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'''[[TubeTK|Home]]'''
*[[TubeTK/About|About]]
*[[TubeTK/Images|Image Gallery]]
*[[TubeTK/Data|Data and Publications]]
<br>
<br>
<b>[http://public.kitware.com/Wiki/TubeTK Home]</b>
----
*[[TubeTK/About | About]]
*[[TubeTK/Images | Image Gallery]]
*[[TubeTK/Data | Data and Publications]]
<br>
<br>
<hr>
'''For Users'''
* [[TubeTK/Installation|Installation]]
* [[TubeTK/Documentation|Methods & Apps]]
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]
* [[TubeTK/OsiriX|TubeTK with OsiriX]]
<br>
<br>
<b>For Users</b>
----
* [[TubeTK/Installation | Installation]]
* [[TubeTK/Documentation | Methods & Apps]]
* [[TubeTK/Slicer | TubeTK with Slicer]]
* [[TubeTK/ImageJ | TubeTK with ImageJ]]
* [[TubeTK/OsiriX | TubeTK with OsiriX]]
<br>
<br>
<hr>
'''For Developers'''
* [[TubeTK/Development|Development Docs]]
<br>
<br>
<b>For Developers</b>
----
* [[TubeTK/Development | Development Docs]]
<br>
<br>
<hr>
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''
<br>
<br>
<b>[http://public.kitware.com/Bug/search.php?project_id=35 Report Bugs<br>Request Features]</b>
<br>
<br>
----
<br>
<br>
<br>
'''[[TubeTK/Contact|Contact Us]]'''
<b>[[TubeTK/Team | Contact Us]]</b>


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= Data =  
= Data =  
* 100 Healthy Normal MRIs and MRAs from UNC
 
** http://insight-journal.org/midas/community/view/21?path_navigation=19-15
=== 100 Healthy Normal MRIs and MRAs from UNC ===
* TubeTK Testing Data
{|width="100%"
** http://midas3.kitware.com/midas/community/7
|[[File:Intracranial-Teaser.jpg|300px|link=https://data.kitware.com/#collection/591086ee8d777f16d01e0724/folder/58a372e38d777f0721a64dc6]]
|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 [https://data.kitware.com/#collection/591086ee8d777f16d01e0724/folder/58a372e38d777f0721a64dc6 here]. A subset of this dataset also includes intra-cranial vasculature (centerline + radius), extracted from the MRA images.  These models are found in each patient's "Auxillary Data" folder, such as [https://data.kitware.com/#collection/591086ee8d777f16d01e0724/folder/58a372fa8d777f0721a64dfb here].
|}
 
 
 
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=== Recognition in Ultrasound (REUS) Database ===
 
{|width="100%"
|[[File:REUS-Teaser.jpg|300px|link=http://midas3.kitware.com/midas/folder/10255]]
|This dataset contains Ultrasound (US) 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 [http://midas3.kitware.com/midas/folder/10255 here].
 
In summary (see included README file for details), the database contains videos from 9 different ''noodle'' structures. We provide 10 templates videos per structure (i.e., 90 templates in total) and 9 ''search path'' videos (i.e., 1 search path video per structure). One task could be, for instance, to localize (temporally) the templates in the corresponding search path videos. Currently, the videos are available in (64x64pixel) and (128x128pixel) spatial resolution.
 
To evaluate recognition algorithms, we further provide human ground truth locations for the search paths, indicating when a structure moves "in" and "out" of the US imaging plane (These annotations were averaged over 5 different persons).
|}
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=== TubeTK Testing Data ===
Another good resource to download data material for experimenting with TubeTK is our testing data, available from [http://midas3.kitware.com/midas/community/7 here].


