Paper Info
Title
Interactive analysis for large volume data from fluorescence microscopy at cellular precision
Abstract
AbstractHighlights •Interactive data analysis based on volume visualizations.•Diffusion calculation for brushing on large volume data of multiple bricks.•Large data support for data analysis.•Demonstration of usability in real-world biomedical research. Graphical abstractDisplay OmittedAbstractThe main objective for understanding fluorescence microscopy data is to investigate and evaluate the fluorescent signal intensity distributions as well as their spatial relationships across multiple channels. The quantitative analysis of 3D fluorescence microscopy data needs interactive tools for researchers to select and focus on relevant biological structures. We developed an interactive tool based on volume visualization techniques and GPU computing for streamlining rapid data analysis. Our main contribution is the implementation of common data quantification functions on streamed volumes, providing interactive analyses on large data without lengthy preprocessing. Data segmentation and quantification are coupled with brushing and executed at an interactive speed. A large volume is partitioned into data bricks, and only user-selected structures are analyzed to constrain the computational load. We designed a framework to assemble a sequence of GPU programs to handle brick borders and stitch analysis results. Our tool was developed in collaboration with domain experts and has been used to identify cell types. We demonstrate a workflow to analyze cells in vestibular epithelia of transgenic mice.
Year
DOI
Venue
2021
10.1016/j.cag.2021.05.006
Periodicals
Keywords
DocType
Volume
Interactive analysis, Volume analysis, Rapid analysis, Cell analysis, Brushing, Fluorescence microscopy, Large data, Streamed processing
Journal
98
Issue
ISSN
Citations 
C
0097-8493
0
PageRank 
References 
Authors
0.34
0
3
Name
Order
Citations
PageRank
Y Wan1274.28
Holly A. Holman200.34
Charles Hansen315710.59