Module 2 · Visual Grammar

Stain and Modality Recognition

Do not ask a stain a question it cannot answer.

LM shows tissue response. IF shows immune reactants and staining pattern. EM shows ultrastructural deposit location and morphology.

Immunofluorescence identifies…

Identifies WHAT is deposited: IgG, IgA, IgM, C3, C1q, kappa/lambda, fibrin.
Identifies the PATTERN: granular, linear, mesangial, capillary wall, full-house, pauci-immune, C3-dominant.

Electron microscopy shows…

Shows ultrastructural LOCATION of electron-dense deposits: mesangial, subendothelial, subepithelial, intramembranous.
Shows MORPHOLOGY: organized fibrils, microtubules, humps, spikes, GBM lamellation, foot process effacement.

Immune deposition is an integrated LM + IF + EM synthesis. Do not teach that immune deposition is seen only on EM.

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Image placeholder — H&E (Hematoxylin & Eosin)

Best for: General survey of architecture, cellularity, and inflammation.
Look for: Nuclear detail, cytoplasmic staining, hypercellularity, crescents, tubular injury, inflammatory infiltrates.
Common mistakes: H&E under-highlights basement membranes and matrix — do not rule out membranous or MPGN patterns on H&E alone.

Quick check

Which finding is H&E LEAST reliable for identifying?

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Image placeholder — PAS (Periodic Acid–Schiff)

Best for: Basement membranes, mesangial matrix, and tubular brush border.
Look for: Mesangial expansion, GBM thickness, double contours, nodular sclerosis, loss of tubular brush border in ATI.
Common mistakes: PAS-positivity is not specific — matrix expansion in diabetes, amyloid, and MPGN can look similar without IF/EM correlation.

Quick check

PAS is most useful for evaluating:

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Image placeholder — Jones Silver

Best for: GBM contours and mesangial outlines with high spatial resolution.
Look for: GBM spikes (membranous), double contours / tram-tracks (MPGN, TMA), fibrillary/discontinuous GBM, mesangial interposition.
Common mistakes: Silver artefact and over-staining can mimic double contours; correlate with PAS and EM.

Quick check

GBM 'spikes' on Jones silver most classically suggest:

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Image placeholder — Masson Trichrome

Best for: Interstitial fibrosis and glomerular/vascular sclerosis (chronicity).
Look for: Blue collagen in interstitium (IFTA), arteriosclerotic intimal fibrosis, segmental scars, fibrocellular crescents.
Common mistakes: Fibrin, immune deposits, and old thrombi can also stain — read trichrome for chronicity, not for immune deposition.

Quick check

The best modality for estimating IFTA at low-power is:

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Image placeholder — Immunofluorescence (IF)

Best for: Identity and pattern of immune reactants in glomeruli and along basement membranes.
Look for: IgG, IgA, IgM, C3, C1q, kappa/lambda, fibrin — and their pattern: granular, linear, mesangial, capillary wall, full-house, pauci-immune, C3-dominant.
Common mistakes: IF identifies WHAT is deposited and WHERE by pattern — it does not, by itself, prove ultrastructural deposit location. Absence of staining does not exclude disease if tissue is inadequate.

Quick check

A biopsy shows granular capillary-wall IgG and C3 with dominant IgG-4 and no light-chain restriction. IF pattern best fits:

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Image placeholder — Electron Microscopy (EM)

Best for: Ultrastructural location and morphology of electron-dense deposits, and podocyte / GBM architecture.
Look for: Deposit location — mesangial, subendothelial, subepithelial, intramembranous; organized substructure — fibrils, microtubules; foot process effacement; GBM lamellation and duplication.
Common mistakes: EM shows ultrastructural location and morphology, not immune identity. Do not confuse 'immune deposits' (an LM/IF/EM synthesis) with 'electron-dense deposits' (an EM finding).

Quick check

Non-branching randomly oriented fibrils ~10 nm in diameter on EM, with Congo-red positivity, best fits: