@article{Dehghan2011a,

title = {Brachytherapy Seed Reconstruction with Joint-Encoded C-Arm Single-Axis Rotation and Motion Compensation},

author = {Ehsan Dehghan and Ameet K. Jain and Mehdi Moradi and Xu Wen and William J. Morris and Septimiu E. Salcudean and Gabor Fichtinger},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Dehghan_etal_US_Fluoro_Reg.pdf},

doi = {10.1016/j.media.2011.05.017},

year  = {2011},

date = {2011-10-01},

urldate = {2011-10-01},

journal = {Medical Image Analysis},

volume = {15},

pages = {760 – 771},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lee2011,

title = {REDMAPS: Reduced-Dimensionality Matching for Prostate Brachytherapy Seed Reconstruction},

author = {Junghoon Lee and Christian Labat and Ameet K. Jain and Danny Y Song and E. Clif Burdette and Gabor Fichtinger and Jerry L. Prince},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Lee2011.pdf},

doi = {10.1109/TMI.2010.2059709},

year  = {2011},

date = {2011-01-01},

urldate = {2011-01-01},

journal = {IEEE Transactions on Medical Imaging},

volume = {30},

pages = {38-51},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Song2008,

title = {Registered ultrasound and fluoroscopy for intraoperative dynamic dosimetry in prostate brachytherapy},

author = {Danny Y Song and Anton Degeut and Iulian Iordachita and Elwood Armour and Ameet K. Jain and E. Clif Burdette and Gabor Fichtinger},

url = {http://www sciencedirect com/science/article/B6X3G-4S86YJ8-1B/2/332751abcc9066ed833bea302ef2f604

https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Song2008a.pdf},

doi = {DOI: 10 1016/j brachy 2008 02 364},

issn = {1538-4721},

year  = {2008},

date = {2008-01-01},

urldate = {2008-01-01},

journal = {Brachytherapy},

volume = {7},

number = {2},

pages = {102 - 102},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jain2007,

title = {Intra-operative 3D guidance in prostate brachytherapy using a non-isocentric C-arm},

author = {Ameet K. Jain and Anton Degeut and Iulian Iordachita and Gouthami Chintalapani and Jack Blevins and Le Yi and Elwood Armour and E. Clif Burdette and Danny Y Song and Gabor Fichtinger},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Jain2007.pdf},

year  = {2007},

date = {2007-01-01},

urldate = {2007-01-01},

journal = {Medical image computing and computer-assisted intervention (MICCAI)},

volume = {10},

number = {Pt 2},

pages = {9–17},

publisher = {Johns Hopkins University, USA},

abstract = {<p>Intra-operative guidance in Transrectal Ultrasound (TRUS) guided prostate brachytherapy requires localization of inserted radioactive seeds relative to the prostate Seeds were reconstructed using a typical C-arm, and exported to a commercial brachytherapy system for dosimetry analysis Technical obstacles for 3D reconstruction on a non-isocentric C-arm included pose-dependent C-arm calibration; distortion correction; pose estimation of C-arm images; seed reconstruction;, C-arm to TRUS registration In precision-machined hard phantoms with 40-100 seeds, we correctly reconstructed 99 8% seeds with a mean 3D accuracy of 0 68 mm In soft tissue phantoms with 45-87 seeds, clinically realistic 15 degrees C-arm motion, we correctly reconstructed 100% seeds with an accuracy of 1 3 mm The reconstructed 3D seed positions were then registered to the prostate segmented from TRUS In a Phase-1 clinical trial, so far on 4 patients with 66-84 seeds, we achieved intra-operative monitoring of seed distribution, dosimetry We optimized the 100% prescribed iso-dose contour by inserting an average of 3 75 additional seeds, making intra-operative dosimetry possible on a typical C-arm, at negligible additional cost to the existing clinical installation</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Liu2007,

title = {Prostate implant reconstruction with discrete tomography},

author = {Xiaofeng Liu and Ameet K. Jain and Gabor Fichtinger},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Liu2007.pdf},

