Publications by authors named "Knut Conradsen"

10 Publications

  • Page 1 of 1

Using virtual reality for anatomical landmark annotation in geometric morphometrics.

PeerJ 2022 7;10:e12869. Epub 2022 Feb 7.

Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark.

To study the shape of objects using geometric morphometrics, landmarks are oftentimes collected digitally from a 3D scanned model. The expert may annotate landmarks using software that visualizes the 3D model on a flat screen, and interaction is achieved with a mouse and a keyboard. However, landmark annotation of a 3D model on a 2D display is a tedious process and potentially introduces error due to the perception and interaction limitations of the flat interface. In addition, digital landmark placement can be more time-consuming than direct annotation on the physical object using a tactile digitizer arm. Since virtual reality (VR) is designed to more closely resemble the real world, we present a VR prototype for annotating landmarks on 3D models. We study the impact of VR on annotation performance by comparing our VR prototype to Stratovan Checkpoint, a commonly used commercial desktop software. We use an experimental setup, where four operators placed six landmarks on six grey seal () skulls in six trials for both systems. This enables us to investigate multiple sources of measurement error. We analyse both for the configuration and for single landmarks. Our analysis shows that annotation in VR is a promising alternative to desktop annotation. We find that annotation precision is comparable between the two systems, with VR being significantly more precise for one of the landmarks. We do not find evidence that annotation in VR is faster than on the desktop, but it is accurate.
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http://dx.doi.org/10.7717/peerj.12869DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8830334PMC
February 2022

Measurement error using a SeeMaLab structured light 3D scanner against a Microscribe 3D digitizer.

PeerJ 2021 20;9:e11804. Epub 2021 Aug 20.

Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.

Background: Geometric morphometrics is a powerful approach to capture and quantify morphological shape variation. Both 3D digitizer arms and structured light surface scanners are portable, easy to use, and relatively cheap, which makes these two capturing devices obvious choices for geometric morphometrics. While digitizer arms have been the "gold standard", benefits of having full 3D models are manifold. We assessed the measurement error and investigate bias associated with the use of an open-source, high-resolution structured light scanner called SeeMaLab against the popular Microscribe 3D digitizer arm.

Methodology: The analyses were based on 22 grey seal () skulls. 31 fixed anatomical landmarks were annotated both directly using a Microscribe 3D digitizer and on reconstructed 3D digital models created from structured light surface scans. Each skull was scanned twice. Two operators annotated the landmarks, each twice on all the skulls and 3D models, allowing for the investigation of multiple sources of measurement error. We performed multiple Procrustes ANOVAs to compare the two devices in terms of within- and between-operator error, to quantify the measurement error induced by device, to compare between-device error with other sources of variation, and to assess the level of scanning-related error. We investigated the presence of general shape bias due to device and operator.

Results: Similar precision was obtained with both devices. If landmarks that were identified as less clearly defined and thus harder to place were omitted, the scanner pipeline would achieve higher precision than the digitizer. Between-operator error was biased and seemed to be smaller when using the scanner pipeline. There were systematic differences between devices, which was mainly driven by landmarks less clearly defined. The factors , and were all statistically significant and of similar size, but were minor sources of total shape variation, compared to the biological variation among grey seal skulls. The scanning-related error was small compared to all other error sources.

Conclusions: As the scanner showed precision similar to the digitizer, a scanner should be used if the advantages of obtaining detailed 3D models of a specimen are desired. To obtain high precision, a pre-study should be conducted to identify difficult landmarks. Due to the observed bias, data from different devices and/or operators should not be combined when the expected biological variation is small, without testing the landmarks for repeatability across platforms and operators. For any study necessitating the combination of landmark measurements from different operators, the scanner pipeline will be better suited. The small scanning-related error indicates that by following the same scanning protocol, different operators can be involved in the scanning process without introducing significant error.
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http://dx.doi.org/10.7717/peerj.11804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8381885PMC
August 2021

Multimodal soft tissue markers for bridging high-resolution diagnostic imaging with therapeutic intervention.

Sci Adv 2020 08 19;6(34):eabb5353. Epub 2020 Aug 19.

DTU Health Technology, Section for Biotherapeutic Engineering and Drug Targeting, Center for Nanomedicine and Theranostics, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.

