ArticleBMC bioinformatics2010
A high-level 3D visualization API for Java and ImageJ.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 212 papers.
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Who cites it
212 citing papers in PubMed.
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- The 3D architecture of the ctenophore aboral organ and the evolution of complex integrative centers in animals.Science advances · 2026Article
- A multi-resolution imaging and analysis pipeline for comparative circuit reconstruction in insects.bioRxiv : the preprint server for biology · 2026Article
- The substance P/ Neurokinin-1 receptor signaling drives perineural invasion in pancreatic ductal adenocarcinoma (PDAC).Frontiers in cell and developmental biology · 2026Article
- Targeting stroma-mediated T-cell exclusion and functional exhaustion in pancreatic ductal adenocarcinoma through CXCR4 and PD-1 blockade.Frontiers in immunology · 2026Article
- Application to developmental toxicity testing of a novel method for whole-brain imaging of microglia in zebrafish.Current research in toxicology · 2026Article
- Topography-driven movement of biomolecular condensates.PloS one · 2026Article
- Two-photon characterisation of long-Stokes-shift dye ATTO 490LS for single-laser multicolour imaging.microPublication biology · 2026Article
- Mapping cell dynamics in human ex vivo hair follicles suggests pulling mechanism of hair growth.Nature communications · 2025Article
- Photon-Counting Micro-CT for Bone Morphometry in Murine Models.Tomography (Ann Arbor, Mich.) · 2025Article
- Exploring neurodevelopment via spatiotemporal collation of anatomical networks with NeuroSC.eLife · 2025Article
- Automated segmentation of soft X-ray tomography: Native cellular structure with submicron resolution at high-throughput for whole-cell quantitative imaging in yeast.Molecular biology of the cell · 2025Article
- Article
- Migration and structural implication of cyanobacteria in biological soil crusts in response to water and particle burial.Innovation (Cambridge (Mass.)) · 2025Article
- NeuroSC: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks.bioRxiv : the preprint server for biology · 2025Article
152 more citing papers are in PubMed but not listed here.
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
No grant is acknowledged in the PubMed record.
Abstract
backgroundCurrent imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.
resultsHere we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts.
conclusionsOur framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.
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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.