Publications

A complete list of my publications is also available via Google Scholar.

2018

  • N. Lichtenberg, N. Smit, C. Hansen, and K. Lawonn, “Real-time field aligned stripe patterns,” Computers & Graphics, vol. 74, p. 137–149, 2018. doi:10.1016/j.cag.2018.04.008
    [BibTeX] [Abstract] [Download PDF]

    In this paper, we present a parameterization technique that can be applied to surface meshes in real-time without time-consuming preprocessing steps. The parameterization is suitable for the display of (un-)oriented patterns and texture patches, and to sample a surface in a periodic fashion. The method is inspired by existing work that solves a global optimization problem to generate a continuous stripe pattern on the surface, from which texture coordinates can be derived. We propose a local optimization approach that is suitable for parallel execution on the GPU, which drastically reduces computation time. With this, we achieve on-the-fly texturing of 3D, medium-sized (up to 70 k vertices) surface meshes. The algorithm takes a tangent vector field as input and aligns the texture coordinates to it. Our technique achieves real-time parameterization of the surface meshes by employing a parallelizable local search algorithm that converges to a local minimum in a few iterations. The calculation in real-time allows for live parameter updates and determination of varying texture coordinates. Furthermore, the method can handle non-manifold meshes. The technique is useful in various applications, e.g., biomedical visualization and flow visualization. We highlight our method{’}s potential by providing usage scenarios for several applications.

    @article{lichtenberg_real-time_2018,
    title = {Real-time field aligned stripe patterns},
    volume = {74},
    issn = {0097-8493},
    url = {http://noeskasmit.com/wp-content/uploads/2018/08/lichtenberg_2018.pdf},
    doi = {10.1016/j.cag.2018.04.008},
    abstract = {In this paper, we present a parameterization technique that can be applied to surface meshes in real-time without time-consuming preprocessing steps. The parameterization is suitable for the display of (un-)oriented patterns and texture patches, and to sample a surface in a periodic fashion. The method is inspired by existing work that solves a global optimization problem to generate a continuous stripe pattern on the surface, from which texture coordinates can be derived. We propose a local optimization approach that is suitable for parallel execution on the GPU, which drastically reduces computation time. With this, we achieve on-the-fly texturing of 3D, medium-sized (up to 70 k vertices) surface meshes. The algorithm takes a tangent vector field as input and aligns the texture coordinates to it. Our technique achieves real-time parameterization of the surface meshes by employing a parallelizable local search algorithm that converges to a local minimum in a few iterations. The calculation in real-time allows for live parameter updates and determination of varying texture coordinates. Furthermore, the method can handle non-manifold meshes. The technique is useful in various applications, e.g., biomedical visualization and flow visualization. We highlight our method{\textquoteright}s potential by providing usage scenarios for several applications.},
    urldate = {2018-07-29},
    journal = {{Computers \& Graphics}},
    author = {Lichtenberg, Nils and Smit, Noeska and Hansen, Christian and Lawonn, Kai},
    month = aug,
    year = {2018},
    keywords = {Computational geometry,, Computer graphics, Parameterization, Visualization},
    pages = {137--149},
    }

2017

  • K. Lawonn, N. Smit, K. Bühler, and B. Preim, “A Survey on Multimodal Medical Data Visualization,” Computer Graphics Forum, 2017. doi:10.1111/cgf.13306
    [BibTeX] [Abstract] [Download PDF]

    Multimodal data of the complex human anatomy contain a wealth of information. To visualize and explore such data, techniques for emphasizing important structures and controlling visibility are essential. Such fused overview visualizations guide physicians to suspicious regions to be analyzed in detail, e.g. with slice-based viewing. We give an overview of state of the art in multimodal medical data visualization techniques. Multimodal medical data consists of multiple scans of the same subject using various acquisition methods, often combining multiple complimentary types of information. Three-dimensional visualization techniques for multimodal medical data can be used in diagnosis, treatment planning, doctor-patient communication as well as interdisciplinary communication. Over the years, multiple techniques have been developed in order to cope with the various associated challenges and present the relevant information from multiple sources in an insightful way. We present an overview of these techniques and analyze the specific challenges that arise in multimodal data visualization and how recent works aimed to solve these, often using smart visibility techniques. We provide a taxonomy of these multimodal visualization applications based on the modalities used and the visualization techniques employed. Additionally, we identify unsolved problems as potential future research directions.

    @article{lawonn_survey_2017,
    title = {A {Survey} on {Multimodal} {Medical} {Data} {Visualization}},
    doi = {10.1111/cgf.13306},
    journal = {{Computer Graphics Forum}},
    author = {Lawonn, Kai and Smit, Noeska and B{\"u}hler, Katja and Preim, Bernhard},
    abstract = {Multimodal data of the complex human anatomy contain a wealth of information. To visualize and explore such data, techniques
    for emphasizing important structures and controlling visibility are essential. Such fused overview visualizations guide
    physicians to suspicious regions to be analyzed in detail, e.g. with slice-based viewing. We give an overview of state of the art
    in multimodal medical data visualization techniques. Multimodal medical data consists of multiple scans of the same subject
    using various acquisition methods, often combining multiple complimentary types of information. Three-dimensional visualization
    techniques for multimodal medical data can be used in diagnosis, treatment planning, doctor-patient communication
    as well as interdisciplinary communication. Over the years, multiple techniques have been developed in order to cope with
    the various associated challenges and present the relevant information from multiple sources in an insightful way. We present
    an overview of these techniques and analyze the specific challenges that arise in multimodal data visualization and how recent
    works aimed to solve these, often using smart visibility techniques. We provide a taxonomy of these multimodal visualization applications
    based on the modalities used and the visualization techniques employed. Additionally, we identify unsolved problems
    as potential future research directions.
    },
    month = oct,
    year = {2017},
    url = {https://vis.uib.no/wp-content/papercite-data/pdfs/LawonnSmit-2017-MULTI.pdf}
    }

  • N. Smit, K. Lawonn, A. Kraima, M. Deruiter, H. Sokooti, S. Bruckner, E. Eisemann, and A. Vilanova, “PelVis: Atlas-based Surgical Planning for Oncological Pelvic Surgery,” IEEE Transactions on Visualization and Computer Graphics (Proceedings of Scientific Visualization 2016), vol. 23, 2017. doi:10.1109/TVCG.2016.2598826
    [BibTeX] [Abstract] [Download PDF]

    Due to the intricate relationship between the pelvic organs and vital structures, such as vessels and nerves, pelvic anatomy is often considered to be complex to comprehend. In oncological pelvic surgery, a trade-off has to be made between complete tumor resection and preserving function by preventing damage to the nerves. Damage to the autonomic nerves causes undesirable post-operative side-effects such as fecal and urinal incontinence, as well as sexual dysfunction in up to 80 percent of the cases. Since these autonomic nerves are not visible in pre-operative MRI scans or during surgery, avoiding nerve damage during such a surgical procedure becomes challenging. In this work, we present visualization methods to represent context, target, and risk structures for surgical planning. We employ distance-based and occlusion management techniques in an atlas-based surgical planning tool for oncological pelvic surgery. Patient-specific pre-operative MRI scans are registered to an atlas model that includes nerve information. Through several interactive linked views, the spatial relationships and distances between the organs, tumor and risk zones are visualized to improve understanding, while avoiding occlusion. In this way, the surgeon can examine surgically relevant structures and plan the procedure before going into the operating theater, thus raising awareness of the autonomic nerve zone regions and potentially reducing post-operative complications. Furthermore, we present the results of a domain expert evaluation with surgical oncologists that demonstrates the advantages of our approach.

