I’m an Associate Professor in Medical Visualization (tenure track position funded by the BFS), with a background in computer science and radiography. My research focuses on model-based visualization for medical applications, as well as multi-modal visualization in the context of computational medicine. My position is also associated to the Mohn Medical Imaging and Visualization (MMIV) centre.
Teaching:
- Continuously INF219, INF319 Project in Visualization
- Spring Semester 2019: INF101 Object-oriented Programming
- Fall Semester 2017/2018: INF358 Seminar in Visualization
This page only displays publications I have authored in my current affiliation. For a full overview, please check my Google Scholar profile.
Publications
2019
![[DOI]](http://vis.uib.no/wp-content/plugins/papercite/img/external.png){kind=small}
[Bibtex] @article{kraima2019role,
title={The role of the longitudinal muscle in the anal sphincter complex: Implications for the Intersphincteric Plane in Low Rectal Cancer Surgery?},
author={Kraima, Anne C and West, Nicholas P and Roberts, Nicholas and Magee, Derek R and Smit, Noeska N and van de Velde, Cornelis JH and DeRuiter, Marco C and Rutten, Harm J and Quirke, Philip},
journal={Clinical Anatomy},
year={2019},
doi="10.1002/ca.23444",
url = "https://onlinelibrary.wiley.com/doi/full/10.1002/ca.23444",
publisher={Wiley Online Library},
project = "ttmedvis",
images = {images/kraima-2019-role.png},
thumbnails = {images/kraima-2019-role.png},
abstract = {Intersphincteric resection (ISR) enables radical sphincter‐preserving surgery in a subset of low rectal tumors impinging on the anal sphincter complex (ASC). Excellent anatomical knowledge is essential for optimal ISR. This study describes the role of the longitudinal muscle (LM) in the ASC and implications for ISR and other low rectal and anal pathologies. Six human adult en bloc cadaveric specimens (three males, three females) were obtained from the University of Leeds GIFT Research Tissue Programme. Paraffin‐embedded mega blocks containing the ASC were produced and serially sectioned at 250 μm intervals. Whole mount microscopic sections were histologically stained and digitally scanned. The intersphincteric plane was shown to be potentially very variable. In some places adipose tissue is located between the external anal sphincter (EAS) and internal anal sphincter (IAS), whereas in others the LM interdigitates to obliterate the plane. Elsewhere the LM is (partly) absent with the intersphincteric plane lying on the IAS. The LM gave rise to the formation of the submucosae and corrugator ani muscles by penetrating the IAS and EAS. In four of six specimens, striated muscle fibers from the EAS curled around the distal IAS reaching the anal submucosa. The ASC formed a complex structure, varying between individuals with an inconstant LM affecting the potential location of the intersphincteric plane as well as a high degree of intermingling striated and smooth muscle fibers potentially further disrupting the plane. The complexity of identifying the correct pathological staging of low rectal cancer is also demonstrated.}
}![[PDF]](http://vis.uib.no/wp-content/plugins/papercite/img/pdf.png)
![[YT]](http://vis.uib.no/wp-content/papercite-data/images/youtube.png)
[Bibtex] @INPROCEEDINGS {Garrison2019SM,
author = {Garrison, Laura and Va\v{s}\'{\i}\v{c}ek, Jakub and Gr\"{u}ner, Renate and Smit, Noeska and Bruckner, Stefan},
title = {SpectraMosaic: An Exploratory Tool for the Interactive Visual Analysis of Magnetic Resonance Spectroscopy Data},
journal = {Computer Graphics Forum},
month = {sep},
year = {2019},
booktitle = {Proceedings of 9th EG Workshop on Visual Computing for Biology and Medicine (VCBM)},
event = "VCBM 2019",
proceedings = "Proceedings of the 9th Eurographics Workshop on Visual Computing in Biology and Medicine",
keywords = {medical visualization, magnetic resonance spectroscopy data, information visualization, user-centered design},
images = "images/garrison_VCBM19spectramosaic_full.PNG",
thumbnails = "images/garrison_VCBM19spectramosaic_thumb.png",
pdf = "pdfs/garrison_VCBM19spectramosaic.pdf",
youtube = "https://youtu.be/Rzl7sl4WvdQ",
abstract = {Magnetic resonance spectroscopy (MRS) allows for assessment of tissue metabolite characteristics used often for early detection and treatment evaluation of brain-related pathologies. However, meaningful variations in ratios of tissue metabolites within a sample area are difficult to capture with current visualization tools. Furthermore, the learning curve to interpretation is steep and limits the more widespread adoption of MRS in clinical practice. In this design study, we collaborated with domain experts to design a novel visualization tool for the exploration of tissue metabolite concentration ratios in spectroscopy clinical and research studies. We present a data and task analysis for this domain, where MRS data attributes can be categorized into tiers of visual priority. We furthermore introduce a novel set of visual encodings for these attributes. Our result is SpectraMosaic (see Figure~\ref{fig:teaser}), an interactive insight-generation tool for rapid exploration and comparison of metabolite ratios. We validate our approach with two case studies from MR spectroscopy experts, providing early qualitative evidence of the efficacy of the system for visualization of spectral data and affording deeper insights into these complex heterogeneous data.},
