Evaluation of Navigation Operations in Immersive Microscopic Visualization

Takashina, Tomomi; Ito, Meguru; Kokumai, Yuji

doi:10.1145/3359996.3364724

Cited by 2 publications

(2 citation statements)

References 4 publications

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“…Arbitrary selection and isolation of a local ROI is one of the tasks where VR provides an advantage over flat screens thanks to its intuitive navigation 9 . We performed the selection of a stalk in a C. crescentus bacterium and isolated its dataset (sample CaulobacterC_2_R09_stalk_MoernerLab.csv) (Fig.…”

Section: Arbitrary Selection and Isolation Of A Roi In Large Complicated Datasetsmentioning

confidence: 99%

“…vLUME has four key features: (1) Data exploration and comparison. The configurable user interface allows researchers, without need for programming, to seamlessly switch back and forth from a global view of the entire captured sample to detailed nanoscale views of molecular elements in any arbitrary orientation, faster than with conventional flat screens 9 . Doing so allows the easy local selection of data for further analysis (Supplementary Videos 2 and 3).…”

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confidence: 99%

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vLUME: 3D virtual reality for single-molecule localization microscopy

Spark¹,

Kitching²,

Esteban-Ferrer

et al. 2020

Nat Methods

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vLUME is a virtual reality software package designed to render large three-dimensional single-molecule localization microscopy datasets. vLUME features include visualization, segmentation, bespoke analysis of complex local geometries and exporting features. vLUME can perform complex analysis on real three-dimensional biological samples that would otherwise be impossible by using regular flat-screen visualization programs.Super-resolution microscopy based on three-dimensional single-molecule localization microscopy (3D-SMLM) is now well established 1,2 , and its widespread adoption has led to the development of more than 36 software packages dedicated to quantitative evaluation of the spatial and temporal detection of fluorophore photoswitching 3 . While the initial emphasis in the 3D-SMLM field has clearly been on improving resolution and data quality, there is now a marked absence of 3D visualization approaches that enable the straightforward, high-fidelity exploration of this type of data. Inspired by the horological phosphorescence points that illuminate watch-faces in the dark, we present vLUME (visualization of the local universe in a micro environment, pronounced 'volume'), an immersive virtual reality (VR)-based visualization software package purposefully designed to render large 3D-SMLM datasets. It is free for academic use. vLUME enables robust visualization, segmentation, annotation and quantification of millions of fluorescence puncta from any 3D-SMLM technique. vLUME has an intuitive user interface and is compatible with all commercial gaming VR hardware (Oculus Rift/Rift S and HTC Vive/Vive Pro; Supplementary Video 1). Although other microscopy data (that is, confocal) visualization tools have previously explored VR technology using volumetric representations 4,5 , vLUME has been specifically and purposefully created for SMLM. It accelerates the analysis of highly complex 3D point-cloud data and the rapid identification of defects that are otherwise neglected in global quality metrics. (A comparison with other VR and non-VR tools can be found in Supplementary Table 1.)vLUME is a point-cloud based 3D-SMLM data visualization tool able to render all pointillism-based multidimensional datasets. It differs from other 3D tools for 3D-SMLM visualization such as ViSP 6 by providing a complete VR interactive environment and intuitive interface for life scientists, dedicated to data visualization, segmentation and analysis. Users load multidimensional particle-list datasets into vLUME (.csv files; Fig. 1a), such as those generated by commonly used 3D-SMLM software 7,8 . This allows users to comprehend the spatial and temporal relation between

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Section: Arbitrary Selection and Isolation Of A Roi In Large Complicated Datasetsmentioning

confidence: 99%

mentioning

confidence: 99%

vLUME: 3D virtual reality for single-molecule localization microscopy

Spark¹,

Kitching²,

Esteban-Ferrer

et al. 2020

Nat Methods

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A Systematic Literature Review of User Evaluation in Immersive Analytics

Friedl‐Knirsch,

Pointecker,

Pfistermüller

et al. 2024

Computer Graphics Forum

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User evaluation is a common and useful tool for systematically generating knowledge and validating novel approaches in the domain of Immersive Analytics. Since this research domain centres around users, user evaluation is of extraordinary relevance. Additionally, Immersive Analytics is an interdisciplinary field of research where different communities bring in their own methodologies. It is vital to investigate and synchronise these different approaches with the long‐term goal to reach a shared evaluation framework. While there have been several studies focusing on Immersive Analytics as a whole or on certain aspects of the domain, this is the first systematic review of the state of evaluation methodology in Immersive Analytics. The main objective of this systematic literature review is to illustrate methodologies and research areas that are still underrepresented in user studies by identifying current practice in user evaluation in the domain of Immersive Analytics in coherence with the PRISMA protocol. (see https://www.acm.org/publications/class-2012)

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Evaluation of Navigation Operations in Immersive Microscopic Visualization

Cited by 2 publications

References 4 publications

vLUME: 3D virtual reality for single-molecule localization microscopy

vLUME: 3D virtual reality for single-molecule localization microscopy

A Systematic Literature Review of User Evaluation in Immersive Analytics

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