    @article{smit_pelvis:_2017,
    title = {{PelVis}: {Atlas}-based {Surgical} {Planning} for {Oncological} {Pelvic} {Surgery}},
    volume = {23},
    shorttitle = {{PelVis}},
    doi = {10.1109/TVCG.2016.2598826},
    abstract = {Due to the intricate relationship between the pelvic organs and vital structures, such as vessels and nerves, pelvic anatomy is often considered to be complex to comprehend. In oncological pelvic surgery, a trade-off has to be made between complete tumor resection and preserving function by preventing damage to the nerves. Damage to the autonomic nerves causes undesirable post-operative side-effects such as fecal and urinal incontinence, as well as sexual dysfunction in up to 80 percent of the cases. Since these autonomic nerves are not visible in pre-operative MRI scans or during surgery, avoiding nerve damage during such a surgical procedure becomes challenging. In this work, we present visualization methods to represent context, target, and risk structures for surgical planning. We employ distance-based and occlusion management techniques in an atlas-based surgical planning tool for oncological pelvic surgery. Patient-specific pre-operative MRI scans are registered to an atlas model that includes nerve information. Through several interactive linked views, the spatial relationships and distances between the organs, tumor and risk zones are visualized to improve understanding, while avoiding occlusion. In this way, the surgeon can examine surgically relevant structures and plan the procedure before going into the operating theater, thus raising awareness of the autonomic nerve zone regions and potentially reducing post-operative complications. Furthermore, we present the results of a domain expert evaluation with surgical oncologists that demonstrates the advantages of our approach.},
    journal = {{IEEE Transactions on Visualization and Computer Graphics (Proceedings of Scientific Visualization 2016)}},
    author = {Smit, Noeska and Lawonn, Kai and Kraima, Annelot and Deruiter, Marco and Sokooti, Hessam and Bruckner, Stefan and Eisemann, Elmar and Vilanova, Anna},
    month = jan,
    year = {2017},
    url = {http://noeskasmit.com/wp-content/uploads/2018/08/smit_pelvis_2017.pdf}
    }

2016

  • A. C. Kraima, M. Derks, N. N. Smit, C. J. H. van de Velde, G. G. Kenter, and M. C. DeRuiter, “Careful Dissection of the Distal Ureter Is Highly Important in Nerve-sparing Radical Pelvic Surgery: A 3d Reconstruction and Immunohistochemical Characterization of the Vesical Plexus,” International Journal of Gynecological Cancer: Official Journal of the International Gynecological Cancer Society, vol. 26, iss. 5, p. 959–966, 2016. doi:10.1097/IGC.0000000000000709
    [BibTeX] [Abstract] [Download PDF]

    OBJECTIVE: Radical hysterectomy with pelvic lymphadenectomy (RHL) is the preferred treatment for early-stage cervical cancer. Although oncological outcome is good with regard to recurrence and survival rates, it is well known that RHL might result in postoperative bladder impairments due to autonomic nerve disruption. The pelvic autonomic network has been extensively studied, but the anatomy of nerve fibers branching off the inferior hypogastric plexus to innervate the bladder is less known. Besides, the pathogenesis of bladder dysfunction after RHL is multifactorial but remains unclear. We studied the 3-dimensional anatomy and neuroanatomical composition of the vesical plexus and describe implications for RHL. MATERIALS AND METHODS: Six female adult cadaveric pelvises were macroscopically dissected. Additionally, a series of 10 female fetal pelvises (embryonic age, 10-22 weeks) was studied. Paraffin-embedded blocks were transversely sliced in 8-$\mu$m sections. (Immuno) histological analysis was performed with hematoxylin and eosin, azan, and antibodies against S-100 (Schwann cells), tyrosine hydroxylase (postganglionic sympathetic fibers), and vasoactive intestinal peptide (postganglionic parasympathetic fibers). The results were 3-dimensionally visualized. RESULTS: The vesical plexus formed a group of nerve fibers branching off the ventral part of the inferior hypogastric plexus to innervate the bladder. In all adult and fetal specimens, the vesical plexus was closely related to the distal ureter and located in both the superficial and deep layers of the vesicouterine ligament. Efferent nerve fibers belonging to the vesical plexus predominantly expressed tyrosine hydroxylase and little vasoactive intestinal peptide. CONCLUSIONS: The vesical plexus is located in both layers of the vesicouterine ligament and has a very close relationship with the distal ureter. Complete mobilization of the ureter in RHL might cause bladder dysfunction due to sympathetic and parasympathetic denervation. Hence, the distal ureter should be regarded as a risk zone in which the vesical plexus can be damaged.

    @article{kraima_careful_2016,
    title = {Careful {Dissection} of the {Distal} {Ureter} {Is} {Highly} {Important} in {Nerve}-sparing {Radical} {Pelvic} {Surgery}: {A} 3D {Reconstruction} and {Immunohistochemical} {Characterization} of the {Vesical} {Plexus}},
    volume = {26},
    issn = {1525-1438},
    shorttitle = {Careful {Dissection} of the {Distal} {Ureter} {Is} {Highly} {Important} in {Nerve}-sparing {Radical} {Pelvic} {Surgery}},
    doi = {10.1097/IGC.0000000000000709},
    url = {http://graphics.tudelft.nl/Publications-new/2016/KDSVKD16/Careful_Dissection_of_the_Distal_Ureter_Is_Highly.98714.pdf},
    abstract = {OBJECTIVE: Radical hysterectomy with pelvic lymphadenectomy (RHL) is the preferred treatment for early-stage cervical cancer. Although oncological outcome is good with regard to recurrence and survival rates, it is well known that RHL might result in postoperative bladder impairments due to autonomic nerve disruption. The pelvic autonomic network has been extensively studied, but the anatomy of nerve fibers branching off the inferior hypogastric plexus to innervate the bladder is less known. Besides, the pathogenesis of bladder dysfunction after RHL is multifactorial but remains unclear. We studied the 3-dimensional anatomy and neuroanatomical composition of the vesical plexus and describe implications for RHL.
    MATERIALS AND METHODS: Six female adult cadaveric pelvises were macroscopically dissected. Additionally, a series of 10 female fetal pelvises (embryonic age, 10-22 weeks) was studied. Paraffin-embedded blocks were transversely sliced in 8-$\mu$m sections. (Immuno) histological analysis was performed with hematoxylin and eosin, azan, and antibodies against S-100 (Schwann cells), tyrosine hydroxylase (postganglionic sympathetic fibers), and vasoactive intestinal peptide (postganglionic parasympathetic fibers). The results were 3-dimensionally visualized.
    RESULTS: The vesical plexus formed a group of nerve fibers branching off the ventral part of the inferior hypogastric plexus to innervate the bladder. In all adult and fetal specimens, the vesical plexus was closely related to the distal ureter and located in both the superficial and deep layers of the vesicouterine ligament. Efferent nerve fibers belonging to the vesical plexus predominantly expressed tyrosine hydroxylase and little vasoactive intestinal peptide.
    CONCLUSIONS: The vesical plexus is located in both layers of the vesicouterine ligament and has a very close relationship with the distal ureter. Complete mobilization of the ureter in RHL might cause bladder dysfunction due to sympathetic and parasympathetic denervation. Hence, the distal ureter should be regarded as a risk zone in which the vesical plexus can be damaged.},
    language = {eng},
    number = {5},
    journal = {{International Journal of Gynecological Cancer: Official Journal of the International Gynecological Cancer Society}},
    author = {Kraima, Anne C. and Derks, Marloes and Smit, Noeska N. and van de Velde, Cornelis J. H. and Kenter, Gemma G. and DeRuiter, Marco C.},
    year = {2016},
    pmid = {27101584},
    keywords = {Autonomic Pathways, Female, Humans, Hypogastric Plexus, Immunohistochemistry, Organ Sparing Treatments, Pelvis, Staining and Labeling, Ureter, Urinary Bladder},
    pages = {959--966}
    }

  • N. Smit, C. Hofstede, A. Kraima, D. Jansma, M. deRuiter, E. Eisemann, and A. Vilanova, “The Online Anatomical Human: Web-based Anatomy Education.” 2016. doi:10.2312/eged.20161025
    [BibTeX] [Abstract] [Download PDF]

    The Online Anatomical Human (OAH) is a web-based viewer for studying anatomy. It is based on real human anatomy and incorporates medical image data in linked 2D and 3D views that students can freely interact with. Our application is the only to support 2D and 3D views based on real medical imaging data. The main goal of this anatomical online resource is to serve as an educational platform available to anyone with access to a modern web browser. Users can annotate regions, add comments, and provide hyperlinks to additional media. By making our work accessible to medical experts, we can ensure an increasing amount of information, leading to an evergrowing gain in educational value. The OAH will be used in an upcoming Massive Open Online Course (MOOC) to teach anatomy of the pelvis and will be made available to students worldwide via the web.

