ArticleBMC bioinformatics2017
FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
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- An algorithmic and software framework to incorporate orientation distribution functions in finite element simulations for biomechanics and biophysics.Acta biomaterialia · 2025Article
- Activity-dependent refinement of axonal projections forms one-to-one connection pattern in the developing chick ciliary ganglion.Frontiers in cellular neuroscience · 2025Article
- Evolution of connectivity architecture in the Drosophila mushroom body.Nature communications · 2024Article
- Sensory innervation in the prostate and a role for calcitonin gene-related peptide in prostatic epithelial proliferation.Frontiers in molecular neuroscience · 2024Article
- The odor of a nontoxic tetrodotoxin analog, 5,6,11-trideoxytetrodotoxin, is detected by specific olfactory sensory neurons of the green spotted puffers.Chemical senses · 2024Article
- u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions.Cell reports methods · 2023Article
- Heterogeneous receptor expression underlies non-uniform peptidergic modulation of olfaction in Drosophila.Nature communications · 2023Article
- Local and long-distance organization of prefrontal cortex circuits in the marmoset brain.Neuron · 2023Article
- Asymmetric Presynaptic Depletion of Dopamine Neurons in aInternational journal of molecular sciences · 2023Article
- OptoRheo: Simultaneous in situ micro-mechanical sensing and imaging of live 3D biological systems.Communications biology · 2023Article
- Mushroom body input connections form independently of sensory activity in Drosophila melanogaster.Current biology : CB · 2022Article
- A neurogenetic mechanism of experience-dependent suppression of aggression.Science advances · 2022Article
- A Novel Gesture-Based Control System for Fluorescence Volumetric Data in Virtual Reality.Sensors (Basel, Switzerland) · 2021Article
- Live imaging of retinotectal mapping reveals topographic map dynamics and a previously undescribed role for Contactin 2 in map sharpening.Development (Cambridge, England) · 2021Article
- Interactive Analysis for Large Volume Data from Fluorescence Microscopy at Cellular Precision.Computers & graphics · 2021Article
- Article
- Layered roles ofeLife · 2020Article
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Authors and funding
10 authors.
Funding
Abstract
backgroundImage segmentation and registration techniques have enabled biologists to place large amounts of volume data from fluorescence microscopy, morphed three-dimensionally, onto a common spatial frame. Existing tools built on volume visualization pipelines for single channel or red-green-blue (RGB) channels have become inadequate for the new challenges of fluorescence microscopy. For a three-dimensional atlas of the insect nervous system, hundreds of volume channels are rendered simultaneously, whereas fluorescence intensity values from each channel need to be preserved for versatile adjustment and analysis. Although several existing tools have incorporated support of multichannel data using various strategies, the lack of a flexible design has made true many-channel visualization and analysis unavailable. The most common practice for many-channel volume data presentation is still converting and rendering pseudosurfaces, which are inaccurate for both qualitative and quantitative evaluations.
resultsHere, we present an alternative design strategy that accommodates the visualization and analysis of about 100 volume channels, each of which can be interactively adjusted, selected, and segmented using freehand tools. Our multichannel visualization includes a multilevel streaming pipeline plus a triple-buffer compositing technique. Our method also preserves original fluorescence intensity values on graphics hardware, a crucial feature that allows graphics-processing-unit (GPU)-based processing for interactive data analysis, such as freehand segmentation. We have implemented the design strategies as a thorough restructuring of our original tool, FluoRender.
conclusionThe redesign of FluoRender not only maintains the existing multichannel capabilities for a greatly extended number of volume channels, but also enables new analysis functions for many-channel data from emerging biomedical-imaging techniques.
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