graph Kernels. In: MICCAI '13 (accepted), 2013 Supplementary Material
  • J. Jomier, E. Bullitt, M. Van Horn, C. Pathak, and S. Aylward: 3D/2D model-to-image registration applied to TIPS surgery. In: MICCAI’06, vol. 4191, pp. 662–669, 2006
  • J. Jomier, V. LeDigarcher, and S. Aylward: Automatic vascular tree formation using the mahalanobis distance. In: MICCAI '05, vol. 3750, pp. 806–812, 2005
  • J. Jomier, V. LeDigarcher, and S. Aylward: Comparison of vessel segmentations using STAPLE. In: MICCAI '05, vol. 3749, pp. 523–530, 2005
  • S. Aylward, J. Jomier, C. Vivert, V. LeDigarcher, and E. Bullitt: Spatial graphs for intra-cranial vascular network characterization, generation, and discrimination. In: MICCAI '05, vol. 3749, pp. 59–66, 2005
  • J. Jomier and S. Aylward: Rigid and deformable vasculature-to-image registration: A hierarchical approach. In: MICCAI '04, vol. 3216, pp. 829–836, 2004
  • E. Bullitt, I. Jung, K. Muller, G. Gerig, S. Aylward, S. Joshi, K. Smith, W. Lin, and M. Ewend: Determining malignancy of brain tumors by analysis of vessel shape. In: MICCAI '04, vol. 3217, pp. 645–653, 2004
  • J. Jomier, D. Wallace, and S. Aylward: Quantification of retinopathy of prematurity via vessel segmentation. In: MICCAI '03, vol. 2879, pp. 620–626, 2003
  • B. Jolly, M. Van Horn, S. Aylward, and E. Bullitt: Needle detection and tracking in the TIPS endovascular procedure. In: MICCAI '03, vol. 2879, pp. 953–954, 2003
  • Y. Fridman, S. Pizer, S. Aylward, and E. Bullitt: Segmenting 3D branching tubular structures using cores. In: MICCAI '03, vol. 2879, pp. 570–577, 2003
  • D. Cool, D. Chillet, J. Kim, J. Guyon, M. Foskey, and S. Aylward: Tissue-based affine registration of brain images to form a vascular density atlas. In: MICCAI '03, vol. 2879, pp. 9–15, 2003
  • D. Chillet, J. Jomier, D. Cool, and S. Aylward: Vascular atlas formation using a vessel-to-image affine registration method. In: MICCAI '03, vol. 2878, pp. 335–342, 2003
  • E. Bullitt, G. Gerig, S. Aylward, S. Joshi, K. Smith, M. Ewend, and W. Lin: Vascular attributes and malignant brain tumors. In: MICCAI '03, vol. 2878, pp. 671–679, 2003
  • S. Aylward, S. Weeks, and E. Bullitt: Analysis of the Parameter Space of a Metric for Registering 3D Vascular Images. In: MICCAI ’01, vol. pp. 932–939, 2001
  • E. Bullitt, S. Aylward, A. Liu, J. Stone, S. Mukherji, C. Coffey, G. Gerig, and S. Pizer: 3D graph description of the intracerebral vasculature from segmented MRA and tests of accuracy by comparison with X-ray angiograms. In: IPMI '99, vol. 1613, pp. 308–321, 1999
  • E. Bullitt, A. Liu, S. Aylward, and S. Pizer: Reconstruction of the intracerebral vasculature from MRA and a pair of projection views. In: IMPI '97, vol. 1230, pp. 537–542, 1997

Other Conference Papers

  • D. F. Pace, A. Enquobahrie, H. Yang, S. R. Aylward, and M. Niethammer: Deformable image registration of sliding organs using anisotropic diffusive regularization. In: IEEE International Symposium on Biomedical Imaging (ISBI), pp. 407–413, 2011
  • D. F. Pace, M. Niethammer, and S. R. Aylward: Sliding geometries in deformable image registration. In: MICCAI ’11 Proceedings of the Third International Conference on Abdominal Imaging, pp. 141–148, 2011
  • R. C. Gessner, R. Kothadia, S. Feingold, S. Aylward, E. Bullitt, and P. A. Dayton: Blood vessel structural morphology derived from 3D dual-frequency ultrasound images. In: IEEE Ultrasonics Symposium (IUS), pp. 209–212, 2010
  • J. Lee, J. Jomier, S. Aylward, M. Tyszka, S. Moy, J. Lauder, and M. Styner: Evaluation of atlas based mouse brain segmentation. In: SPIE Medical Imaging, 2009
  • Z. Zhao, D. K. Wallace, S. F. Freedman, and S. R. Aylward: A tool for computer-aided diagnosis of retinopathy of prematurity. In: SPIE Medical Imaging, 2008
  • E. Bullitt and S. Aylward: Visualizing blood vessel trees in three dimensions: clinical applications. In: SPIE Medical Imaging, 2005
  • S. R. Aylward, J. Jomier, J. P. Guyon, and S. Weeks: Intra-operative 3D ultrasound augmentation. In: IEEE International Symposium on Biomedical Imaging (ISBI), pp. 421–424, 2002
  • E. Bullitt, SR Aylward: Patient-specific vascular models for endovascular and open operative procedures. In: Proceedings of the 2nd International Mt. BANDAI Symposium for Neuroscience, pp. 88-94, 2001
  • E. Bullitt and S. R. Aylward: Analysis of Time-Varing Images Using 3-D Vascular Models. In: Proceedings of the 30th on Applied Imagery Pattern Recognition Workshop (AIPR), p. 9-14, 2001 (Keynote Address)
  • S. Aylward, S. Pizer, D. Eberly, and E. Bullitt: Intensity Ridge and Widths for Tubular Object Segmentation and Description. In: MMBIA ’96 p. 131-138, 1996