    @inproceedings{smit_online_2016,
    title = {The {Online} {Anatomical} {Human}: {Web}-based {Anatomy} {Education}},
    shorttitle = {The {Online} {Anatomical} {Human}},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/NoeskaSmitAnatomyEducation.pdf},
    doi = {10.2312/eged.20161025},
    abstract = {The Online Anatomical Human (OAH) is a web-based viewer for studying anatomy. It is based on real human anatomy and incorporates medical image data in linked 2D and 3D views that students can freely interact with. Our application is the only to support 2D and 3D views based on real medical imaging data. The main goal of this anatomical online resource is to serve as an educational platform available to anyone with access to a modern web browser. Users can annotate regions, add comments, and provide hyperlinks to additional media. By making our work accessible to medical experts, we can ensure an increasing amount of information, leading to an evergrowing gain in educational value. The OAH will be used in an upcoming Massive Open Online Course (MOOC) to teach anatomy of the pelvis and will be made available to students worldwide via the web.},
    language = {en},
    urldate = {2018-07-29},
    author = {Smit, Noeska and Hofstede, Cees-Willem and Kraima, Annelot and Jansma, Daniel and deRuiter, Marco and Eisemann, Elmar and Vilanova, Anna},
    year = {2016}
    }

  • N. Smit, A. Kraima, D. Jansma, M. deRuiter, E. Eisemann, and A. Vilanova, “VarVis: Visualizing Anatomical Variation in Branching Structures,” in Proceedings of the Eurographics / IEEE VGTC Conference on Visualization: Short Papers, 2016, p. 49–53. doi:10.2312/eurovisshort.20161160
    [BibTeX] [Abstract] [Download PDF]

    Anatomical variations are naturally-occurring deviations from typical human anatomy. While these variations are considered normal and non-pathological, they are still of interest in clinical practice for medical specialists such as radiologists and transplantation surgeons. The complex variations in branching structures, for instance in arteries or nerves, are currently visualized side-by-side in illustrations or expressed using plain text in medical publications. In this work, we present a novel way of visualizing anatomical variations in complex branching structures for educational purposes: VarVis. VarVis consists of several linked views that reveal global and local similarities and differences in the variations. We propose a novel graph representation to provide an overview of the topological changes. Our solution involves a topological similarity measure, which allows the user to select variations at a global level based on their degree of similarity. After a selection is made, local topological differences can be interactively explored using illustrations and topology graphs. We also incorporate additional information regarding the probability of the various cases. Our solution has several advantages over traditional approaches, which we demonstrate in an evaluation.

    @inproceedings{smit_varvis:_2016,
    series = {{EuroVis} '16},
    title = {{VarVis}: {Visualizing} {Anatomical} {Variation} in {Branching} {Structures}},
    shorttitle = {{VarVis}},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/NoeskaSmitVarVis.pdf},
    doi = {10.2312/eurovisshort.20161160},
    abstract = {Anatomical variations are naturally-occurring deviations from typical human anatomy. While these variations are considered
    normal and non-pathological, they are still of interest in clinical practice for medical specialists such as radiologists and
    transplantation surgeons. The complex variations in branching structures, for instance in arteries or nerves, are currently
    visualized side-by-side in illustrations or expressed using plain text in medical publications.
    In this work, we present a novel way of visualizing anatomical variations in complex branching structures for educational purposes:
    VarVis. VarVis consists of several linked views that reveal global and local similarities and differences in the variations.
    We propose a novel graph representation to provide an overview of the topological changes. Our solution involves a topological
    similarity measure, which allows the user to select variations at a global level based on their degree of similarity. After a
    selection is made, local topological differences can be interactively explored using illustrations and topology graphs. We also
    incorporate additional information regarding the probability of the various cases. Our solution has several advantages over
    traditional approaches, which we demonstrate in an evaluation.
    },
    urldate = {2018-07-29},
    booktitle = {{Proceedings of the {Eurographics} / {IEEE} {VGTC} {Conference} on {Visualization}: {Short} {Papers}}},
    publisher = {Eurographics Association},
    author = {Smit, Noeska and Kraima, Annelot and Jansma, Daniel and deRuiter, Marco and Eisemann, Elmar and Vilanova, Anna},
    year = {2016},
    pages = {49--53}
    }

  • N. Smit and K. Lawonn, “An Introduction to Evaluation in Medical Visualization,” in Proceedings of the EuroVis Workshop on Reproducibility, Verification, and Validation in Visualization, 2016, p. 41–43. doi:10.2312/eurorv3.20161115
    [BibTeX] [Abstract] [Download PDF]

    Medical visualization papers often deal with data that is interpreted by medical domain experts in a research or clinical context. Since visualizations are by definition designed to be interpreted by a human observer, often an evaluation is performed to confirm the utility of a presented method. The exact type of evaluation required is not always clear, especially to new researchers. With this paper, we hope to clarify the different types of evaluation methods that exist and provide practical guidelines to choose the most suitable evaluation method to increase the value of the work.

    @inproceedings{smit_introduction_2016,
    series = {{EuroRv}{\textasciicircum}3 '16},
    title = {An {Introduction} to {Evaluation} in {Medical} {Visualization}},
    isbn = {978-3-03868-017-8},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/NoeskaSmitEvaluationMedicalVisualization.pdf},
    doi = {10.2312/eurorv3.20161115},
    abstract = {Medical visualization papers often deal with data that is interpreted by medical domain experts in a research or clinical context. Since visualizations are by definition designed to be interpreted by a human observer, often an evaluation is performed to confirm the utility of a presented method. The exact type of evaluation required is not always clear, especially to new researchers. With this paper, we hope to clarify the different types of evaluation methods that exist and provide practical guidelines to choose the most suitable evaluation method to increase the value of the work.},
    urldate = {2018-07-29},
    booktitle = {Proceedings of the {EuroVis} {Workshop} on {Reproducibility}, {Verification}, and {Validation} in {Visualization}},
    publisher = {Eurographics Association},
    author = {Smit, Noeska and Lawonn, Kai},
    year = {2016},
    pages = {41--43}
    }

  • N. Lichtenberg, N. Smit, C. Hansen, and K. Lawonn, Sline: Seamless Line Illustration for Interactive Biomedical Visualization, The Eurographics Association, 2016. doi:10.2312/vcbm.20161281
    [BibTeX] [Abstract] [Download PDF]

    In medical visualization of surface information, problems often arise when visualizing several overlapping structures simultaneously. There is a trade-off between visualizing multiple structures in a detailed way and limiting visual clutter, in order to allow users to focus on the main structures. Illustrative visualization techniques can help alleviate these problems by defining a level of abstraction per structure. However, clinical uptake of these advanced visualization techniques so far has been limited due to the complex parameter settings required. To bring advanced medical visualization closer to clinical application, we propose a novel illustrative technique that offers a seamless transition between various levels of abstraction and detail. Using a single comprehensive parameter, users are able to quickly define a visual representation per structure that fits the visualization requirements for focus and context structures. This technique can be applied to any biomedical context in which multiple surfaces are routinely visualized, such as neurosurgery, radiotherapy planning or drug design. Additionally, we introduce a novel hatching technique, that runs in real-time and does not require texture coordinates. An informal evaluation with experts from different biomedical domains reveals that our technique allows users to design focus-and-context visualizations in a fast and intuitive manner.

