A living cell

A human fibroblast, the cell that builds skin and scar tissue, crawling across a glass coverslip. It is about 70 µm long and only a few micrometres thick: thin at its spreading front edge, thickest over the nucleus.

Everything is moving

Microtubules grow from the centrosome at a fifth of a micrometre per second, then suddenly collapse and regrow. Lysosomes race along them, mitochondria crawl, divide and fuse, and the leading edge ruffles forward while the tail lets go. Collapsing ruffles gulp the surrounding medium into bright vacuoles (macropinosomes) that drift inward and shrink. Time runs faster than life (the clock shows how much); slow it to real time under Settings.

The colours

Fluorescent labels each make one structure glow: DNA in the nucleus, microtubules and actin filaments by default. The colours are false, chosen for contrast, as in published images. Add mitochondria, the ER, the Golgi, lysosomes or growing microtubule tips under Stains, or roll the dice for another cell in another staining.

Focus

A confocal microscope sees a slice about 0.8 µm thick. Focus down onto the glass for the lamellipodium and stress fibres, or up through the nucleus. A widefield microscope collects out-of-focus light too, as haze. TIRF lights only the first tenth of a micrometre above the glass.

Resolution

Light blurs every point into a spot about a quarter of a micrometre across, wider for red light than for blue. A microtubule is only 25 nm thick, so what you see is the blur. Super-resolution (structured illumination) halves it.

Without stains

Living cells are nearly transparent, so plain brightfield shows almost nothing in focus. Phase contrast turns small delays of the light into darkness, with its telltale bright halo round the edges; vacuoles full of medium look bright. DIC shows the same delays as a relief, as if lit from one side. Darkfield blocks the direct light, so only what the cell scatters glows. Interference reflection looks at the glass from below: where the cell grips it at focal adhesions the reflections cancel, leaving black streaks.

Things to find

Focus up beside the nucleus to find the primary cilium, the cell’s antenna, lying on its upper surface. Specks of protein lie on the glass round the cell, and blurry particles drift through the medium far above it.

The cell is simulated: its shape, motion and every structure are modelled on measurements of living fibroblasts, and imaged through a model of a 1.4 NA oil objective. Labels are placed where the structures really are in the simulation.