Chemistry

Ultrastructure

Fluorescence

Compartmentalization (fire protection)

Philosophy

Artificial intelligence

Biochemistry

Physics

Fluorescence microscope

Enzyme

Anatomy

Biology

Image (mathematics)

Optics

Biophysics

Endoplasmic reticulum

Electron microscope

Cell biology

STED microscopy

Correlative

Computer science

Resolution (logic)

Microscopy

Linguistics

Computational biology

Superresolution

Chromatin

Science

Within cells, the spatial compartmentalization of thousands of distinct proteins serves a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) can elucidate protein spatial relationships to global ultrastructure, but has suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional cryogenic SR and focused ion beam-milled block-face EM across entire vitreously frozen cells. The approach preserves ultrastructure while enabling independent SR and EM workflow optimization. We discovered unexpected protein-ultrastructure relationships in mammalian cells including intranuclear vesicles containing endoplasmic reticulum-associated proteins, web-like adhesions between cultured neurons, and chromatin domains subclassified on the basis of transcriptional activity. Our findings illustrate the value of a comprehensive multimodal view of ultrastructural variability across whole cells.

Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells