A visual key for every category on the submission form, in the same order it appears there — read alongside a paper's figures to standardise how different people call the same features.
Classify what the image actually shows, not what you'd expect from the species. Imaging artefacts, growth-condition effects, and mis-speciation in older literature will exist, but should be corrected post-hoc. The diagrams below are schematic, guided by real TEM observations, but will inevitably not cover all possibilities. This is a working draft: expect it to keep changing as edge cases turn up, and please feedback!.
The shape of the chloroplast itself, independent of the pyrenoid. Sets the context for what "central" or "bulged" means and is often useful as a taxonomic marker too.
Discoid / lens-shaped
Flattened, disc-like — as in most Rhodophyta.
Star-shaped (stellate)
Extensively lobed, radiating — e.g. Zygnema, Porphyridium, Rhodella.
Cup-shaped
Open, bowl-like cross-section — e.g. Chlamydomonas, Chlorella.
Two-lobed (butterfly)
Two lobes joined by a central/basal pyrenoid — e.g. Cryptomonas, Pavlova.
Lobed
Many small, irregular lobes — distinct from the broader radiating pattern of stellate.
Cuboid (axial plate)
Flat, plate-like.
Reticulate
Net-like, perforated.
Other
Includes ring-shaped and ribbon-shaped/helical — rare enough in TEM data that they're not worth separate categories. Describe in notes.
Pyrenoids per chloroplast: most unicellular algae have one, but note how many are visible if more.
Cell type: only fill in if presence or form is cell-type specific (e.g. "gametes only") — leave blank otherwise.
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Intraplastid pyrenoid location
The pyrenoid's position relative to the chloroplast body.
Central (embedded)
Not in contact with the chloroplast envelope — e.g. Chlamydomonas, Porphyridium, Thalassiosira. Shown here across several chloroplast shapes. Also called "embedded" in some literature.
Stalked
Bulges out through the envelope via a narrow constriction — apical or lateral.
Bulged
Same idea, but no constriction — wide-based from where it leaves the chloroplast.
Junctional
Sits at the junction where lobes meet — a constricted region. Butterfly/stellate chloroplasts.
Transverse
Centred along the chloroplast's long axis, but spans the full width along the short axis — touching the envelope on both sides. Distinct from central, which touches neither.
Other
Doesn't fit the options above — describe in the free-text field.
Position (stalked/bulged only):
Apical
At the end of the chloroplast.
Lateral
From the side of the chloroplast.
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Matrix shape
The shape of the pyrenoid matrix itself, separate from the chloroplast or the general class above.
Spherical / pseudo-spherical
Broadly rounded — includes matrices that appear slightly misshapen only due to constriction or other seemingly transient effect.
Lenticular
Elongated — noticeably longer in one direction, distinguishing it from spherical/pseudo-spherical. Can be lens-shaped (e.g. diatom pyrenoids) or more stretched.
Lobed
One continuous matrix, several rounded lobes.
Multinucleate
Segments appear as individual separate blobs — not just one matrix transected by thylakoids, as with the others above. E.g. Anthoceros.
Amorphous
Continuous but not spherical and not clearly lobed. More commonly associated with stalked pyrenoids
Other
Describe in the notes field.
Diameter: estimate in µm from the image if a scale bar is present — even a rough figure is useful.
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Traversing membranes
Whether membranes penetrate through the matrix itself, or approach it closely. These are the common categories, including an explicit "Absent" (naked) option for when no membrane traverses the matrix at all. More than one can apply — select all that fit, e.g. an invagination that also looks fenestrated in section.
Sheets
Continuous, unbroken sheets spanning the matrix — e.g. P. bulbiculosus (multiple sheets).
Fenestrated
Appears fenestrated (perforated) in 2D section.
Curved
Follows a curved path — e.g. Porphyridium.
Invaginated
Folds inward from the boundary — usually can't resolve which membrane (envelope vs. other) at typical resolution, so just call it invagination.
Proximal
Thylakoids very close to entering the matrix, approaching perpendicular to the condensate — mainly in stalked/bulged pyrenoids.
Peripheral
Enters the matrix only near its edge, not through the centre. Rare — confirm carefully, and don't confuse with a surrounding membrane (below), which never enters the matrix at all.
Peripheral vs. surrounding membrane: a peripheral traversing membrane still crosses into the dense matrix, just close to its boundary. A surrounding membrane (see below) stays entirely outside the matrix, enclosing it without entering. Only pick "Peripheral" when the membrane is clearly seen crossing into the matrix, not merely abutting it — it's an uncommon call.
Continuous with external thylakoid network? Only asked for sheets, fenestrated, or curved — not invaginations or proximal approaches, which by definition aren't continuous with the network as they are invaginations of the encasing membranes (e.g. chloroplast envolope).
Extent:
Complete
Spans the whole matrix — usual for sheets/curved.
Partial
Enters from the edge, doesn't reach the other side — usual for fenestrations.
Discontinuous
Breaks partway rather than running continuously.
Number of traversions: count the number of individual traversions (e.g. Porphyridium's curved traversions, or multiple sheets as in P. bulbiculosus).
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Surrounding feature
Three independent yes/no/unclear questions, not mutually exclusive — a pyrenoid could plausibly have more than one of these at once.
Carbohydrate barrier
Present
Starch — also called capping vesicle / pyrenoid sac / pyrenoid cap in older TEMs.
Location:
Chloroplastic
Starch sits inside the chloroplast envelope (green line) — usually central pyrenoids.
Extra-chloroplastic
Starch sits outside the envelope (cytosolic) — a membrane separates it from the matrix. Usually stalked/bulged pyrenoids.
Number of granules/plates:count number of plates/granules.
Morphology:
Plate
Continuous, shaped feature — often hugging the matrix periphery.
Granule
Adjacent, more amorphous features.
Coverage: judged relative to the full 360° circumference of the matrix, in cross-section — not against a "complete" ideal. Bucketed as <25%, 25–50%, 50–75%, or 75%+. Full coverage is essentially impossible for stalked/bulged pyrenoids, since the stalk itself is never covered — so don't expect the top bucket there.
Surrounding membrane
Present
A distinct membrane boundary directly enclosing the matrix — including thylakoids running close/appressed to it.
Origin: thylakoid / envelope / other — if other, specify.
Morphology: appressed (flat against the matrix) / curved / other.
Shell
Present
Thin protein layer — often hard to observe, and rare to confidently designate. Only designate if it's clearly visible.
Reference: Shimakawa et al. (2024) Cell.
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Plastoglobuli
Small, roughly spherical lipid droplets, sometimes visible in or around the pyrenoid.
Present
Small dark globules — note the actual location seen (often peripheral).
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Nucleomorph
A vestigial nucleus retained from a secondary endosymbiosis — present in some lineages (e.g. cryptophytes, chlorarachniophytes), never in others. Same yes/no + location pattern as plastoglobuli above.
Present
Note its location relative to the pyrenoid if visible (e.g. adjacent).