ECS preservation

Analysis

Every per-crop measurement the pipeline has produced, live at the top and as standing panels below. Each dot is one crop, chemical above the line and HPF below, with groups sharing one scale so they can be read against each other. How to read this.

loading…

Run

Metric family

Metric

Group by

Tissue

Region

Analysis voxel

At a glance

Order

One card per headline metric: each dot a crop, chemical above and rapid HPF below, medians ticked. The bar is Cliff's δ, drawn from the centre — longer means the two preparations separate further. Click a card to open that metric in full. What δ means.

One metric at a time

Pick any of the 60-odd measurements above. Each dot is one crop — chemical on the upper line, rapid HPF on the lower — and the thick tick is that arm's median. Groups share one scale so they can be read against each other.

Chemical, one crop Rapid HPF, one crop group median n arm with one crop or none

Scale Axis range to

Loading…

The standing panels for this family

Pre-rendered by the pipeline, one for each resolution. The matched panel exists to be read against the native one: a difference that survives downsampling to 8 nm is not explained by voxel size. These change with the family above.

Volume fraction

ECS and cell volume fractions per crop. The most resolution-robust family, so the native panel can be read fairly directly. Native only: the matched run reads zarr metadata that is valid at native resolution alone.

Draw this live — any metric in the family, any grouping, one dot per crop.

Volume fraction, native resolution — Native resolution

ECS width

Distance from each extracellular voxel to the nearest cell. Distance to the wall, not channel width — roughly a quarter of it.

Draw this live — any metric in the family, any grouping, one dot per crop.

ECS width, native resolution — Native resolution

ECS width, matched to 8 nm — Matched to 8 nm

Cell-to-cell gap

Gap between neighbouring cells. Hard floor of three voxels, so the left tail is the measurement, not the tissue; at 8 nm that floor is 24 nm.

Draw this live — any metric in the family, any grouping, one dot per crop.

Cell-to-cell gap, native resolution — Native resolution

Cell-to-cell gap, matched to 8 nm — Matched to 8 nm

Surface area to volume

ECS-facing membrane per unit cell volume, pooled across the cells in each crop.

Draw this live — any metric in the family, any grouping, one dot per crop.

Surface area to volume, native resolution — Native resolution

Surface area to volume, matched to 8 nm — Matched to 8 nm

Membrane shape

Curvature, roughness and protrusion density on the ECS-facing membrane. The 30 nm roughness scale is not honestly resolvable in the matched panel.

Draw this live — any metric in the family, any grouping, one dot per crop.

Membrane shape, native resolution — Native resolution

Membrane shape, matched to 8 nm — Matched to 8 nm

The same crops, as numbers

Every crop behind the plot above, for the metric you have selected. Click a heading to sort; the ▾ on a column filters it; a crop name opens that crop in the 3D viewer.

Download every metric for every crop — one CSV, the same file this page reads.

Every metric at once

Standing panels, rendered by the pipeline rather than drawn in the page. These are the whole study on one sheet: the summary restricted to regions that have crops on both sides, the same again at a common 8 nm voxel, and the effect sizes behind both.

Effect-size matrix — Effect-size matrixCliff's delta for every metric family across the region-matched comparison. Delta runs from -1 to 1; zero means the two preparations are indistinguishable. Direction and size, not significance — several regions have an arm of one, so read the effect, not the p.

Anatomy-matched summary — Anatomy-matched summaryEvery metric, restricted to the region groups where both preparations have crops. Native resolution.

Anatomy-matched, at 8 nm — Anatomy-matched, at 8 nmThe same again with every crop downsampled to 8 nm first — the most conservative view on the site: same regions, same voxel size.

One region, every metric

The same comparison one anatomical region at a time. A region only appears here if both preparations have crops in it — six of them do.

Bile canaliculus — Bile canaliculusLiver, chemical vs HPF.

Hepatocyte lateral — Hepatocyte lateralLiver, the largest matched group.

Glomerular — GlomerularKidney.

Tubule basal — Tubule basalKidney, DCT base and PCT base pooled — the pooling is what gives this region an arm on both sides.

Cardiac interstitial — Cardiac interstitialHeart.

Intercalated disc — Intercalated discHeart.

Pictures of the geometry

What the measurements are measuring. Membrane surfaces coloured by curvature, and the extracellular space rendered as the solid object it is.

These are stills. Paired 3D views puts one crop of each preparation side by side per region, and the crop page will load any two of the 55 into a viewer you can turn.

Extracellular space in 3D — Extracellular space in 3DThe space itself rendered as a solid, rather than the membranes around it.

Cell surface — Cell surfaceA single segmented cell.

Membrane patch, crop1039 — Membrane patch, crop1039Curvature on one ECS-facing patch.

Membrane patch, crop1072 — Membrane patch, crop1072The same view in another crop.

Where to next