year  = {2007},

date = {2007-01-01},

urldate = {2007-01-01},

journal = {Medical image computing and computer-assisted intervention (MICCAI)},

volume = {10},

number = {Pt 1},

pages = {734–742},

publisher = {Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA},

abstract = {<p>We developed a discrete tomography method for prostate implant reconstructions using only a limited number of X-ray projection images A 3D voxel volume is reconstructed by back-projection, using distance maps generated from the projection images The true seed locations are extracted from the voxel volume while false positive seeds are eliminated using a novel optimal geometry coverage model The attractive feature of our method is that it does not require exact seed segmentation of the X-ray images, it yields near 100% correct reconstruction from only six images with an average reconstruction accuracy of 0 86 mm (std = 0 46mm)</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Labat2007,

title = {Toward optimal matching for 3D reconstruction of brachytherapy seeds},

author = {Christian Labat and Ameet K. Jain and Gabor Fichtinger and Jerry L. Prince},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Labat2007.pdf},

year  = {2007},

date = {2007-01-01},

urldate = {2007-01-01},

journal = {Medical image computing and computer-assisted intervention (MICCAI)},

volume = {10},

number = {Pt 2},

pages = {701–709},

publisher = {Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA},

abstract = {<p>X-ray C-arm fluoroscopy is a natural choice for intra-operative seed localization in prostate brachytherapy Resolving the correspondence of seeds in the projection images can be modeled as an assignment problem that is NP-hard Our approach rests on the practical observation that the optimal solution has almost zero cost if the pose of the C-arm is known accurately This allowed us to to derive an equivalent problem of reduced dimensionality that, with linear programming, can be solved efficiently in polynomial time Additionally, our method demonstrates significantly increased robustness to C-arm pose errors when compared to the prior art Because under actual clinical circumstances it is exceedingly difficult to track the C-arm, easing on this constraint has additional practical utility</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jain2006a,

title = {C-arm tracking and reconstruction without an external tracker},

author = {Ameet K. Jain and Gabor Fichtinger},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Jain2006a.pdf},

year  = {2006},

date = {2006-01-01},

urldate = {2006-01-01},

journal = {Medical image computing and computer-assisted intervention (MICCAI)},

volume = {9},

number = {Pt 1},

pages = {494–502},

publisher = {Department of Computer Science, Johns Hopkins University, USA},

abstract = {<p>For quantitative C-arm fluoroscopy, we have developed a unified mathematical framework to tackle the issues of intra-operative calibration, pose estimation, correspondence, reconstruction, without the use of optical/electromagnetic trackers or precision-made fiducial fixtures Our method uses randomly distributed unknown points in the imaging volume, either naturally present or induced by randomly sticking beads or other simple markers in the image pace After these points are segmented, a high dimensional non-linear optimization computes all unknown parameters for calibration, C-arm pose, correspondence, reconstruction Preliminary phantom experiments indicate an average C-arm tracking accuracy of 0 9 degrees, a 3D reconstruction error of 0 8 mm, with an 80 region of convergence for both the AP, lateral axes The method appears to be sufficiently accurate for many clinical applications, and appealing since it works without any external instrumentation, does not interfere with the workspace</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vikal2006a,

title = {Seed Segmentation in C-Arm Fluoroscopy for Brachytherapy Implant Reconstruction},

author = {Siddharth Vikal and Ameet K. Jain and Anton Degeut and Danny Y Song and Gabor Fichtinger},

url = {http://link aip org/link/?MPH/33/2229/2

https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Vikal2006a.pdf},

doi = {10 1118/1 2241679},

year  = {2006},

date = {2006-01-01},

urldate = {2006-01-01},

journal = {Journal of Medical Physics},

volume = {33},

number = {6},

pages = {2229-2229},

publisher = {AAPM},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vikal2006,

title = {Automated Segmentation of Radiographic Fiducials for C-Arm Tracking},

author = {Siddharth Vikal and Ameet K. Jain and Anton Degeut and Danny Y Song and Gabor Fichtinger},

