ArticleBMC bioinformatics2012
Web tools for large-scale 3D biological images and atlases.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed.
- Internal state affects local neuron function in an early sensory processing center to shape olfactory behavior in Drosophila larvae.Scientific reports · 2022Article
- Integrated analysis of Wnt signalling system component gene expression.Development (Cambridge, England) · 2022Article
- CloudReg: automatic terabyte-scale cross-modal brain volume registration.Nature methods · 2021Article
- A collection of yeast cellular electron cryotomography data.GigaScience · 2019Article
- Geppetto: a reusable modular open platform for exploring neuroscience data and models.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis.Developmental biology · 2017Review
- Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design.BMC developmental biology · 2016Article
- Deciphering the mechanisms of developmental disorders: phenotype analysis of embryos from mutant mouse lines.Nucleic acids research · 2016Article
- Live imaging of Tribolium castaneum embryonic development using light-sheet-based fluorescence microscopy.Nature protocols · 2015Article
- eMouseAtlas informatics: embryo atlas and gene expression database.Mammalian genome : official journal of the International Mammalian Genome Society · 2015Article
- Deducing the stage of origin of Wilms' tumours from a developmental series of Wt1-mutant mice.Disease models & mechanisms · 2015Article
- BigDataViewer: visualization and processing for large image data sets.Nature methods · 2015Article
- Developing the eHistology Atlas.Database : the journal of biological databases and curation · 2015Article
- The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units.Frontiers in physiology · 2015Article
- EMAGE mouse embryo spatial gene expression database: 2014 update.Nucleic acids research · 2014Article
- eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome.Mammalian genome : official journal of the International Mammalian Genome Society · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
backgroundLarge-scale volumetric biomedical image data of three or more dimensions are a significant challenge for distributed browsing and visualisation. Many images now exceed 10GB which for most users is too large to handle in terms of computer RAM and network bandwidth. This is aggravated when users need to access tens or hundreds of such images from an archive. Here we solve the problem for 2D section views through archive data delivering compressed tiled images enabling users to browse through very-large volume data in the context of a standard web-browser. The system provides an interactive visualisation for grey-level and colour 3D images including multiple image layers and spatial-data overlay.
resultsThe standard Internet Imaging Protocol (IIP) has been extended to enable arbitrary 2D sectioning of 3D data as well a multi-layered images and indexed overlays. The extended protocol is termed IIP3D and we have implemented a matching server to deliver the protocol and a series of Ajax/Javascript client codes that will run in an Internet browser. We have tested the server software on a low-cost linux-based server for image volumes up to 135GB and 64 simultaneous users. The section views are delivered with response times independent of scale and orientation. The exemplar client provided multi-layer image views with user-controlled colour-filtering and overlays.
conclusionsInteractive browsing of arbitrary sections through large biomedical-image volumes is made possible by use of an extended internet protocol and efficient server-based image tiling. The tools open the possibility of enabling fast access to large image archives without the requirement of whole image download and client computers with very large memory configurations. The system was demonstrated using a range of medical and biomedical image data extending up to 135GB for a single image volume.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.