cyto.site

Cytology, specimen prep, and the cell atlas

Building the model…

Living model of the pluripotent stem cell: the cell. Zoom between the stages. Morphology after Becker et al 2006, J Cell Physiol (cell cycle of H1 and H9); Ponsaerts et al 2004 and Denning et al 2006 (feeder-free culture on Matrigel); Adewumi et al 2007, Nat Biotechnol (pluripotency markers across 59 lines). Cell and nuclear size are not measured: no measured H1 or H9 diameter was found, as the twin on the front page also states..

Welcome. I can help you find any cell, understand what you are seeing, or connect you with the right helper. What are we looking at?

The cell on the front page is a human pluripotent stem cell, grown without feeder cells. Its lines were first derived from human blastocysts, and what makes it what it is are its markers, POU5F1, NANOG, SSEA-4 and TRA-1-60, and its clock: one division every 15 to 16 hours, with a G1 phase of only 2.5 to 3 hours, far shorter than a somatic cell's. It can form derivatives of all three embryonic germ layers, which is why it stands at the door of cyto.site. Sources: Thomson 1998, https://pubmed.ncbi.nlm.nih.gov/9804556/ ; Becker 2006, https://pubmed.ncbi.nlm.nih.gov/16972248/ ; Adewumi 2007, https://pubmed.ncbi.nlm.nih.gov/17572666/ ; Ponsaerts 2004, https://pubmed.ncbi.nlm.nih.gov/15671669/

Gallery 510

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One picture per organelle here; the full gallery holds every picture from every cell site as well, filterable by cell and by organelle.

Panel N (LC3): autophagosome marker as magenta puncta, inset with arrowheads. composite of 14 immunofluorescence panels, mouse choroid plexus epithelial cells; magenta channel is the named organelle marker

Autophagosome · Ono, Shishido, Yamagishi et al 2026, The FEBS Journal

A centriole and its procentriole in human RPE1 cells, both marked in red, seen by expansion microscopy. The physical enlargement of the sample is what makes the pair separable by light; the nine-fold symmetry the copy draws is below this resolution and is not visible here.

Centrosome · EPFL-MEDIACOM

Panel E, "iHTM Control" column: gamma-tubulin (red, basal body), ARL13B (green, ciliary axoneme) and DAPI (blue) in human iPSC-derived trabecular meshwork cells, showing a normal primary cilium. Part of a composite figure on OCRL mutations in Lowe syndrome.

Cilia and flagella · Chen, Liu, Wang et al 2026, Advanced Science

HeLa cells with actin filaments in red and microtubules in green. A wide field down the eyepiece rather than a confocal section, so individual filaments are not resolved and the nuclei dominate; it shows where the networks sit in a cell, not what a filament looks like.

Cytoskeleton · Mariantonietta L.

Panel D (EEA1): early endosome marker as magenta puncta, inset with arrowheads. composite of 14 immunofluorescence panels, mouse choroid plexus epithelial cells; magenta channel is the named organelle marker

Endosomes and vesicles · Ono, Shishido, Yamagishi et al 2026, The FEBS Journal

Panels A (GM130) and B (TGN46): Golgi apparatus markers as magenta puncta, insets with arrowheads. composite of 14 immunofluorescence panels, mouse choroid plexus epithelial cells; magenta channel is the named organelle marker

Golgi · Ono, Shishido, Yamagishi et al 2026, The FEBS Journal

A lipid droplet in lean mouse liver, raw on the left and the depositors' own hand tracing on the right. The droplet is the smooth featureless body: neutral lipid has no internal structure to resolve, which is what distinguishes it from every membrane-bound organelle around it. The ER membranes crowding it are visible as the fine parallel lines. Measured from the tracing, this droplet is 353 nm across at the widest of its 25 slices.

Lipid droplet · Parlakgul G, Arruda AP, Pang S, Cagampan E, Min N, Guney E, Lee Y, Inouye K, Hess HF, Xu CS, Hotamisligil GS

Panel I (LAMP1): lysosome marker as magenta puncta, inset with arrowheads. composite of 14 immunofluorescence panels, mouse choroid plexus epithelial cells; magenta channel is the named organelle marker

Lysosome · Ono, Shishido, Yamagishi et al 2026, The FEBS Journal

Two mitochondria in a thin section of mammalian lung, cristae resolved as folds of the inner membrane and the double membrane visible at the rim. The scale bar is 50 nm, so the whole frame is about a micrometre across: this is roughly the size the copy beside it is shown at.

Mitochondrion · Louisa Howard

Panel A, row "3M Control": Lamin B1 (red) at the nuclear rim, HA (cyan, LINC-DN reporter, not expressed in this row) and Hoechst (blue) in mouse cortical neurons, showing normal nuclear lamina morphology. Part of a composite figure on LINC complex disruption and ageing.