url = {http://link aip org/link/?MPH/33/2208/3

https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Vikal2006a.pdf},

doi = {10 1118/1 2241601},

year  = {2006},

date = {2006-01-01},

urldate = {2006-01-01},

journal = {Journal of Medical Physics},

volume = {33},

number = {6},

pages = {2208-2208},

publisher = {AAPM},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jain2005e,

title = {Matching and reconstruction of brachytherapy seeds using the Hungarian algorithm (MARSHAL)},

author = {Ameet K. Jain and Yu Zhou and Tabish Mustufa and E. Clif Burdette and Gregory Chirikjian and Gabor Fichtinger},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Jain2005d.pdf},

year  = {2005},

date = {2005-11-01},

urldate = {2005-11-01},

journal = {Journal of Medical Physics},

volume = {32},

number = {11},

pages = {3475–3492},

abstract = {<p>Intraoperative dosimetric quality assurance in prostate brachytherapy critically depends on discerning the three-dimensional (3D) locations of implanted seeds The ability to reconstruct the implanted seeds intraoperatively will allow us to make immediate provisions for dosimetric deviations from the optimal implant plan A method for seed reconstruction from segmented C-arm fluoroscopy images is proposed The 3D coordinates of the implanted seeds can be calculated upon resolving the correspondence of seeds in multiple x-ray images We formalize seed-matching as a combinatorial optimization problem, which has salient features: (a) extensively studied solutions by the computer science community; (b) proof for the nonexistence of any polynomial time exact algorithm;, (c) a practical pseudo-polynomial algorithm that mostly runs in O(N3) time using any number of images We prove that two images are insufficient to correctly match the seeds, while a third image renders the matching problem to be of nonpolynomial complexity We utilize the special structure of the problem, propose a pseudopolynomial time algorithm Using three presegmented images, matching, reconstruction of brachytherapy seeds using the Hungarian algorithm achieved complete matching in simulation experiments;, 98 5% in phantom experiments 3D reconstruction error for correctly matched seeds has a mean of 0 63 mm, and 0 9 mm for incorrectly matched seeds The maximum seed reconstruction error in each implant was typically around 1 32 mm Both on synthetic data, in phantom experiments, matching rate, reconstruction error achieved using presegmented images was found to be sufficient for prostate brachytherapy The algorithm is extendable to deal with arbitrary number of images without any loss in speed or accuracy The algorithm is sufficiently generic to provide a practical solution to any correspondence problem, across different imaging modalities, features</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jain2005a,

title = {FTRAC},

author = {Ameet K. Jain and Tabish Mustufa and Yu Zhou and E. Clif Burdette and Gregory Chirikjian and Gabor Fichtinger},

year  = {2005},

date = {2005-10-01},

journal = {Journal of Medical Physics},

volume = {32},

number = {10},

pages = {3185–3198},

abstract = {<p>C-arm fluoroscopy is ubiquitous in contemporary surgery, but it lacks the ability to accurately reconstruct three-dimensional (3D) information A major obstacle in fluoroscopic reconstruction is discerning the pose of the x-ray image, in 3D space Optical/magnetic trackers tend to be prohibitively expensive, intrusive, cumbersome in many applications We present single-image-based fluoroscope tracking (FTRAC) with the use of an external radiographic fiducial consisting of a mathematically optimized set of ellipses, lines, and points This is an improvement over contemporary fiducials, which use only points The fiducial encodes six degrees of freedom in a single image by creating a unique view from any direction A nonlinear optimizer can rapidly compute the pose of the fiducial using this image The current embodiment has salient attributes: small dimensions (3 x 3 x 5 cm); need not be close to the anatomy of interest;, accurately segmentable We tested the fiducial, the pose recovery method on synthetic data, also experimentally on a precisely machined mechanical phantom Pose recovery in phantom experiments had an accuracy of 0 56 mm in translation, 0 33 degrees in orientation Object reconstruction had a mean error of 0 53 mm with 0 16 mm STD The method offers accuracies similar to commercial tracking systems, and appears to be sufficiently robust for intraoperative quantitative C-arm fluoroscopy Simulation experiments indicate that the size can be further reduced to 1 x 1 X 2 cm, with only a marginal drop in accuracy</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jain2005,

