Virtual reality assisted microscopy data visualization and colocalization analysis

Theart, Rensu P.; Loos, Ben; Niesler, Thomas

doi:10.1186/s12859-016-1446-2

Cited by 42 publications

(36 citation statements)

References 18 publications

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“…A recent application paper presented a 3D scatterplot and coordinated views in virtual reality, using a head-mounted display and a Leap Motion controller [37]. Using mid-air interactions a user can scale and rotate the visualisation as well as select data points by defining volumes inside the visualisation.…”

Section: Mid-air Interfacesmentioning

confidence: 99%

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Design space for spatio-data coordination: Tangible interaction devices for immersive information visualisation

Cordeil

Bach

et al. 2017

2017 IEEE Pacific Visualization Symposium (PacificVis)

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We introduce the concept of "spatio-data coordination" (SD coordination) which defines the mapping of user actions in physical space into the space of data in a visualisation. SD coordination is intended to lower the user's cognitive load when exploring complex multidimensional data such as biomedical data, multiple data attributes vs time in a space-time-cube visualisation, or three-dimensional projections of three-or-higher-dimensional data sets. To inform the design of interaction devices to allow for SD coordination, we define a design space and demonstrate it with sketches and early prototypes of three exemplar devices for SD coordinated interaction.

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Section: Mid-air Interfacesmentioning

confidence: 99%

“…Moreover, accurate head-tracking enables embodied navigation in a visualisation; allowing the viewer to walk around the data, switch from overview to detail and to "step-inside" the data. Mid-air interaction with accurately tracked hand-held controllers further allows users to point, select or otherwise interact in V/AR [37].…”

Section: Introductionmentioning

confidence: 99%

Design space for spatio-data coordination: Tangible interaction devices for immersive information visualisation

Cordeil

Bach

et al. 2017

2017 IEEE Pacific Visualization Symposium (PacificVis)

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“…Such high-dimensional data also represent an exciting challenge for new ways of scientific visualization based e.g. on virtual reality techniques ( Calì et al , 2016 ; Ledford, 2017 ; Theart et al , 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of tissue reconstruction algorithms for 3D histology

et al. 2018

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MotivationDigital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking.ResultsWe developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches.Availability and implementationCode: https://github.com/BioimageInformaticsTampere/RegBenchmark. Whole slide image datasets: http://urn.fi/urn: nbn: fi: csc-kata20170705131652639702.Supplementary information Supplementary data are available at Bioinformatics online.

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“…We employ a recently developed virtual reality (VR) system that allows sample visualization and ROI selection in true 3D, thereby achieving an unambiguous representation of the data [ 11 ]. Since more data points are taken into account when using a 3D ROI, the statistical uncertainty associated with the colocalization metrics will also be reduced [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Improved region of interest selection and colocalization analysis in three-dimensional fluorescence microscopy samples using virtual reality

et al. 2018

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Although modern fluorescence microscopy produces detailed three-dimensional (3D) datasets, colocalization analysis and region of interest (ROI) selection is most commonly performed two-dimensionally (2D) using maximum intensity projections (MIP). However, these 2D projections exclude much of the available data. Furthermore, 2D ROI selections cannot adequately select complex 3D structures which may inadvertently lead to either the exclusion of relevant or the inclusion of irrelevant data points, consequently affecting the accuracy of the colocalization analysis. Using a virtual reality (VR) enabled system, we demonstrate that 3D visualization, sample interrogation and analysis can be achieved in a highly controlled and precise manner. We calculate several key colocalization metrics using both 2D and 3D derived super-resolved structured illumination-based data sets. Using a neuronal injury model, we investigate the change in colocalization between Tau and acetylated α-tubulin at control conditions, after 6 hours and again after 24 hours. We demonstrate that performing colocalization analysis in 3D enhances its sensitivity, leading to a greater number of statistically significant differences than could be established when using 2D methods. Moreover, by carefully delimiting the 3D structures under analysis using the 3D VR system, we were able to reveal a time dependent loss in colocalization between the Tau and microtubule network as an early event in neuronal injury. This behavior could not be reliably detected using a 2D based projection. We conclude that, using 3D colocalization analysis, biologically relevant samples can be interrogated and assessed with greater precision, thereby better exploiting the potential of fluorescence-based image analysis in biomedical research.

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Virtual reality assisted microscopy data visualization and colocalization analysis

Cited by 42 publications

References 18 publications

Design space for spatio-data coordination: Tangible interaction devices for immersive information visualisation

Design space for spatio-data coordination: Tangible interaction devices for immersive information visualisation

Comparative analysis of tissue reconstruction algorithms for 3D histology

Improved region of interest selection and colocalization analysis in three-dimensional fluorescence microscopy samples using virtual reality

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