    @book{lichtenberg_sline:_2016,
    title = {Sline: {Seamless} {Line} {Illustration} for {Interactive} {Biomedical} {Visualization}},
    isbn = {978-3-03868-010-9},
    shorttitle = {Sline},
    url = {http://noeskasmit.com/wp-content/uploads/2018/08/Lichtenberg_2016.pdf},
    abstract = {In medical visualization of surface information, problems often arise when visualizing several overlapping structures simultaneously. There is a trade-off between visualizing multiple structures in a detailed way and limiting visual clutter, in order to allow users to focus on the main structures. Illustrative visualization techniques can help alleviate these problems by defining a level of abstraction per structure. However, clinical uptake of these advanced visualization techniques so far has been limited due to the complex parameter settings required. To bring advanced medical visualization closer to clinical application, we propose a novel illustrative technique that offers a seamless transition between various levels of abstraction and detail. Using a single comprehensive parameter, users are able to quickly define a visual representation per structure that fits the visualization requirements for focus and context structures. This technique can be applied to any biomedical context in which multiple surfaces are routinely visualized, such as neurosurgery, radiotherapy planning or drug design. Additionally, we introduce a novel hatching technique, that runs in real-time and does not require texture coordinates. An informal evaluation with experts from different biomedical domains reveals that our technique allows users to design focus-and-context visualizations in a fast and intuitive manner.},
    language = {en},
    urldate = {2018-07-29},
    publisher = {The Eurographics Association},
    author = {Lichtenberg, Nils and Smit, Noeska and Hansen, Christian and Lawonn, Kai},
    year = {2016},
    doi = {10.2312/vcbm.20161281}
    }

  • N. Smit, “The Virtual Surgical Pelvis: Anatomy Visualization for Education and Surgical Planning,” PhD Thesis, 2016. doi:10.4233/uuid:b065ea24-0fb8-4cab-b427-9612ae6a2113
    [BibTeX] [Abstract] [Download PDF]

    This thesis deals with visualizing anatomical data for medical education and surgical planning purposes. To this end, we have developed a detailed virtual atlas, the Virtual Surgical Pelvis (VSP), which unifies surgically relevant knowledge on pelvic anatomy. We provide methods to share the knowledge contained in the VSP for educational purposes, and to visualize the VSP in the context of individual patients for pre-operative planning purposes.

    @phdthesis{smit_virtual_2016,
    title = {The {Virtual} {Surgical} {Pelvis}: {Anatomy} {Visualization} for {Education} and {Surgical} {Planning}},
    shorttitle = {The {Virtual} {Surgical} {Pelvis}},
    abstract = {This thesis deals with visualizing anatomical data for medical education and surgical planning purposes. To this end, we have developed a detailed virtual atlas, the Virtual Surgical Pelvis (VSP), which unifies surgically relevant knowledge on pelvic anatomy. We provide methods to share the knowledge contained in the VSP for educational purposes, and to visualize the VSP in the context of individual patients for pre-operative planning purposes.},
    author = {Smit, Noeska},
    month = oct,
    year = {2016},
    doi = {10.4233/uuid:b065ea24-0fb8-4cab-b427-9612ae6a2113},
    abstract = {This thesis deals with visualizing anatomical data for medical education and surgical planning purposes. To this end, we have developed a detailed virtual atlas, the Virtual Surgical Pelvis (VSP), which unifies surgically relevant knowledge on pelvic anatomy. We provide methods to share the knowledge contained in the VSP for educational purposes, and to visualize the VSP in the context of individual patients for pre-operative planning purposes.},
    url = {http://repository.tudelft.nl/islandora/object/uuid:b065ea24-0fb8-4cab-b427-9612ae6a2113/datastream/OBJ/download}
    }

2015

  • M. Kleppe, A. C. Kraima, R. F. P. M. Kruitwagen, T. Van Gorp, N. N. Smit, J. C. van Munsteren, and M. C. DeRuiter, “Understanding Lymphatic Drainage Pathways of the Ovaries to Predict Sites for Sentinel Nodes in Ovarian Cancer,” International Journal of Gynecological Cancer: Official Journal of the International Gynecological Cancer Society, vol. 25, iss. 8, p. 1405–1414, 2015. doi:10.1097/IGC.0000000000000514
    [BibTeX] [Abstract] [Download PDF]

    OBJECTIVE: In ovarian cancer, detection of sentinel nodes is an upcoming procedure. Perioperative determination of the patient’s sentinel node(s) might prevent a radical lymphadenectomy and associated morbidity. It is essential to understand the lymphatic drainage pathways of the ovaries, which are surprisingly up till now poorly investigated, to predict the anatomical regions where sentinel nodes can be found. We aimed to describe the lymphatic drainage pathways of the human ovaries including their compartmental fascia borders. METHODS: A series of 3 human female fetuses and tissues samples from 1 human cadaveric specimen were studied. Immunohistochemical analysis was performed on paraffin-embedded transverse sections (8 or 10 $\mu$m) using antibodies against Lyve-1, S100, and $\alpha$-smooth muscle actin to identify the lymphatic endothelium, Schwann, and smooth muscle cells, respectively. Three-dimensional reconstructions were created. RESULTS: Two major and 1 minor lymphatic drainage pathways from the ovaries were detected. One pathway drained via the proper ligament of the ovaries (ovarian ligament) toward the lymph nodes in the obturator fossa and the internal iliac artery. Another pathway drained the ovaries via the suspensory ligament (infundibulopelvic ligament) toward the para-aortic and paracaval lymph nodes. A third minor pathway drained the ovaries via the round ligament to the inguinal lymph nodes. Lymph vessels draining the fallopian tube all followed the lymphatic drainage pathways of the ovaries. CONCLUSIONS: The lymphatic drainage pathways of the ovaries invariably run via the suspensory ligament (infundibulopelvic ligament) and the proper ligament of the ovaries (ovarian ligament), as well as through the round ligament of the uterus. Because ovarian cancer might spread lymphogenously via these routes, the sentinel node can be detected in the para-aortic and paracaval regions, obturator fossa and surrounding internal iliac arteries, and inguinal regions. These findings support the strategy of injecting tracers in both ovarian ligaments to identify sentinel nodes.

    @article{kleppe_understanding_2015,
    title = {Understanding {Lymphatic} {Drainage} {Pathways} of the {Ovaries} to {Predict} {Sites} for {Sentinel} {Nodes} in {Ovarian} {Cancer}},
    volume = {25},
    issn = {1525-1438},
    doi = {10.1097/IGC.0000000000000514},
    abstract = {OBJECTIVE: In ovarian cancer, detection of sentinel nodes is an upcoming procedure. Perioperative determination of the patient's sentinel node(s) might prevent a radical lymphadenectomy and associated morbidity. It is essential to understand the lymphatic drainage pathways of the ovaries, which are surprisingly up till now poorly investigated, to predict the anatomical regions where sentinel nodes can be found. We aimed to describe the lymphatic drainage pathways of the human ovaries including their compartmental fascia borders.
    METHODS: A series of 3 human female fetuses and tissues samples from 1 human cadaveric specimen were studied. Immunohistochemical analysis was performed on paraffin-embedded transverse sections (8 or 10 $\mu$m) using antibodies against Lyve-1, S100, and $\alpha$-smooth muscle actin to identify the lymphatic endothelium, Schwann, and smooth muscle cells, respectively. Three-dimensional reconstructions were created.
    RESULTS: Two major and 1 minor lymphatic drainage pathways from the ovaries were detected. One pathway drained via the proper ligament of the ovaries (ovarian ligament) toward the lymph nodes in the obturator fossa and the internal iliac artery. Another pathway drained the ovaries via the suspensory ligament (infundibulopelvic ligament) toward the para-aortic and paracaval lymph nodes. A third minor pathway drained the ovaries via the round ligament to the inguinal lymph nodes. Lymph vessels draining the fallopian tube all followed the lymphatic drainage pathways of the ovaries.
    CONCLUSIONS: The lymphatic drainage pathways of the ovaries invariably run via the suspensory ligament (infundibulopelvic ligament) and the proper ligament of the ovaries (ovarian ligament), as well as through the round ligament of the uterus. Because ovarian cancer might spread lymphogenously via these routes, the sentinel node can be detected in the para-aortic and paracaval regions, obturator fossa and surrounding internal iliac arteries, and inguinal regions. These findings support the strategy of injecting tracers in both ovarian ligaments to identify sentinel nodes.},
    language = {eng},
    number = {8},
    journal = {{International Journal of Gynecological Cancer: Official Journal of the International Gynecological Cancer Society}},
    author = {Kleppe, Marjolein and Kraima, Anne C. and Kruitwagen, Roy F. P. M. and Van Gorp, Toon and Smit, Noeska N. and van Munsteren, Jacoba C. and DeRuiter, Marco C.},
    month = oct,
    year = {2015},
    pmid = {26397066},
    pmcid = {PMC5106084},
    keywords = {Biomarkers, Tumor, Drainage, Female, Fetus, Gestational Age, Humans, Immunoenzyme Techniques, Lymph Nodes, Lymphatic Vessels, Neoplasm Staging, Ovarian Neoplasms, Pelvis, Prognosis},
    pages = {1405--1414},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/kraima_lymphatic_2014.pdf}
    }