git = "https://git.app.uib.no/Laura.Garrison/spectramosaic",
project = "VIDI"
}@incollection{Smit-2019-AtlasVis,
title={Towards Advanced Interactive Visualization for Virtual Atlases},
author={Smit, Noeska and Bruckner, Stefan},
booktitle={Biomedical Visualisation},
pages={85--96},
year={2019},
publisher={Springer},
doi = {10.1007/978-3-030-19385-0_6},
url = "http://noeskasmit.com/wp-content/uploads/2019/07/Smit_AtlasVis_2019.pdf",
images = "images/Smit-2019-AtlasVis.png",
thumbnails = "images/Smit-2019-AtlasVis.png",
abstract = "An atlas is generally defined as a bound collection of tables, charts or illustrations describing a phenomenon. In an anatomical atlas for example, a collection of representative illustrations and text describes anatomy for the purpose of communicating anatomical knowledge. The atlas serves as reference frame for comparing and integrating data from different sources by spatially or semantically relating collections of drawings, imaging data, and/or text. In the field of medical image processing, atlas information is often constructed from a collection of regions of interest, which are based on medical images that are annotated by domain experts. Such an atlas may be employed for example for automatic segmentation of medical imaging data. The combination of interactive visualization techniques with atlas information opens up new possibilities for content creation, curation, and navigation in virtual atlases. With interactive visualization of atlas information, students are able to inspect and explore anatomical atlases in ways that were not possible with the traditional method of presenting anatomical atlases in book format, such as viewing the illustrations from other viewpoints. With advanced interaction techniques, it becomes possible to query the data that forms the basis for the atlas, thus empowering researchers to access a wealth of information in new ways. So far, atlasbased visualization has been employed for mainly medical education, as well as biological research. In this survey, we provide an overview of current digital biomedical atlas tasks and applications and summarize relevant visualization techniques. We discuss recent approaches for providing next-generation visual interfaces to navigate atlas data that go beyond common text-based search and hierarchical lists. Finally, we reflect on open challenges and opportunities for the next steps in interactive atlas visualization. ",
project = "ttmedvis,MetaVis,VIDI"
}@article{Solteszova-2019-MLT,
author = {Solteszova, V. and Smit, N. N. and Stoppel, S. and Grüner, R. and Bruckner, S.},
title = {Memento: Localized Time-Warping for Spatio-Temporal Selection},
journal = {Computer Graphics Forum},
volume = {0},
number = {0},
pages = {},
year = {2019},
keywords = {interaction, temporal data, visualization, spatio-temporal projection, • Human-centred computing → Visualization techniques, Scientific visualization, • Mathematics of computing → Time series analysis},
images = "images/Solteszova-2019-MLT.jpg",
thumbnails = "images/Solteszova-2019-MLT-1.jpg",
doi = {10.1111/cgf.13763},
abstract = {Abstract Interaction techniques for temporal data are often focused on affecting the spatial aspects of the data, for instance through the use of transfer functions, camera navigation or clipping planes. However, the temporal aspect of the data interaction is often neglected. The temporal component is either visualized as individual time steps, an animation or a static summary over the temporal domain. When dealing with streaming data, these techniques are unable to cope with the task of re-viewing an interesting local spatio-temporal event, while continuing to observe the rest of the feed. We propose a novel technique that allows users to interactively specify areas of interest in the spatio-temporal domain. By employing a time-warp function, we are able to slow down time, freeze time or even travel back in time, around spatio-temporal events of interest. The combination of such a (pre-defined) time-warp function and brushing directly in the data to select regions of interest allows for a detailed review of temporally and spatially localized events, while maintaining an overview of the global spatio-temporal data. We demonstrate the utility of our technique with several usage scenarios.},
