ArticleNature methods2023
Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- SIMworks-an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy.Nature protocols · 2026Review
- Chem-SIM: SIM-resolved chemical imaging via wide-field mid-infrared photothermal modulation of fluorescence.Nature communications · 2026Article
- Super-Resolution Structured Illumination Microscopy to Study Endocytosis and Cellular Nanoparticle Uptake.ACS nano · 2026Review
- Visualizing intraorganellar ultrastructures, dynamics, and interactions with open-access background-free Lock-in-SIM.Nature communications · 2025Article
- Low-Cost Spinning Disk Confocal Microscopy with a 25-Megapixel Camera.Sensors (Basel, Switzerland) · 2025Article
- Deep3DSIM: Super-resolution imaging of thick tissue using 3D structured illumination with adaptive optics.eLife · 2025Article
- Principal component analysis for three-dimensional structured illumination microscopy (PCA-3DSIM).Light, science & applications · 2025Article
- High-fidelity tissue super-resolution imaging achieved with confocalLight, science & applications · 2025Article
- A gentle palette of plasma membrane dyes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Dark-based optical sectioning assists background removal in fluorescence microscopy.Nature methods · 2025Article
- Bayesian deep-learning structured illumination microscopy enables reliable super-resolution imaging with uncertainty quantification.Nature communications · 2025Article
- LED-based multicolor extended resolution transmission fluorescence microscopy.Journal of biomedical optics · 2025Article
- Fast segmentation and multiplexing imaging of organelles in live cells.Nature communications · 2025Article
- Fast reconstruction and optical-sectioning three-dimensional structured illumination microscopy.Innovation (Cambridge (Mass.)) · 2025Article
- Metasurface-Coated Liquid Microlens for Super Resolution Imaging.Micromachines · 2024Article
- Expanding super-resolution imaging versatility in organisms with multi-confocal image scanning microscopy.National science review · 2024Article
- Efficient high-resolution fluorescence projection imaging over an extended depth of field through optical hardware and deep learning optimizations.Biomedical optics express · 2024Article
- Ultra-high spatio-temporal resolution imaging with parallel acquisition-readout structured illumination microscopy (PAR-SIM).Light, science & applications · 2024Article
- Visualization of cristae and mtDNA interactions via STED nanoscopy using a low saturation power probe.Light, science & applications · 2024Article
- Super-Resolution Imaging of Neuronal Structures with Structured Illumination Microscopy.Bioengineering (Basel, Switzerland) · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Open-3DSIM is an open-source reconstruction platform for three-dimensional structured illumination microscopy. We demonstrate its superior performance for artifact suppression and high-fidelity reconstruction relative to other algorithms on various specimens and over a range of signal-to-noise levels. Open-3DSIM also offers the capacity to extract dipole orientation, paving a new avenue for interpreting subcellular structures in six dimensions (xyzθλt). The platform is available as MATLAB code, a Fiji plugin and an Exe application to maximize user-friendliness.
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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.