  • K. Lawonn, N. Smit, B. Preim, and A. Vilanova, “Illustrative Multi-volume Rendering for PET/CT Scans,” in Proceedings of the Eurographics Workshop on Visual Computing for Biology and Medicine, 2015, p. 103–112. doi:10.2312/vcbm.20151213
    [BibTeX] [Abstract] [Download PDF]

    In this paper we present illustrative visualization techniques for PET/CT datasets. PET/CT scanners acquire both PET and CT image data in order to combine functional metabolic information with structural anatomical information. Current visualization techniques mainly rely on 2D image fusion techniques to convey this combined information to physicians. We introduce an illustrative 3D visualization technique, specifically designed for use with PET/CT datasets. This allows the user to easily detect foci in the PET data and to localize these regions by providing anatomical contextual information from the CT data. Furthermore, we provide transfer function specifically designed for PET data that facilitates the investigation of interesting regions. Our technique allows users to get a quick overview of regions of interest and can be used in treatment planning, doctor-patient communication and interdisciplinary communication. We conducted a qualitative evaluation with medical experts to validate the utility of our method in clinical practice.

    @inproceedings{lawonn_illustrative_2015,
    series = {{VCBM} '15},
    title = {Illustrative {Multi}-volume {Rendering} for {PET}/{CT} {Scans}},
    isbn = {978-3-905674-82-8},
    url = {http://noeskasmit.com/wp-content/uploads/2018/08/Lawonn_2015.pdf},
    doi = {10.2312/vcbm.20151213},
    abstract = {In this paper we present illustrative visualization techniques for PET/CT datasets. PET/CT scanners acquire both PET and CT image data in order to combine functional metabolic information with structural anatomical information. Current visualization techniques mainly rely on 2D image fusion techniques to convey this combined information to physicians. We introduce an illustrative 3D visualization technique, specifically designed for use with PET/CT datasets. This allows the user to easily detect foci in the PET data and to localize these regions by providing anatomical contextual information from the CT data. Furthermore, we provide transfer function specifically designed for PET data that facilitates the investigation of interesting regions. Our technique allows users to get a quick overview of regions of interest and can be used in treatment planning, doctor-patient communication and interdisciplinary communication. We conducted a qualitative evaluation with medical experts to validate the utility of our method in clinical practice.},
    urldate = {2018-07-29},
    booktitle = {Proceedings of the {Eurographics} {Workshop} on {Visual} {Computing} for {Biology} and {Medicine}},
    publisher = {Eurographics Association},
    author = {Lawonn, Kai and Smit, Noeska and Preim, Bernhard and Vilanova, Anna},
    year = {2015},
    pages = {103--112}
    }

  • A. Kraima, N. Smit, D. Jansma, E. Eisemann, H. S. Park, M. S. Chung, N. West, P. Quirke, H. Rutten, A. Vilanova, V. C. de Velde, and M. DeRuiter, “2087 The development of a 3d anatomical atlas of the pelvis: Taking the next step in enhancing surgical anatomical education and clinical guidance,” European Journal of Cancer, vol. 51, p. S357, 2015. doi:10.1016/S0959-8049(16)31009-7
    [BibTeX] [Abstract] [Download PDF]

    The surgical anatomy of the pelvis is very complex. Due to the funnel-shaped pelvis there is an intricate anatomical arrangement. In case of rectal cancer, surgeons are challenged to perform a total mesorectal excision (TME), involving radical en-bloc removal of tumour and surrounding structures, and preservation of autonomic nerves. Excellent anatomical knowledge of the pelvis is essential to obtain good oncological and functional results in TME. However, contradicting descriptions on the arrangement of fasciae and nerves create confusion. As incomplete mesorectal excisions and iatrogenic nerve disruption are still reported, there is a need to optimise treatment by enhancing the anatomical knowledge among surgeons. We aimed to develop the Virtual Surgical Pelvis (VSP): an anatomical atlas representing the female pelvis in a virtual 3D context. Cadaveric specimens were histologically analysed to reveal the precise arrangement of fasciae and autonomic nerves.

    @article{kraima_2087_2015,
    title = {2087 {The} development of a 3D anatomical atlas of the pelvis: {Taking} the next step in enhancing surgical anatomical education and clinical guidance},
    volume = {51},
    issn = {0959-8049, 1879-0852},
    shorttitle = {2087 {The} development of a {3D} anatomical atlas of the pelvis},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/development3Datlaspelvis.pdf},
    doi = {10.1016/S0959-8049(16)31009-7},
    language = {English},
    urldate = {2018-07-29},
    journal = {{European Journal of Cancer}},
    author = {Kraima, A. and Smit, N. and Jansma, D. and Eisemann, E. and Park, H. S. and Chung, M. S. and West, N. and Quirke, P. and Rutten, H. and Vilanova, A. and Velde, C. Van de and DeRuiter, M.},
    month = sep,
    year = {2015},
    pages = {S357},
    abstract = {The surgical anatomy of the pelvis is very complex. Due
    to the funnel-shaped pelvis there is an intricate anatomical arrangement.
    In case of rectal cancer, surgeons are challenged to perform a total
    mesorectal excision (TME), involving radical en-bloc removal of tumour and
    surrounding structures, and preservation of autonomic nerves. Excellent
    anatomical knowledge of the pelvis is essential to obtain good oncological
    and functional results in TME. However, contradicting descriptions on
    the arrangement of fasciae and nerves create confusion. As incomplete
    mesorectal excisions and iatrogenic nerve disruption are still reported,
    there is a need to optimise treatment by enhancing the anatomical
    knowledge among surgeons. We aimed to develop the Virtual Surgical
    Pelvis (VSP): an anatomical atlas representing the female pelvis in a virtual
    3D context. Cadaveric specimens were histologically analysed to reveal the
    precise arrangement of fasciae and autonomic nerves.}
    }

  • A. Kraima, N. West, D. Treanor, N. Roberts, D. Magee, N. Smit, C. Van de Velde, M. Deruiter, H. Rutten, and P. Quirke, “The Three-Dimensional Anatomy of the Anal Sphincter Complex and its Relevance to Low Rectal and Anal Pathology.” 2015.
    [BibTeX] [Abstract] [Download PDF]

    The surgical anatomy of the pelvis is highly complex. In case of rectal cancer the surgeon is challenged to perform a total mesorectal excision (TME) warranting complete removal of the tumor and preservation of the autonomic nerves. However, incomplete TME specimens and surgical damage to the nerves are still part of clinical reality. A highly-detailed 3D pelvic model would be an excellent tool to increase anatomical knowledge of the surgical anatomy of the pelvis. Visible Human Datasets (VHDs) are often used to create a 3D model, but they lack anatomical detail such as autonomic nerves and fasciae. Immunohistochemistry is an ideal method to study those key surgical structures at microscopic level. Recently, the Unified Anatomical Human (UAH) has been developed. UAH integrates heterogeneous anatomical data and will allow registration of patient-specific diagnostic images. In this study, we describe the development of The Virtual Surgical Pelvis (VSP) and its potential clinical value in anatomical education and surgical simulation.