project = "MetaVis,ttmedvis,VIDI"
}@article{Meuschke-2019-EvalViz,
title = {EvalViz--Surface Visualization Evaluation Wizard for Depth and Shape Perception Tasks},
author = {Meuschke, Monique and Smit, Noeska N and Lichtenberg, Nils and Preim, Bernhard and Lawonn, Kai},
journal = {Computers \& Graphics},
year = {2019},
publisher = {Elsevier},
number = "1",
volume = "82",
DOI = {10.1016/j.cag.2019.05.022},
images = "images/Meuschke_EvalViz_2019.png",
thumbnails = "images/Meuschke_EvalViz_2019.png",
abstract = "User studies are indispensable for visualization application papers in order to assess the value and limitations of the presented approach. Important aspects are how well depth and shape information can be perceived, as coding of these aspects is essential to enable an understandable representation of complex 3D data. In practice, there is usually little time to perform such studies, and the establishment and conduction of user studies can be labour-intensive. In addition, it can be difficult to reach enough participants to obtain expressive results regarding the quality of different visualization techniques.
In this paper, we propose a framework that allows visualization researchers to quickly create task-based user studies on depth and shape perception for different surface visualizations and perform the resulting tasks via a web interface. With our approach, the effort for generating user studies is reduced and at the same time the web-based component allows researchers to attract more participants to their study. We demonstrate our framework by applying shape and depth evaluation tasks to visualizations of various surface representations used in many technical and biomedical applications.",
project = "ttmedvis"
}@MISC {Garrison2019SM_eurovis,
title = {A Visual Encoding System for Comparative Exploration of Magnetic Resonance Spectroscopy Data},
author = {Garrison, Laura and Va\v{s}\'{\i}\v{c}ek, Jakub and Gr\"{u}ner, Renate and Smit, Noeska and Bruckner, Stefan},
abstract = "Magnetic resonance spectroscopy (MRS) allows for assessment of tissue metabolite characteristics used often for early detection and treatment evaluation of intracranial pathologies. In particular, this non-invasive technique is important in the study of metabolic changes related to brain tumors, strokes, seizure disorders, Alzheimer's disease, depression, as well as other diseases and disorders affecting the brain. However, meaningful variations in ratios of tissue metabolites within a sample area are difficult to capture with current visualization tools. Furthermore, the learning curve to interpretation is steep and limits the more widespread adoption of MRS in clinical practice. In this work we present a novel, tiered visual encoding system for multi-dimensional MRS data to aid in the visual exploration of metabolite concentration ratios. Our system was developed in close collaboration with domain experts including detailed data and task analyses. This visual encoding system was subsequently realized as part of an interactive insight-generation tool for rapid exploration and comparison of metabolite ratio variation for deeper insights to these complex data.",
booktitle = {Proceedings of the EuroVis Conference - Posters (EuroVis ’19)},
year = {2019},
howpublished = "Poster presented at the EuroVis conference 2019",
keywords = {medical visualization, magnetic resonance spectroscopy data, information visualization, user-centered design},
images = "images/garrison_eurovis2019_SM_encodings.png",
thumbnails = "images/garrison_eurovis2019_SM_encodings.png",
pdf = "pdfs/garrison_eurovis2019_SM.pdf",
youtube = "https://youtu.be/Rzl7sl4WvdQ",
project = "VIDI"
}@inproceedings {Smit-2019-DBP,
booktitle = {Eurographics 2019 - Dirk Bartz Prize},
editor = {Bruckner, Stefan and Oeltze-Jafra, Steffen},
title = {{Model-based Visualization for Medical Education and Training}},
author = {Smit, Noeska and Lawonn, Kai and Kraima, Annelot and deRuiter, Marco and Bruckner, Stefan and Eisemann, Elmar and Vilanova, Anna},
year = {2019},
publisher = {The Eurographics Association},
ISSN = {1017-4656},
DOI = {10.2312/egm.20191033},
pdf = "pdfs/Smit_DBPrize_2019.pdf",
images = "images/Smit_DBPrize_2019.png",
thumbnails = "images/Smit_DBPrize_2019.png",
abstract = "Anatomy, or the study of the structure of the human body, is an essential component of medical education. Certain parts of human anatomy are considered to be more complex to understand than others, due to a multitude of closely related structures. Furthermore, there are many potential variations in anatomy, e.g., different topologies of vessels, and knowledge of these variations is critical for many in medical practice.