Diagnostic imaging often outperforms the surgeon's ability to identify small structures during therapeutic procedures. Smart soft tissue markers that translate the sensitivity of diagnostic imaging into optimal therapeutic intervention are therefore highly warranted. This paper presents a unique adaptable liquid soft tissue marker system based on functionalized carbohydrates (Carbo-gel). The liquid state of these markers allows for high-precision placement under image guidance using thin needles. Based on step-by-step modifications, the image features and mechanical properties of markers can be optimized to bridge diagnostic imaging and specific therapeutic interventions. The performance of Carbo-gel is demonstrated for markers that (i) have radiographic, magnetic resonance, and ultrasound visibility; (ii) are palpable and visible; and (iii) are localizable by near-infrared fluorescence and radio guidance. The study demonstrates encouraging proof of concept for the liquid marker system as a well-tolerated multimodal imaging marker that can improve image-guided radiotherapy and surgical interventions, including robotic surgery.
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http://dx.doi.org/10.1126/sciadv.abb5353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7438096PMC
August 2020

Investigation of pausing fermentation of salamis with multispectral imaging for optimal sensory evaluations.

Meat Sci 2018 Dec 25;146:9-17. Epub 2018 Jul 25.

Technical University of Denmark, Richard Petersens Plads, 2800 Kgs. Lyngby, Denmark. Electronic address:

The fermentation process of salamis involves several parameters influencing taste, texture, and color of the salami. One significant parameter is the fermentation time. It is difficult to conduct sensory evaluations to assess the effect of time without introducing variation between observation days. It may be possible to overcome this by stalling or pausing the fermentation by deep-chilling the salamis. This study investigates the difference of non- and deep-chilled salamis with the use of a multispectral imaging system. The statistical investigation, based on image features relating to size, visual texture, and color of the sausages over time, showed that it may be possible to stall the fermentation process. It was shown that a statistical difference in the two kinds of samples is present. For the size feature the difference could be quantified into a number of days. However, for the important color feature only a statistical difference was observed, whereas the visual difference expressed in terms of ΔE was barely present.
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http://dx.doi.org/10.1016/j.meatsci.2018.07.029DOI Listing
December 2018

A multimodal data-set of a unidirectional glass fibre reinforced polymer composite.

Data Brief 2018 Jun 14;18:1388-1393. Epub 2018 Apr 14.

Department of Applied Mathematics and Computer Science, Technical University of Denmark, Denmark.

A unidirectional (UD) glass fibre reinforced polymer (GFRP) composite was scanned at varying resolutions in the micro-scale with several imaging modalities. All six scans capture the same region of the sample, containing well-aligned fibres inside a UD load-carrying bundle. Two scans of the cross-sectional surface of the bundle were acquired at a high resolution, by means of scanning electron microscopy (SEM) and optical microscopy (OM), and four volumetric scans were acquired through X-ray computed tomography (CT) at different resolutions. Individual fibres can be resolved from these scans to investigate the micro-structure of the UD bundle. The data is hosted at https://doi.org/10.5281/zenodo.1195879 and it was used in Emerson et al. (2018) [1] to demonstrate that precise and representative characterisations of fibre geometry are possible with relatively low X-ray CT resolutions if the analysis method is robust to image quality.
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http://dx.doi.org/10.1016/j.dib.2018.04.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060273PMC
June 2018

Integrated Brain Atlas for Unbiased Mapping of Nervous System Effects Following Liraglutide Treatment.

Sci Rep 2018 07 9;8(1):10310. Epub 2018 Jul 9.

Global Research, Novo Nordisk A/S, Måløv, Denmark.

Light Sheet Fluorescence Microscopy (LSFM) of whole organs, in particular the brain, offers a plethora of biological data imaged in 3D. This technique is however often hindered by cumbersome non-automated analysis methods. Here we describe an approach to fully automate the analysis by integrating with data from the Allen Institute of Brain Science (AIBS), to provide precise assessment of the distribution and action of peptide-based pharmaceuticals in the brain. To illustrate this approach, we examined the acute central nervous system effects of the glucagon-like peptide-1 (GLP-1) receptor agonist liraglutide. Peripherally administered liraglutide accessed the hypothalamus and brainstem, and led to activation in several brain regions of which most were intersected by projections from neurons in the lateral parabrachial nucleus. Collectively, we provide a rapid and unbiased analytical framework for LSFM data which enables quantification and exploration based on data from AIBS to support basic and translational discovery.
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http://dx.doi.org/10.1038/s41598-018-28496-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037685PMC
July 2018

Scene reassembly after multimodal digitization and pipeline evaluation using photorealistic rendering.

Appl Opt 2017 Sep;56(27):7679-7690

Transparent objects require acquisition modalities that are very different from the ones used for objects with more diffuse reflectance properties. Digitizing a scene where objects must be acquired with different modalities requires scene reassembly after reconstruction of the object surfaces. This reassembly of a scene that was picked apart for scanning seems unexplored. We contribute with a multimodal digitization pipeline for scenes that require this step of reassembly. Our pipeline includes measurement of bidirectional reflectance distribution functions and high dynamic range imaging of the lighting environment. This enables pixelwise comparison of photographs of the real scene with renderings of the digital version of the scene. Such quantitative evaluation is useful for verifying acquired material appearance and reconstructed surface geometry, which is an important aspect of digital content creation. It is also useful for identifying and improving issues in the different steps of the pipeline. In this work, we use it to improve reconstruction, apply analysis by synthesis to estimate optical properties, and to develop our method for scene reassembly.
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http://dx.doi.org/10.1364/AO.56.007679DOI Listing
September 2017

Quantitative tumor heterogeneity assessment on a nuclear population basis.