    @inproceedings{kraima_three-dimensional_2015,
    title = {The {Three}-{Dimensional} {Anatomy} of the {Anal} {Sphincter} {Complex} and its {Relevance} to {Low} {Rectal} and {Anal} {Pathology}},
    author = {Kraima, Anne and West, Nicholas and Treanor, D and Roberts, N and Magee, Derek and Smit, Noeska and Van de Velde, CJH and Deruiter, Marco and Rutten, Harm and Quirke, Philip},
    month = sep,
    year = {2015},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/kraima_anal_2016.pdf},
    abstract = {The surgical anatomy of the pelvis is highly complex.
    In case of rectal cancer the surgeon is challenged to perform a total mesorectal
    excision (TME) warranting complete removal of the tumor and
    preservation of the autonomic nerves. However, incomplete TME specimens
    and surgical damage to the nerves are still part of clinical reality.
    A highly-detailed 3D pelvic model would be an excellent tool to increase
    anatomical knowledge of the surgical anatomy of the pelvis. Visible Human
    Datasets (VHDs) are often used to create a 3D model, but they lack
    anatomical detail such as autonomic nerves and fasciae. Immunohistochemistry
    is an ideal method to study those key surgical structures at
    microscopic level. Recently, the Unified Anatomical Human (UAH)
    has been developed. UAH integrates heterogeneous anatomical data
    and will allow registration of patient-specific diagnostic images. In
    this study, we describe the development of The Virtual Surgical Pelvis
    (VSP) and its potential clinical value in anatomical education and surgical
    simulation.}
    }

2014

  • A. Kraima, N. N. Smit, D. Jansma, N. P. West, P. Quirke, H. J. Rutten, A. Vilanova, V. C. J. H. de Velde, and M. C. DeRuiter, “62. The virtual surgical pelvis: A highly-detailed 3d pelvic model for anatomical education and surgical simulation,” European Journal of Surgical Oncology, vol. 40, iss. 11, p. S32, 2014. doi:10.1016/j.ejso.2014.08.059
    [BibTeX] [Abstract] [Download PDF]

    The surgical anatomy of the pelvis is highly complex. In case of rectal cancer the surgeon is challenged to perform a total mesorectal excision (TME) warranting complete removal of the tumor and preservation of the autonomic nerves. However, incomplete TME specimens and surgical damage to the nerves are still part of clinical reality. A highly-detailed 3D pelvic model would be an excellent tool to increase anatomical knowledge of the surgical anatomy of the pelvis. Visible Human Datasets (VHDs) are often used to create a 3D model, but they lack anatomical detail such as autonomic nerves and fasciae. Immunohistochemistry is an ideal method to study those key surgical structures at microscopic level. Recently, the Unified Anatomical Human (UAH) has been developed. UAH integrates heterogeneous anatomical data and will allow registration of patient-specific diagnostic images. In this study, we describe the development of The Virtual Surgical Pelvis (VSP) and its potential clinical value in anatomical education and surgical simulation

    @article{kraima_62._2014,
    title = {62. {The} virtual surgical pelvis: {A} highly-detailed 3D pelvic model for anatomical education and surgical simulation},
    volume = {40},
    issn = {0748-7983, 1532-2157},
    shorttitle = {62. {The} virtual surgical pelvis},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/ejso.pdf},
    abstract = {The surgical anatomy of the pelvis is highly complex.
    In case of rectal cancer the surgeon is challenged to perform a total mesorectal
    excision (TME) warranting complete removal of the tumor and
    preservation of the autonomic nerves. However, incomplete TME specimens
    and surgical damage to the nerves are still part of clinical reality.
    A highly-detailed 3D pelvic model would be an excellent tool to increase
    anatomical knowledge of the surgical anatomy of the pelvis. Visible Human
    Datasets (VHDs) are often used to create a 3D model, but they lack
    anatomical detail such as autonomic nerves and fasciae. Immunohistochemistry
    is an ideal method to study those key surgical structures at
    microscopic level. Recently, the Unified Anatomical Human (UAH)
    has been developed. UAH integrates heterogeneous anatomical data
    and will allow registration of patient-specific diagnostic images. In
    this study, we describe the development of The Virtual Surgical Pelvis
    (VSP) and its potential clinical value in anatomical education and surgical
    simulation},
    doi = {10.1016/j.ejso.2014.08.059},
    language = {English},
    number = {11},
    urldate = {2018-07-29},
    journal = {{European Journal of Surgical Oncology}},
    author = {Kraima, A. and Smit, N. N. and Jansma, D. and West, N. P. and Quirke, P. and Rutten, H. J. and Vilanova, A. and Velde, C. J. H. Van de and DeRuiter, M. C.},
    month = nov,
    year = {2014},
    pages = {S32},
    }

  • A. C. Kraima, M. Derks, N. N. Smit, J. C. Van Munsteren, J. Van der Velden, G. G. Kenter, and M. C. DeRuiter, “Lymphatic drainage pathways from the cervix uteri: implications for radical hysterectomy?,” Gynecologic Oncology, vol. 132, iss. 1, p. 107–113, 2014. doi:10.1016/j.ygyno.2013.10.030
    [BibTeX] [Abstract] [Download PDF]

    OBJECTIVE: Radical hysterectomy with pelvic lymphadenectomy is the treatment of choice for early-stage cervical cancer. Wertheim’s original technique has been often modified, mainly in the extent of parametrectomy. Okabayashi’s technique is considered as the most radical variant regarding removal of the ventral parametrium and paracolpal tissues. Surgical outcome concerning recurrence and survival is good, but morbidity is high due to autonomic nerve damage. While the autonomic network has been studied extensively, the lymphatic system is less understood. This study describes the lymphatic drainage pathways of the cervix uteri and specifically the presence of lymphatics in the vesico-uterine ligament (VUL). METHODS: A developmental series of 10 human female fetal pelves was studied. Paraffin embedded blocks were sliced in transverse sections of 8 or 10 $\mu$m. Analysis was performed by staining with antibodies against LYVE-1 (lymphatic endothelium), S100 (Schwann cells), alpha-Smooth Muscle Actin (smooth muscle cells) and CD68 (macrophages). The results were three-dimensionally represented. RESULTS: Two major pathways drained the cervix uteri: a supra-ureteral pathway, running in the cardinal ligament superior to the ureter, and a dorsal pathway, running in the utero-sacral ligament towards the rectal pillars. No lymph vessels draining the cervix uteri were detected in the VUL. In the paracolpal parametrium lymph vessels draining the upper vagina fused with those from the bladder. CONCLUSIONS: The VUL does not contain lymphatics from the cervix uteri. Hence, the favorable survival outcomes of the Okabayashi technique cannot be explained by radical removal of lymphatic pathways in the ventrocaudal parametrium.

    @article{kraima_lymphatic_2014,
    title = {Lymphatic drainage pathways from the cervix uteri: implications for radical hysterectomy?},
    volume = {132},
    issn = {1095-6859},
    shorttitle = {Lymphatic drainage pathways from the cervix uteri},
    doi = {10.1016/j.ygyno.2013.10.030},
    abstract = {OBJECTIVE: Radical hysterectomy with pelvic lymphadenectomy is the treatment of choice for early-stage cervical cancer. Wertheim's original technique has been often modified, mainly in the extent of parametrectomy. Okabayashi's technique is considered as the most radical variant regarding removal of the ventral parametrium and paracolpal tissues. Surgical outcome concerning recurrence and survival is good, but morbidity is high due to autonomic nerve damage. While the autonomic network has been studied extensively, the lymphatic system is less understood. This study describes the lymphatic drainage pathways of the cervix uteri and specifically the presence of lymphatics in the vesico-uterine ligament (VUL).
    METHODS: A developmental series of 10 human female fetal pelves was studied. Paraffin embedded blocks were sliced in transverse sections of 8 or 10 $\mu$m. Analysis was performed by staining with antibodies against LYVE-1 (lymphatic endothelium), S100 (Schwann cells), alpha-Smooth Muscle Actin (smooth muscle cells) and CD68 (macrophages). The results were three-dimensionally represented.
    RESULTS: Two major pathways drained the cervix uteri: a supra-ureteral pathway, running in the cardinal ligament superior to the ureter, and a dorsal pathway, running in the utero-sacral ligament towards the rectal pillars. No lymph vessels draining the cervix uteri were detected in the VUL. In the paracolpal parametrium lymph vessels draining the upper vagina fused with those from the bladder.
    CONCLUSIONS: The VUL does not contain lymphatics from the cervix uteri. Hence, the favorable survival outcomes of the Okabayashi technique cannot be explained by radical removal of lymphatic pathways in the ventrocaudal parametrium.},
    language = {eng},
    number = {1},
    journal = {{Gynecologic Oncology}},
    author = {Kraima, A. C. and Derks, M. and Smit, N. N. and Van Munsteren, J. C. and Van der Velden, J. and Kenter, G. G. and DeRuiter, M. C.},
    month = jan,
    year = {2014},
    pmid = {24201016},
    keywords = {Cervical cancer, Drainage, Female, Humans, Hysterectomy, Lymphatic drainage pathways, Lymphatic Vessels, Parametrium, Radical hysterectomy, Uterine Cervical Neoplasms, Utero-sacral ligament, Vesicouterine ligament, Vesicular Transport Proteins},
    pages = {107--113},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/kraima_lymphatic_2014.pdf}
    }