Some aspects of individual anatomy, such as the autonomic nerves, are not visible in individuals through medical imaging techniques or even during surgery, placing these nerves at risk for damage.
3D models and interactive visualization techniques can be used to improve understanding of this complex anatomy, in combination with traditional medical education paradigms.
We present a framework incorporating several advanced medical visualization techniques and applications for teaching and training purposes, which is the result of an interdisciplinary project.
In contrast to previous approaches which focus on general anatomy visualization or direct visualization of medical imaging data, we employ model-based techniques to represent variational anatomy, as well as anatomy not visible from imaging. Our framework covers the complete spectrum including general anatomy, anatomical variations, and anatomy in individual patients.
Applications within our framework were evaluated positively with medical users, and our educational tool for general anatomy is in use in a Massive Open Online Course (MOOC) on anatomy, which had over 17000 participants worldwide in the first run.",
project = "ttmedvis,VIDI"
}@inproceedings {Moerth-2019-VCBM,
booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine",
editor = "Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia",
abstract = "Three-dimensional (3D) ultrasound imaging and visualization
is often used in medical diagnostics, especially in prenatal
screening. Screening the development of the fetus is
important to assess possible complications early on. State
of the art approaches involve taking standardized
measurements to compare them with standardized tables. The
measurements are taken in a 2D slice view, where precise
measurements can be difficult to acquire due to the fetal
pose. Performing the analysis in a 3D view would enable the
viewer to better discriminate between artefacts and
representative information. Additionally making data
comparable between different investigations and patients is
a goal in medical imaging techniques and is often achieved
by standardization. With this paper, we introduce a novel
approach to provide a standardization method for 3D
ultrasound fetus screenings. Our approach is called “The
Vitruvian Baby” and incorporates a complete pipeline for
standardized measuring in fetal 3D ultrasound. The input of
the method is a 3D ultrasound screening of a fetus and the
output is the fetus in a standardized T-pose. In this pose,
taking measurements is easier and comparison of different
fetuses is possible. In addition to the transformation of
the 3D ultrasound data, we create an abstract representation
of the fetus based on accurate measurements. We demonstrate
the accuracy of our approach on simulated data where the
ground truth is known.",
title = "The Vitruvian Baby: Interactive Reformation of Fetal Ultrasound Data to a T-Position",
author = "Mörth, Eric and Raidou, Renata Georgia and Viola, Ivan and Smit, Noeska",
year = "2019",
publisher = "The Eurographics Association",
ISSN = "2070-5786",
ISBN = "978-3-03868-081-9",
DOI = "10.2312/vcbm.20191245",
pdf = "pdfs/VCBM_TheVitruvianBaby_ShortPaper_201-205.pdf",
images = "images/vcbmVitruvianBaby.jpg",
thumbnails = "images/vcbmVitruvianBaby.jpg",
url = "https://diglib.eg.org/handle/10.2312/vcbm20191245",
project = {VIDI}
}