FIB-SEM intake prototype
A guided visual page using OpenOrganelle-derived FIB-SEM example figures to explain nuclear envelope context, chromatin texture, nucleoli, nuclear bodies, and cell-type variation.
Intake analysis
The collection is strongest as an interpretive teaching set. It repeatedly shows segmented or panel-based FIB-SEM views of nuclei from HeLa, Jurkat, macrophage, COS-7, kidney, liver, and immune-contact examples. These exports use darkfield-style contrast: bright structures sit on black backgrounds. The page below uses visible patterns and filename context, but formal figure legends should be checked against the original OpenOrganelle dataset metadata before publication.
Guided readouts
Envelope and periphery
FIB-SEM sections place the nuclear boundary inside the surrounding cytoplasm, making the envelope, adjacent organelles, and peripheral chromatin context easier to discuss together. This is useful for explaining why nuclear architecture is both a genome-organization problem and a cell-geometry problem. Volume EM atlas study.
Related nuclear envelope review
Chromatin texture
The high-magnification panels show heterogeneous electron density inside the nucleus. Used carefully, these views help introduce the visual difference between compacted material, less-dense regions, and the problem of mapping EM contrast onto molecular chromatin states. Volume EM atlas study. Primary segmentation study.
Related heterochromatin review
Nucleolus
Nucleolus-labeled examples from different cell contexts give the page a direct route into ribosome-biogenesis compartments, nuclear body organization, and the limits of identifying compartments from morphology alone. Primary nucleolar study. Primary segmentation study.
Related nucleolus review
Nuclear bodies
The macrophage examples are useful for showing how the same region can be presented as raw slices or as a more segmented visual. That contrast supports a stronger teaching point: nuclear body interpretation depends on imaging, annotation, and biological context. Primary segmentation study.
Explore nuclear body reviewsNanoscale Visualization
Explore rotation and slice movies of fixed-cell volume EM exports labeled as pancreatic islet and T-cell examples. Rotation and Z-slice traversal are display motions; they do not measure biological dynamics. Dataset identities and annotations still need to be matched to the original records. Volume EM atlas study.
Pancreas Islet Chromatin (FIB-SEM 3D): This rotation movie shows a rendered peripheral dense region and less-dense channels in a nuclear volume. EM morphology alone does not establish heterochromatin identity, transcriptional activity, or correspondence to nuclear pores; those interpretations require source annotations or correlative markers.
Gemini Flash triage
Model-generated labels and filenames are hypotheses for expert review, not validated annotations. None of the molecular identities below is confirmed by this page. Match each crop to its original dataset and annotation, and use correlative markers where identity is not resolved by ultrastructure. Primary segmentation study.
Unverified candidate
The crop shows granule-like contrast. A filename or model label does not confirm an IGC or nuclear-speckle identity.
Unverified candidate
Gemini flagged a discrete textured body near an IGC-like region, but the call depends on the SUBZCB label.
Unverified candidate
A nucleolus-like crop with internal contrast variation; fibrillar-center, dense-fibrillar and granular-component assignments require source or expert confirmation.
Unverified candidate
A clear nuclear boundary with coarse dense material at the periphery and throughout the nucleoplasm.
Unverified candidate
A dense subregion in an export whose filename includes PcG. Polycomb proteins, histone modifications and silencing activity cannot be identified from this morphology alone; the original annotation and molecular evidence remain unverified.
Cell-type variation
The selected batch includes immune cells, epithelial-like cells, tissue sections, and infection or contact contexts. The safest public framing is comparative: the images show that nuclear shape, surrounding cytoplasm, and internal density patterns vary across preparations. Volume EM atlas study.
A compact example for discussing nuclear boundary, adjacent membranes, and local chromatin density.
A useful contrast against larger adherent-cell examples, especially for immune-cell nuclear shape.
A scene-level example for placing nuclear ultrastructure inside a larger cell-cell interaction.
A tissue-scale counterpoint for showing how nuclei sit among dense organelle-rich cytoplasm.
Reusable page modules
Best used when discussing nuclear speckles or IGC-like domains with clear source confirmation.
mouse-liver-igc-render.jpg
A practical supporting image for transport, cargo, or punctate nuclear structure explainers.
hela-cargo-particles.jpg
Strongest reusable candidate for explaining raw slices versus annotated nuclear compartments.
macrophage-nuclear-body-slices.jpg
Model-assisted surface rendering of nuclear contrast; genomic domain boundaries and molecular identity have not been verified.
hela-cell3-chromatin-3d.jpg
A pancreatic-islet-labeled export showing dense nuclear regions; heterochromatin identity requires source confirmation.
pancreas-islet-chromatin-overview.jpgCredit and evidence
This page is an intake prototype using local example images collected from the OpenOrganelle public resource. Individual image-to-dataset provenance, molecular annotations, and reuse licenses remain unresolved. The linked atlas and segmentation studies describe methods; they do not authenticate every local crop or model-generated label.
OpenOrganelle provides public visualization access to cloud-hosted FIB-SEM datasets through the CellMap data portal.
openorganelle.orgXu and colleagues described an open-access FIB-SEM atlas of whole cells and tissues, with datasets deposited to OpenOrganelle. Volume EM atlas study.
Nature 2021 atlas DOIHeinrich and colleagues reported segmentation of many organelle classes in 4 nm and 8 nm voxel FIB-SEM volumes. Primary segmentation study.
Nature 2021 segmentation DOIThe public OpenOrganelle code repository describes the app as a gateway for visualizing large cloud-hosted FIB-SEM datasets.
Janelia CellMap GitHubScite publication metadata independently confirms Xu et al., the volume EM atlas and Heinrich et al., whole-cell organelle segmentation as separate Nature papers. These method papers establish the resource and reported segmentation work; they do not validate every local crop, model-generated label or molecular assignment.
The atlas has a publisher correction, whose notice was read directly. It replaces a damaged Supplementary Video 2 and corrects axis-label formatting in Extended Data Fig. 2. It does not supply missing provenance for the local example movies. Use the corrected publisher supplements when comparing the original data.
This update checks publication identities and the correction notice. Original full Methods, all dataset annotations, raw-volume segmentation accuracy and individual image reuse permissions remain outside the verified scope. Rotation and slice traversal are display motions of fixed-cell volumes.