  • N. N. Smit, B. K. Haneveld, M. Staring, E. Eisemann, C. P. Botha, and A. Vilanova, “RegistrationShop: An Interactive 3D Medical Volume Registration System.” 2014. doi:http://hdl.handle.net/10.2312/vcbm.20141193.145-153
    [BibTeX] [Abstract] [Download PDF]

    In medical imaging, registration is used to combine images containing information from different modalities or to track treatment effects over time in individual patients. Most registration software packages do not provide an easy-to-use interface that facilitates the use of registration. 2D visualization techniques are often used for visualizing 3D datasets. RegistrationShop was developed to improve and ease the process of volume registration using 3D visualizations and intuitive interactive tools. It supports several basic visualizations of 3D volumetric data. Interactive rigid and non-rigid transformation tools can be used to manipulate the volumes and immediate visual feedback for all rigid transformation tools allows the user to examine the current result in real-time. In this context, we introduce 3D comparative visualization techniques, as well as a way of placing landmarks in 3D volumes. Finally, we evaluated our approach with domain experts, who underlined the potential and usefulness of RegistrationShop.

    @inproceedings{smit_registrationshop:_2014,
    title = {{RegistrationShop}: {An} {Interactive} {3D} {Medical} {Volume} {Registration} {System}},
    isbn = {978-3-905674-62-0},
    shorttitle = {{RegistrationShop}},
    abstract = {In medical imaging, registration is used to combine images containing information from different modalities or to track treatment effects over time in individual patients. Most registration software packages do not provide an easy-to-use interface that facilitates the use of registration. 2D visualization techniques are often used for visualizing 3D datasets. RegistrationShop was developed to improve and ease the process of volume registration using 3D visualizations and intuitive interactive tools. It supports several basic visualizations of 3D volumetric data. Interactive rigid and non-rigid transformation tools can be used to manipulate the volumes and immediate visual feedback for all rigid transformation tools allows the user to examine the current result in real-time. In this context, we introduce 3D comparative visualization techniques, as well as a way of placing landmarks in 3D volumes. Finally, we evaluated our approach with domain experts, who underlined the potential and usefulness of RegistrationShop.},
    language = {en},
    urldate = {2018-07-29},
    publisher = {The Eurographics Association},
    author = {Smit, Noeska N. and Haneveld, Berend Klein and Staring, Marius and Eisemann, Elmar and Botha, Charl P. and Vilanova, Anna},
    year = {2014},
    doi = {http://hdl.handle.net/10.2312/vcbm.20141193.145-153},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/RegistrationShop.pdf}
    }

2012

  • N. N. Smit, A. C. Kraima, D. Jansma, M. C. de Ruiter, and C. P. Botha, “A unified representation for the model-based visualization of heterogeneous anatomy data,” in EuroVis-Short Papers, 2012, p. 85–89.
    [BibTeX] [Abstract] [Download PDF]

    In the course of anatomical research, anatomists acquire and attempt to organize a great deal of heterogeneous data from different sources, such as MRI and CT data, cryosections, immunohistochemistry, manual and automatic segmentations of various structures, related literature, the relations between all of these items, and so forth. Currently, there is no way of storing, accessing and visualizing these heterogeneous datasets in an integrated fashion. Such capabilities would have great potential to empower anatomy research. In this work, we present methods for the integration of heterogeneous spatial and non-spatial data from different sources, as well as the complex relations between them, into a single model with standardized anatomical coordinates. All captured data can then be interactively visualized in various ways, depending on the anatomical question. Furthermore, our model enables data to be queried both structurally, i.e., relative to existing anatomical structures, and spatially, i.e., with anatomical coordinates. When new patient-specific medical scans are added to the model, all available model information can be mapped to them. Using this mapping, model information can be transferred back to the new scans, thus enabling the creation of visualizations enriched with information not available in the scans themselves.

    @inproceedings{smit_unified_2012,
    title = {A unified representation for the model-based visualization of heterogeneous anatomy data},
    booktitle = {{EuroVis}-{Short} {Papers}},
    author = {Smit, N. N. and Kraima, A. C. and Jansma, D. and de Ruiter, M. C. and Botha, C. P.},
    year = {2012},
    pages = {85--89},
    abstract = {In the course of anatomical research, anatomists acquire and attempt to organize a great deal of heterogeneous
    data from different sources, such as MRI and CT data, cryosections, immunohistochemistry, manual and automatic
    segmentations of various structures, related literature, the relations between all of these items, and so forth. Currently,
    there is no way of storing, accessing and visualizing these heterogeneous datasets in an integrated fashion.
    Such capabilities would have great potential to empower anatomy research. In this work, we present methods for
    the integration of heterogeneous spatial and non-spatial data from different sources, as well as the complex relations
    between them, into a single model with standardized anatomical coordinates. All captured data can then be
    interactively visualized in various ways, depending on the anatomical question. Furthermore, our model enables
    data to be queried both structurally, i.e., relative to existing anatomical structures, and spatially, i.e., with anatomical
    coordinates. When new patient-specific medical scans are added to the model, all available model information
    can be mapped to them. Using this mapping, model information can be transferred back to the new scans, thus
    enabling the creation of visualizations enriched with information not available in the scans themselves.
    },
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/smit_unified_2012.pdf}
    }

  • N. N. Smit, A. C. Kraima, D. Jansma, M. C. DeRuiter, and C. P. Botha, “The unified anatomical human (beta): Model-based representation of heterogeneous anatomical data,” in Workshop 3D Physiological Human (3DPH), CASA, 2012.
    [BibTeX] [Abstract] [Download PDF]

    Three-dimensional anatomical models can be of great clinical value in surgical and educational applications. Mostly, three-dimensional models are reconstructed from Visible Human Datasets (VHDs). In the current VHDs, problems may arise in detecting finer anatomical structures, as is the case in the complex pelvic anatomy. Other datasources, such as CT, MR or immunohistochemistry, may reveal more detailed information about specific relevant anatomical structures. At this moment, there is no way of storing, accessing and visualizing all this information in one single solution. In this work, we present The Unified Anatomical Human: a method for the integration of heterogeneous anatomical data from different sources into a single model. This model allows for storage, retrieval and interactive visualization of arbitrary anatomical data sets. It forms an ideal foundation for further surgical and educational applications in any anatomical region of interest in the human body. Furthermore, we present the foundations for a highly detailed three-dimensional model of the human pelvis. This anatomically realistic model can serve as a solid basis for surgical training, pre-operative planning and medical education.