title = {C-arm calibration-is it really necessary?},

author = {Ameet K. Jain and Ryan Kon and Yu Zhou and Gabor Fichtinger},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Jain2005c.pdf},

year  = {2005},

date = {2005-01-01},

urldate = {2005-01-01},

journal = {Medical image computing and computer-assisted intervention (MICCAI)},

volume = {8},

number = {Pt 1},

pages = {639–646},

abstract = {<p>C-arm fluoroscopy is modelled as a perspective projection, the parameters of which are estimated through a calibration procedure It has been universally accepted that precise intra-procedural calibration is a prerequisite for accurate quantitative C-arm fluoroscopy guidance Calibration, however, significantly adds to system complexity, which is a major impediment to clinical practice We challenge the status quo by questioning the assumption that precise intra-procedural calibration is really necessary We derived theoretical bounds for the sensitivity of 3D measurements to mis-calibration Experimental results corroborated the theory in that mis-calibration in the focal spot by as much as 50 mm still allows for tracking with an accuracy of 0 5 mm in translation, 0 65 degrees in rotation, and such mis-calibration does not impose any additional error on the reconstruction of small objects</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jain2005c,

title = {Towards Intra-Operative Dosimetry in Prostate Brachytherapy},

author = {Ameet K. Jain and Yu Zhou and Christopher Kennedy and Tabish Mustufa and E. Clif Burdette and Gregory Chirikjian and Gabor Fichtinger},

url = {http://link aip org/link/?MPH/32/2159/1

https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Jain2005c.pdf},

doi = {10 1118/1 1998646},

year  = {2005},

date = {2005-01-01},

urldate = {2005-01-01},

journal = {Journal of Medical Physics},

volume = {32},

number = {6},

pages = {2159-2159},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kemper2005,

title = {Transrectal Fiducial Carrier for Radiographic Image Registration in Prostate Brachytherapy},

author = {Jacob Kemper and Astrid Burkholder and Ameet K. Jain and Tabish Mustufa and Keenan Wyrobek and E. Clif Burdette and Danny Y Song and Allison Okamura and Gabor Fichtinger},

url = {http://link aip org/link/?MPH/32/2108/2

https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Kemper2005.pdf},

doi = {10 1118/1 1998447},

year  = {2005},

date = {2005-01-01},

urldate = {2005-01-01},

journal = {Journal of Medical Physics},

volume = {32},

number = {6},

pages = {2108-2108},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jain2004,

title = {Brachytherapy seed reconstruction from fluoroscopic images using network flow algorithms},

author = {Ameet K. Jain and Yu Zhou and Tabish Mustufa and E. Clif Burdette and Christian Scheideler and Gregory Chirikjian and Gabor Fichtinger},

url = {http://www sciencedirect com/science/article/B6T7X-4D93P8D-YJ/2/5a75b8f5680b69fa4a2ea65491763c4b

https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Jain2004.pdf},

doi = {DOI: 10 1016/j ijrobp 2004 07 594},

issn = {0360-3016},

year  = {2004},

date = {2004-01-01},

urldate = {2004-01-01},

journal = {International Journal of Radiation Oncology*Biology*Physics},

volume = {60},

number = {Supplement 1},

pages = {S594 - S595},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fichtinger2003,

title = {Image Registration of multiple medical imaging modalities using a multiple degree-of-freedom-encoded fiducial},

author = {Gabor Fichtinger and Ameet K. Jain and Tabish Mustufa and Keenan Wyrobek and Gregory Chirikjian and Yu Zhou and E. Clif Burdette},

year  = {2003},

date = {2003-01-01},

urldate = {2003-01-01},

number = {60/493,406},

keywords = {},

pubstate = {published},

tppubtype = {article}

}