Nuclear envelope · Hasegawa, Hama, Amemiya et al 2026, EMBO Reports

Representative electron micrographs illustrating the ultrastructural nucleolar characteristics of dorsal root ganglia neurons after administration of miR-30c-5p mimic or inhibitor to SNI rats. Sham (A) and SNI rats treated with miR-30c-5p inhibitor (C) exhibit the typical nucleolar organisation of DRG neurons, characterised by the presence of numerous small-sized fibrillar centres (*, FCs), surrounded by a ring of dense fibrillar component (DFC), and areas of granular component (GC), preferentially at the nucleolar periphery. SNI rats treated with vehicle (B) or with miR-30c-5p mimic (D) present severe nucleolar alterations, including the formation of enlarged FCs and segregation of large masses of GC and DFC at the nucleolar periphery. Scale bar: 2 um.

Nucleolus · Frances, Mata-Garrido, Lafarga et al 2024, International Journal of Molecular Sciences. Figure 4

Panel of a six-part figure, cropped to this panel and otherwise unaltered, which CC BY allows with attribution. Human astrocyte differentiated from induced pluripotent stem cells of a healthy donor, 25 days in vitro. The authors describe it as a typical cell nucleus with an eccentrically located nucleolus, marked by the yellow arrow, and shallow invaginations of the envelope, marked by the red arrow. Scale bar 2 micrometres. The invaginations are worth noticing: the envelope shown as a smooth sphere on most diagrams is not smooth here.

Nucleus · Kutukova, Ivanov, Novosadova et al 2026, Modern Technologies in Medicine

Peroxisomal membrane protein PMP70 by MINFLUX. In the confocal panel each peroxisome is a blob; in the MINFLUX panels the same organelles resolve into rings and arcs, so the membrane is seen as a surface rather than a point. The crystalloid core the copy draws is not visible here, because this marker labels the membrane.

Peroxisome · abberior Instruments GmbH, contact person: Dr. Frederik Köpper

Ultrastructural analysis of VAC exocytosis and lateral lumen formation. A Principle of APEX2-TEM labeling. A brief (2-5 min) incubation of fixed cells with diaminobenzidine (DAB) and hydrogen peroxide (H2O2) results in the deposition of a DAB polymer that upon binding to OsO4 produces an electron-dense stain. B APEX2 TEM labeling of Pals1-A2E at different time points of the calcium switch assay. White arrowheads indicate small vesicles close to VACs, black arrowheads indicate enhanced contrast of microvilli inside the VACs produced by APEX2 labeling. LM = lateral membrane. C Serial section TEM of a VAC fusion event with the lateral membrane.

Plasma membrane · Ghosh, Martin, Chen et al 2026, Nature Communications

Three major conformational states of the 26S proteasome determined by electron cryomicroscopy. The copy beside this is shown in one fixed conformation; the complex actually moves between states, and that motion is what this figure is about.

Proteasome · FridoFoe

Ribosome · Kutukova, Ivanov, Novosadova et al 2026, Modern Technologies in Medicine

The left panel is the depositors' own "raw" file for this evaluation set and is already a thresholded membrane image, white on black, not greyscale electron microscopy. The tracing marks the sheets, the stacked parallel cisternae this copy draws, and leaves the small round tubule profiles unmarked. Sheets occupy 12.4 percent of this 6 um crop of lean mouse liver. Ribosomes are below the resolution of this segmentation, so the sheet is identified by its geometry here, not by studding.

Rough ER · Parlakgul G, Arruda AP, Pang S, Cagampan E, Min N, Guney E, Lee Y, Inouye K, Hess HF, Xu CS, Hotamisligil GS

Smooth endoplasmic reticulum · Parlakgul G, Arruda AP, Pang S, Cagampan E, Min N, Guney E, Lee Y, Inouye K, Hess HF, Xu CS, Hotamisligil GS

Library 8518

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Galleries and publication lists for every organelle and every cell: 8518 papers in Vancouver style, each PMID linked to PubMed, 23 cell galleries. Every PMID cyto.site cites is checked for retraction at each build; 2 retracted, each tagged.

Digital twin

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G1 phase length 2.71 h 2.62 to 2.79

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Organelles 18

Autophagosome 11 pictures Centrosome 14 pictures Cilia and flagella 14 pictures Cytoskeleton 10 pictures Endosomes and vesicles 15 pictures Golgi 15 pictures Lipid droplet 12 pictures Lysosome 10 pictures Mitochondrion 12 pictures Nuclear envelope 15 pictures Nucleolus 12 pictures Nucleus 15 pictures Peroxisome 10 pictures Plasma membrane 11 pictures Proteasome 10 pictures Ribosome 12 pictures Rough ER 12 pictures Smooth endoplasmic reticulum 12 pictures

Knowledge bases 8

adipocyte adipo.site chondrocyte chondro.site granulocyte granulo.site hepatocyte hepato.site myelocyte myelo.site oligodendrocyte oligodendro.site phagocyte phago.site plasmocyte plasmo.site