    @inproceedings{smit_unified_2012-1,
    title = {The unified anatomical human (beta): {Model}-based representation of heterogeneous anatomical data},
    shorttitle = {The unified anatomical human (beta)},
    booktitle = {{Workshop 3D Physiological Human (3DPH), CASA}},
    author = {Smit, N. N. and Kraima, A. C. and Jansma, D. and DeRuiter, M. C. and Botha, C. P.},
    year = {2012},
    abstract = {Three-dimensional anatomical models can be of great clinical value in
    surgical and educational applications. Mostly, three-dimensional models are reconstructed
    from Visible Human Datasets (VHDs). In the current VHDs, problems
    may arise in detecting finer anatomical structures, as is the case in the complex
    pelvic anatomy. Other datasources, such as CT, MR or immunohistochemistry,
    may reveal more detailed information about specific relevant anatomical structures.
    At this moment, there is no way of storing, accessing and visualizing all this
    information in one single solution. In this work, we present The Unified Anatomical
    Human: a method for the integration of heterogeneous anatomical data from
    different sources into a single model. This model allows for storage, retrieval and
    interactive visualization of arbitrary anatomical data sets. It forms an ideal foundation
    for further surgical and educational applications in any anatomical region of
    interest in the human body. Furthermore, we present the foundations for a highly
    detailed three-dimensional model of the human pelvis. This anatomically realistic
    model can serve as a solid basis for surgical training, pre-operative planning and
    medical education.},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/smit_UAH_2012.pdf}
    }

  • A. C. Kraima, N. N. Smit, D. Jansma, C. Wallner, R. L. W. a. Bleys, C. J. H. van de Velde, C. P. Botha, and M. C. DeRuiter, “Toward a highly-detailed 3D pelvic model: Approaching an ultra-specific level for surgical simulation and anatomical education,” Clinical Anatomy, vol. 26, iss. 3, p. 333–338, 2012. doi:10.1002/ca.22207
    [BibTeX] [Abstract] [Download PDF]

    The surgical anatomy of the pelvis is highly complex. Anorectal and urogenital dysfunctions occur frequently after pelvic oncological surgery and are mainly caused by surgical damage of the autonomic nerves. A highly-detailed 3D pelvic model could increase the anatomical knowledge and form a solid basis for a surgical simulation system. Currently, pelvic surgeons still rely on the preoperative interpretation of 2D diagnostic images. With a 3D simulation system, pelvic surgeons could simulate and train different scenes to enhance their preoperative knowledge and improve surgical outcome. To substantially enrich pelvic surgery and anatomical education, such a system must provide insight into the relation between the autonomic network, the lymphatic system, and endopelvic fasciae. Besides CT and MR images, Visible Human Datasets (VHDs) are widely used for 3D modeling, due to the high degree of anatomical detail represented in the cryosectional images. However, key surgical structures cannot be fully identified using VHDs and radiologic imaging techniques alone. Several unsolved anatomical problems must be elucidated as well. Therefore, adequate analysis on a microscopic level is inevitable. The development of a comprehensive anatomical atlas of the pelvis is no straightforward task. Such an endeavor involves several anatomical and technical challenges. This article surveys all existing 3D pelvic models, focusing on the level of anatomical detail. The use of VHDs in the 3D reconstruction of a highly-detailed pelvic model and the accompanying anatomical challenges will be discussed Clin. Anat., 2013. {\textcopyright} 2012 Wiley Periodicals, Inc.

    @article{kraima_toward_2012,
    title = {Toward a highly-detailed {3D} pelvic model: {Approaching} an ultra-specific level for surgical simulation and anatomical education},
    volume = {26},
    copyright = {Copyright {\textcopyright} 2012 Wiley Periodicals, Inc.},
    issn = {1098-2353},
    shorttitle = {Toward a highly-detailed 3D pelvic model},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/TaHD3PM.pdf},
    doi = {10.1002/ca.22207},
    abstract = {The surgical anatomy of the pelvis is highly complex. Anorectal and urogenital dysfunctions occur frequently after pelvic oncological surgery and are mainly caused by surgical damage of the autonomic nerves. A highly-detailed 3D pelvic model could increase the anatomical knowledge and form a solid basis for a surgical simulation system. Currently, pelvic surgeons still rely on the preoperative interpretation of 2D diagnostic images. With a 3D simulation system, pelvic surgeons could simulate and train different scenes to enhance their preoperative knowledge and improve surgical outcome. To substantially enrich pelvic surgery and anatomical education, such a system must provide insight into the relation between the autonomic network, the lymphatic system, and endopelvic fasciae. Besides CT and MR images, Visible Human Datasets (VHDs) are widely used for 3D modeling, due to the high degree of anatomical detail represented in the cryosectional images. However, key surgical structures cannot be fully identified using VHDs and radiologic imaging techniques alone. Several unsolved anatomical problems must be elucidated as well. Therefore, adequate analysis on a microscopic level is inevitable. The development of a comprehensive anatomical atlas of the pelvis is no straightforward task. Such an endeavor involves several anatomical and technical challenges. This article surveys all existing 3D pelvic models, focusing on the level of anatomical detail. The use of VHDs in the 3D reconstruction of a highly-detailed pelvic model and the accompanying anatomical challenges will be discussed Clin. Anat., 2013. {\textcopyright} 2012 Wiley Periodicals, Inc.},
    language = {en},
    number = {3},
    urldate = {2018-07-29},
    journal = {{Clinical Anatomy}},
    author = {Kraima, A. C. and Smit, N. N. and Jansma, D. and Wallner, C. and Bleys, R. L. a. W. and Velde, C. J. H. van de and Botha, C. P. and DeRuiter, M. C.},
    year = {2012},
    keywords = {3D anatomical model, autonomic nerves, endopelvic fasciae, pelvis, surgical simulation, visible human datasets},
    pages = {333--338}
    }

2010

  • A. L. A. Kerver, G. J. Kleinrensink, N. N. Smit, S. Rabbelier, B. M. W. Sedee, and C. P. Botha, “Web-Based ‘Computer Assisted Surgical Anatomy Mapping’.,” in WEBIST, 2010, p. 244–247.
    [BibTeX] [Abstract] [Download PDF]

    In surgery one of the major problems is a safe approach of the operation site. For surgeons it is paramount to know the location of surgically relevant nerves and vessels. Especially in surgery of the lateral (outside) foot, the anatomy is not always completely clear since the location of nerves and vessels is highly variable. Therefore CASAM is developed by students in Delft and Rotterdam (Netherlands). This web-application is based on the Django-framework and is a useful tool for three usergroups: 1) Researchers: After photographing dissected specimen a Thin Plate Spline transformation is used to compute an average foot and the pictures of individual specimen are warped to match this reference, average-foot. Renditions can be made to depict relevant surgical anatomy. Finally the researchers can define a zone in the lateral foot in which it is safe to approach the operation site. 2) Surgeons: Relevant anatomy (gathered by the researcher) can be warped over the picture of the patient. This pre-operative planning using CASAM assists the surgeon in determining a ‘tailor made’ safe-zone for each patient. 3) Students: For educational purposes, a drawn incision line can be compared to the computed location of nerves and vessels, thus providing personal feedback.

    @inproceedings{kerver_web-basedcomputer_2010,
    title = {Web-{Based} '{Computer} {Assisted} {Surgical} {Anatomy} {Mapping}'.},
    booktitle = {{WEBIST}},
    author = {Kerver, A. L. A. and Kleinrensink, Gert Jan and Smit, Noeska N. and Rabbelier, S. and Sedee, B. M. W. and Botha, Charl P.},
    year = {2010},
    pages = {244--247},
    abstract = {In surgery one of the major problems is a safe approach of the operation site. For surgeons it is paramount to
    know the location of surgically relevant nerves and vessels. Especially in surgery of the lateral (outside)
    foot, the anatomy is not always completely clear since the location of nerves and vessels is highly variable.
    Therefore CASAM is developed by students in Delft and Rotterdam (Netherlands). This web-application is
    based on the Django-framework and is a useful tool for three usergroups: 1) Researchers: After
    photographing dissected specimen a Thin Plate Spline transformation is used to compute an average foot
    and the pictures of individual specimen are warped to match this reference, average-foot. Renditions can be
    made to depict relevant surgical anatomy. Finally the researchers can define a zone in the lateral foot in
    which it is safe to approach the operation site. 2) Surgeons: Relevant anatomy (gathered by the researcher)
    can be warped over the picture of the patient. This pre-operative planning using CASAM assists the surgeon
    in determining a ‘tailor made’ safe-zone for each patient. 3) Students: For educational purposes, a drawn
    incision line can be compared to the computed location of nerves and vessels, thus providing personal
    feedback.},
    url = {http://noeskasmit.com/wp-content/uploads/2018/07/kerver_2010.pdf}
    }