= Patents =
= Patents =
Line 47: Line 70:


= Books =
= Books =
* Aylward S, Bullitt E, “Chapter 11: Clinical Applications Involving Vascular Image Segmentation and Registration” in Angiography and Plaque Imaging: A Segmentation Perspective, Academic Press, 2002 pp. 529-579  
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 =
= 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.  
* R. Kwitt, N. Vasconcelos, S. Razzaque and S.R. Aylard: '''Localizing Target Structures in Ultrasound Video - A Phantom Study''', Medical Image Analysis, vol. 17, no 7., pp. 7127-22, 2013 [http://www.medicalimageanalysisjournal.com/article/S1361-8415(13)00069-8/abstract Publisher Link] [http://public.kitware.com/Wiki/images/3/33/Kwitt13aMedIA.pdf Preprint]
* E. Bullitt, D. Zeng, B. Mortamet, A. Ghosh, S. R. 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, Feb. 2010.  
* 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, M. Ewend, J. Vredenburgh, A. Friedman, W. Lin, K. Wilber, D. Zeng, S. R. 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, Aug. 2009.  
* 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.  
* 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, Jun. 2009.  
* 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.  
* 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, Sep. 2007.  
* 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.  
* 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, Nov. 2005.  
* 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.  
* 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, Oct. 2005. Winner 2006 Herbert M. Stauffer Award by the Association of University Radiologists PMID: 16179200
* 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, K. Muller, I. Jung, W. Lin, and S. Aylward, “Analyzing attributes of vessel populations,” MEDICAL IMAGE ANALYSIS, vol. 9, no. 1, pp. 39–49, Feb. 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, 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, Dec. 2004.  
* 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.  
* 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, Sep. 2004.  
* 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.  
* 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.  
* 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.  
* 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, Dec. 2003.  
* 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.  
* 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, Sep. 2003.  
* 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.  
* 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 OPHTHALMOLOGY & VISUAL SCIENCE, vol. 44, no. 1, p. U116, May 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, 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, Apr. 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.  
* E. Bullitt and S. Aylward, “Patient-specific vascular models for endovascular and open operative procedures,” International Congress Series, vol. 1247, pp. 129–138, 2002.  
* 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.  
* S. R. Aylward and E. Bullitt, “Initialization, noise, singularities, and scale in height ridge traversal for tubular object centerline extraction,” Medical Imaging, IEEE Transactions on, vol. 21, no. 2, pp. 61–75, 2002.  
* E. Bullitt and S. Aylward: '''Patient-specific vascular models for endovascular and open operative procedures'''. International Congress Series, vol. 1247, pp. 129–138, 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, Jun. 2001.  
* 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, E. Bernard, and G. Gerig, “Computer-assisted visualization of arteriovenous malformations on the home personal computer,” NEUROSURGERY, vol. 48, no. 3, pp. 576–582, Mar. 2001.  
* 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, 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, Sep. 1999.  
* 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.  
* 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, Nov. 1998.  
* 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.  
* E. Bullitt, A. Liu, S. Aylward, M. Soltys, J. Rosenman, and S. Pizer, “Methods for displaying intracerebral vascular anatomy,” AMERICAN JOURNAL OF NEURORADIOLOGY, vol. 18, no. 3, pp. 417–420, Mar. 1997.  
* 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 =
= IPMI and MICCAI Publications =
* J. Jomier, E. Bullitt, M. Van Horn, C. Pathak, and S. R. Aylward, “3D/2D model-to-image registration applied to TIPS surgery,” in MICCAI’06: Proceedings of the 9th international conference on Medical Image Computing and Computer-Assisted Intervention, Berlin, Heidelberg, 2006, pp. 662–669.
* R. Kwitt, D. Pace, M. Niethammer and S. Aylward: '''Studying Cerebral Vasculature Using Structure Proximity and Graph Kernels'''. In: MICCAI '13, vol. 8150, pp. 534-541, 2013 [http://public.kitware.com/Wiki/images/3/3f/SupplementaryMaterial.pdf Supplementary Material] [http://public.kitware.com/Wiki/images/e/e5/Kwitt13bMICCAI.pdf PDF]
* J. Jomier, V. LeDigarcher, and S. Aylward, “Automatic vascular tree formation using the mahalanobis distance,” in Medical Image Computing and Computer-Assisted Intervention–MICCAI 2005, 2005, pp. 806–812.
 