Cytometry A 2017 06 31;91(6):574-584. Epub 2017 Jan 31.

Institute of Pathology, Aalborg University Hospital, DK-9100, Aalborg, Denmark.

Immunohistochemistry Ki-67 stain is widely used for visualizing cell proliferation. The common method for scoring the proliferation is to manually select and score a hot spot. This method is time-consuming and will often not give reproducible results due to subjective selection of the hotspots and subjective scoring. An automatic hotspot detection and proliferative index scoring would be time-saving, make the determination of the Ki-67 score easier and minimize the uncertainty of the score by introducing a more objective and standardized score. Tissue Micro Array cores stained for Ki-67 and their neighbor slide stained for Pan Cytokeratin were aligned and Ki-67 positive and negative nuclei were identified inside tumor regions. A heatmap was calculated based on these and illustrates the distribution of the heterogenous response of Ki-67 positive nuclei in the tumor tissue. An automatic hot spot detection was developed and the Ki-67 score was calculated. All scores were compared with scores provided by a pathologist using linear regression models. No significant difference was found between the Ki-67 scores guided by the developed heatmap and the scores provided by a pathologist. For comparison, scores were also calculated at a random place outside the hot spot and these scores were found to be significantly different from the pathologist scores. A heatmap visualizing the heterogeneity in tumor tissue expressed by Ki-67 was developed and used for an automatic identification of hot spots in which a Ki-67 score was calculated. The Ki-67 scores did not differ significantly from scores provided by a pathologist. © 2017 International Society for Advancement of Cytometry.
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http://dx.doi.org/10.1002/cyto.a.23047DOI Listing
June 2017

Injectable Colloidal Gold for Use in Intrafractional 2D Image-Guided Radiation Therapy.

Adv Healthc Mater 2015 Apr 21;4(6):856-63. Epub 2015 Jan 21.

DTU Nanotech, Department of Micro-and Nanotechnology, Center for Nanomedicine and Theranostics Technical University of Denmark, Building 345E, Ørsteds Plads, 2800, Lyngby, Denmark.

In the western world, approximately 50% of all cancer patients receive radiotherapy alone or in combination with surgery or chemotherapy. Image-guided radiotherapy (IGRT) has in recent years been introduced to enhance precision of the delivery of radiation dose to tumor tissue. Fiducial markers are often inserted inside the tumor to improve IGRT precision and to enable monitoring of the tumor position during radiation therapy. In the present article, a liquid fiducial tissue marker is presented, which can be injected into tumor tissue using thin and flexible needles. The liquid fiducial has high radio-opacity, which allows for marker-based image guidance in 2D and 3D X-ray imaging during radiation therapy. This is achieved by surface-engineering gold nanoparticles to be highly compatible with a carbohydrate-based gelation matrix. The new fiducial marker is investigated in mice where they are highly biocompatible and stable after implantation. To investigate the clinical potential, a study is conducted in a canine cancer patient with spontaneous developed solid tumor in which the marker is successfully injected and used to align and image-guide radiation treatment of the canine patient. It is concluded that the new fiducial marker has highly interesting properties that warrant investigations in cancer patients.
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http://dx.doi.org/10.1002/adhm.201400651DOI Listing
April 2015

Comparison of a multispectral vision system and a colorimeter for the assessment of meat color.

Meat Sci 2015 Apr 5;102:1-7. Epub 2014 Dec 5.

Technical University of Denmark, Richard Petersens Plads, 2800 Kongens Lyngby, Denmark. Electronic address:

The color assessment ability of a multispectral vision system is investigated by a comparison study with color measurements from a traditional colorimeter. The experiment involves fresh and processed meat samples. Meat is a complex material; heterogeneous with varying scattering and reflectance properties, so several factors can influence the instrumental assessment of meat color. In order to assess whether two methods are equivalent, the variation due to these factors must be taken into account. A statistical analysis was conducted and showed that on a calibration sheet the two instruments are equally capable of measuring color. Moreover the vision system provides a more color rich assessment of fresh meat samples with a glossier surface, than the colorimeter. Careful studies of the different sources of variation enable an assessment of the order of magnitude of the variability between methods accounting for other sources of variation leading to the conclusion that color assessment using a multispectral vision system is superior to traditional colorimeter assessments.
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http://dx.doi.org/10.1016/j.meatsci.2014.11.012DOI Listing
April 2015
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