ReviewNature protocols2017
Quantitative 3D structured illumination microscopy of nuclear structures.
Review in Nature protocols, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 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.
The trial behind it
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
44 citing papers in PubMed.
- SIMworks-an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy.Nature protocols · 2026Review
- TEAD1 condensates are transcriptionally inactive storage sites on the pericentromeric heterochromatin in cancer cells.Nature cell biology · 2026Article
- Astrocyte Enrichment of 3D Cortical Constructs Enhances Brain Repair.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Methods to Determine the Role of MIF in Cilia Biogenesis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Advanced Imaging for Live-Cell Spatiotemporal Monitoring: Technologies and Applications.Research (Washington, D.C.) · 2026Review
- High-resolution imaging mass cytometry to map subcellular structures.Nature methods · 2025Article
- Visualizing intraorganellar ultrastructures, dynamics, and interactions with open-access background-free Lock-in-SIM.Nature communications · 2025Article
- Enhanced optical imaging and fluorescent labeling for visualizing drug molecules within living organisms.Acta pharmaceutica Sinica. B · 2024Review
- Non-random spatial organization of telomeres varies during the cell cycle and requires LAP2 and BAF.iScience · 2024Article
- Profiling Chromosome Topological Features by Super-Resolution 3D Structured Illumination Microscopy.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Proteomic profiling of centrosomes across multiple mammalian cell and tissue types by an affinity capture method.Developmental cell · 2023Article
- PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems.EMBO reports · 2023Article
- Caldesmon controls stress fiber force-balance through dynamic cross-linking of myosin II and actin-tropomyosin filaments.Nature communications · 2022Article
- RASER-FISH: non-denaturing fluorescence in situ hybridization for preservation of three-dimensional interphase chromatin structure.Nature protocols · 2022Review
- A Transient Mystery: Nucleolar Channel Systems.Results and problems in cell differentiation · 2022Article
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- RIF1 Links Replication Timing with Fork Reactivation and DNA Double-Strand Break Repair.International journal of molecular sciences · 2021Review
- Piwi-piRNA complexes induce stepwise changes in nuclear architecture at target loci.The EMBO journal · 2021Article
- Review of bio-optical imaging systems with a high space-bandwidth product.Advanced photonics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
3D structured illumination microscopy (3D-SIM) is the super-resolution technique of choice for multicolor volumetric imaging. Here we provide a validated sample preparation protocol for labeling nuclei of cultured mammalian cells, image acquisition and registration practices, and downstream image analysis of nuclear structures and epigenetic marks. Using immunostaining and replication labeling combined with image segmentation, centroid mapping and nearest-neighbor analyses in open-source environments, 3D maps of nuclear structures are analyzed in individual cells and normalized to fluorescence standards on the nanometer scale. This protocol fills an unmet need for the application of 3D-SIM to the technically challenging nuclear environment, and subsequent quantitative analysis of 3D nuclear structures and epigenetic modifications. In addition, it establishes practical guidelines and open-source solutions using ImageJ/Fiji and the TANGO plugin for high-quality and routinely comparable data generation in immunostaining experiments that apply across model systems. From sample preparation through image analysis, the protocol can be executed within one week.
Indexed as
Identifiers
28406495What OpenQuestion holds
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.