* J. Jomier, V. LeDigarcher, and S. Aylward, “Comparison of vessel segmentations using STAPLE,” in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2005, PT 1, 2005, vol. 3749, pp. 523–530.
* R. Kwitt, N. Vasconcelos, S. Razzaque and S. Aylward: '''Recognition in Ultrasound Videos: Where am'''. In: MICCAI '12, vol. 7512, pp. pp 83-90, 2013 ('''Oral presentation''' ; Acceptance rate < 5%; Winner of the '''MICCAI Young Scientist Award''') [http://public.kitware.com/Wiki/images/a/af/Kwitt12aMICCAI.pdf PDF]
* S. Aylward, J. Jomier, C. Vivert, V. LeDigarcher, and E. Bullitt, “Spatial graphs for intra-cranial vascular network characterization, generation, and discrimination,” in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2005, PT 1, 2005, vol. 3749, pp. 59–66.
 
* J. Jomier and S. Aylward, “Rigid and deformable vasculature-to-image registration: A hierarchical approach,” in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2004, PT 1, PROCEEDINGS, 2004, vol. 3216, pp. 829–836.
* 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
* 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 MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2004, PT 2, PROCEEDINGS, 2004, vol. 3217, pp. 645–653.
 
* J. Jomier, D. Wallace, and S. Aylward, “Quantification of retinopathy of prematurity via vessel segmentation,” in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2003, PT 2, 2003, vol. 2879, pp. 620–626.
* J. Jomier, V. LeDigarcher, and S. Aylward: '''Automatic vascular tree formation using the mahalanobis distance'''. In: MICCAI '05, vol. 3750, pp. 806–812, 2005
* B. Jolly, M. Van Horn, S. Aylward, and E. Bullitt, “Needle detection and tracking in the TIPS endovascular procedure,” in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2003, PT 2, 2003, vol. 2879, pp. 953–954.
 
* Y. Fridman, S. Pizer, S. Aylward, and E. Bullitt, “Segmenting 3D branching tubular structures using cores,” in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2003, PT 2, 2003, vol. 2879, pp. 570–577.
* J. Jomier, V. LeDigarcher, and S. Aylward: '''Comparison of vessel segmentations using STAPLE'''. In: MICCAI '05, vol. 3749, pp. 523–530, 2005
* 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 MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2003, PT 2, 2003, vol. 2879, pp. 9–15.
 
* D. Chillet, J. Jomier, D. Cool, and S. Aylward, “Vascular atlas formation using a vessel-to-image affine registration method,” in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2003, PT 1, 2003, vol. 2878, pp. 335–342.
* 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
* E. Bullitt, G. Gerig, S. Aylward, S. Joshi, K. Smith, M. Ewend, and W. Lin, “Vascular attributes and malignant brain tumors,” in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION - MICCAI 2003, PT 1, 2003, vol. 2878, pp. 671–679.
 
* S. Aylward, S. Weeks, and E. Bullitt, “Analysis of the Parameter Space of a Metric for Registering 3D Vascular Images,” in MICCAI ’01: Proceedings of the 4th International Conference on Medical Image Computing and Computer-Assisted Intervention, London, UK, UK, 2001, pp. 932–939.
* 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, 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 INFORMATION PROCESSING IN MEDICAL IMAGING, PROCEEDINGS, 1999, vol. 1613, pp. 308–321.
 
* E. Bullitt, A. Liu, S. Aylward, and S. Pizer, “Reconstruction of the intracerebral vasculature from MRA and a pair of projection views,” in INFORMATION PROCESSING IN MEDICAL IMAGING, 1997, vol. 1230, pp. 537–542.
* 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 =
= 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 Biomedical Imaging: From Nano to Macro, 2011 IEEE International Symposium on, 2011, pp. 407–413.
* 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, Berlin, Heidelberg, 2011, pp. 141–148.
 
* 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 Ultrasonics Symposium (IUS), 2010 IEEE, 2010, pp. 209–212.
* 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
* J. Lee, J. Jomier, S. Aylward, M. Tyszka, S. Moy, J. Lauder, and M. Styner, “Evaluation of atlas based mouse brain segmentation,” SPIE Medical Imaging, 2009, pp. 725943–9
 
* Z. Zhao, D. K. Wallace, S. F. Freedman, and S. R. Aylward, “A tool for computer-aided diagnosis of retinopathy of prematurity,” in Proceedings of SPIE, 2008, vol. 6915, p. 69152W–69152W–7.
* 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
* E. Bullitt and S. Aylward, “Visualizing blood vessel trees in three dimensions: clinical applications,” in Proceedings of SPIE, 2005, vol. 5749, pp. 67–78.
 
* S. R. Aylward, J. Jomier, J. P. Guyon, and S. Weeks, “Intra-operative 3D ultrasound augmentation,” in Biomedical Imaging, 2002. Proceedings. 2002 IEEE International Symposium on, 2002, pp. 421–424.
* 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
* E. Bullitt, SR Aylward, “Patient-specific vascular models for endovascular and open operative procedures.” Proceedings of the 2nd International Mt. BANDAI Symposium for Neuroscience. Southern Tohoku Research Institute for Neuroscience, Fukushima Japan, 2001, pp. 88-94.
 
* E. Bullitt and S. R. Aylward, “Analysis of Time-Varing Images Using 3-D Vascular Models,” in AIPR ’01: Proceedings of the 30th on Applied Imagery Pattern Recognition Workshop, Washington, DC, USA, 2001, p. 9-14 (Keynote Address)
* 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
* S. Aylward, S. Pizer, D. Eberly, and E. Bullitt, “Intensity Ridge and Widths for Tubular Object Segmentation and Description,” in MMBIA ’96: Proceedings of the 1996 Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA ’96), Washington, DC, USA, 1996, p. 131.
 
* 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
 
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[[Category: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 also includes intra-cranial vasculature (centerline + radius), extracted from the MRA images. These models are found in each patient's "Auxillary Data" folder, such as here.



Recognition in Ultrasound (REUS) Database

REUS-Teaser.jpg This dataset contains Ultrasound (US) 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.

In summary (see included README file for details), the database contains videos from 9 different noodle structures. We provide 10 templates videos per structure (i.e., 90 templates in total) and 9 search path videos (i.e., 1 search path video per structure). One task could be, for instance, to localize (temporally) the templates in the corresponding search path videos. Currently, the videos are available in (64x64pixel) and (128x128pixel) spatial resolution.

To evaluate recognition algorithms, we further provide human ground truth locations for the search paths, indicating when a structure moves "in" and "out" of the US imaging plane (These annotations were averaged over 5 different persons).


TubeTK Testing Data

Another good resource to download data material for experimenting with TubeTK is our 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. Kwitt, N. Vasconcelos, S. Razzaque and S.R. Aylard: Localizing Target Structures in Ultrasound Video - A Phantom Study, Medical Image Analysis, vol. 17, no 7., pp. 7127-22, 2013 Publisher Link Preprint
  • 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, vol. 8150, pp. 534-541, 2013 Supplementary Material PDF
  • R. Kwitt, N. Vasconcelos, S. Razzaque and S. Aylward: Recognition in Ultrasound Videos: Where am. In: MICCAI '12, vol. 7512, pp. pp 83-90, 2013 (Oral presentation ; Acceptance rate < 5%; Winner of the MICCAI Young Scientist Award) PDF
  • 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