Cell Types

Amacrine cells are a diverse group of inhibitory interneurons in the retina's inner nuclear layer. They form lateral connections within the inner plexiform layer, modulating signals between bipolar cells and ganglion cells. Lacking long axons, they use their processes for local circuit integration. They are crucial for complex visual processing, including motion detection, directional selectivity, and temporal adaptation, shaping the retina's output before it reaches the brain.

Neurons are electrically excitable cells that transmit information through electrochemical signals across synapses. As the principal functional units of the nervous system, they integrate synaptic inputs and relay outputs via axons to other neurons, muscles, or glands. Neuronal subtypes differ widely in morphology, neurotransmitter identity, connectivity, and firing properties.

Astrocytes are star-shaped glial cells, the most abundant in the central nervous system (CNS). They are vital for homeostasis: they form part of the blood-brain barrier, regulate blood flow, control extracellular ion/neurotransmitter balance (e.g., glutamate uptake), and provide metabolic support to neurons. Through the "tripartite synapse," they modulate synaptic strength and plasticity. They also respond to injury via reactive astrogliosis, playing dual roles in scar formation and neuroprotection.

Bipolar cells are retinal neurons that relay visual information directly from photoreceptors (rods and cones) to ganglion cells. They have a characteristic morphology with one dendrite connecting to photoreceptors and one axon synapsing in the inner plexiform layer. They are functionally divided into ON and OFF types, responding to light increments and decrements, respectively. This segregation initiates the parallel pathways essential for contrast perception and visual processing.

Cone cells are photoreceptors specialized for bright-light (photopic) vision, high visual acuity, and color perception. They are concentrated in the fovea centralis. Humans possess three types, each containing a photopigment sensitive to short (blue), medium (green), or long (red) wavelengths, enabling trichromatic color vision. Cones are less light-sensitive than rods but provide fine spatial detail and are critical for tasks like reading, driving, and recognizing faces and colors.

Enteric glial cells (EGCs) are the resident glia of the enteric nervous system (ENS), the "gut brain." They resemble CNS astrocytes and are integral to gastrointestinal homeostasis. EGCs support enteric neurons, regulate intestinal barrier integrity, modulate immune responses within the gut wall, and influence motility. Their dysfunction is implicated in inflammatory bowel diseases (IBD), infections, and functional GI disorders, highlighting their role beyond mere structural support.

Excitatory neurons are nerve cells that, when activated, increase the likelihood of their target neuron firing an action potential. They primarily release the neurotransmitter glutamate at their synapses. They form the primary driving force in neural circuits throughout the brain (e.g., cortical pyramidal neurons) and are fundamental for information propagation, synaptic plasticity (like LTP), and processes such as learning, memory, and cognition.

Granule cells are small, numerous excitatory neurons with a characteristic granular appearance. Key populations exist in the cerebellum (input neurons of the cortical layer), dentate gyrus of the hippocampus (forming new memories), and olfactory bulb. They typically receive multiple inputs, process information in a dense network, and project to larger principal cells (e.g., Purkinje cells, pyramidal cells), playing crucial roles in motor coordination, learning, and sensory processing.

Inhibitory neurons reduce the probability of their postsynaptic target neuron firing an action potential. They primarily release the neurotransmitters GABA (in the brain) or glycine (in the spinal cord/brainstem). They are crucial for balancing neural circuit activity, preventing runaway excitation, generating rhythmic outputs (e.g., in pacemaker circuits), and shaping the temporal and spatial precision of neural computations. Types include interneurons like basket cells and Purkinje cells.

Muller cells are specialized radial glial cells that span the entire thickness of the retina, from the inner to the outer limiting membrane. They are the principal support cells of the retina, maintaining its structural integrity and homeostasis. They regulate extracellular ion and water balance, recycle neurotransmitters (especially glutamate), store glycogen for energy, and guide light to photoreceptors. Their dysfunction is involved in many retinal diseases.

Oligodendrocyte progenitor cells (OPCs), also called NG2-glia, are a population of glial cells found throughout the CNS. They are proliferative and maintain the capacity to differentiate into mature, myelinating oligodendrocytes. OPCs are critical for developmental myelination and remain in the adult CNS, where they contribute to remyelination after demyelinating injuries (e.g., in Multiple Sclerosis) and may have additional roles in monitoring neural circuits.

Oligodendrocytes are the myelinating glial cells of the central nervous system (CNS). Each oligodendrocyte extends multiple processes to wrap and insulate segments of several different axons with concentric layers of myelin membrane. This myelin sheath greatly increases the speed of action potential propagation (saltatory conduction). They also provide metabolic support to the axons they enwrap. Loss of oligodendrocytes or myelin disrupts nerve signaling.

Purkinje cells are large, GABAergic inhibitory neurons that form a single layer in the cerebellar cortex. They are the sole output neurons of the cerebellar cortex, projecting to the deep cerebellar nuclei. They receive massive excitatory input from parallel fibers (granule cell axons) and powerful, instructive input from a single climbing fiber. Their complex dendritic tree integrates these signals to fine-tune motor coordination, balance, and motor learning.

Rod cells are photoreceptors specialized for low-light (scotopic) vision. They are extremely light-sensitive, containing the pigment rhodopsin, and are responsible for night vision and peripheral vision. Rods do not mediate color perception, providing monochromatic (black-and-white) vision. Their signals converge heavily onto bipolar cells, maximizing sensitivity at the expense of fine detail. They are more numerous than cones and are absent from the central fovea.

Schwann cells are the principal glial cells of the peripheral nervous system (PNS). Myelinating Schwann cells wrap around single axons to form the myelin sheath, enabling fast saltatory conduction. Non-myelinating Schwann cells ensheath multiple small-diameter axons. Schwann cells are crucial for supporting axon health and guiding regeneration after PNS injury, forming regeneration tubes (Bands of Büngner) that direct axonal regrowth.

Microglia are the resident macrophages and primary immune cells of the central nervous system (CNS). In their resting state, they constantly survey the parenchyma. Upon detecting injury, infection, or pathological signals, they activate, becoming phagocytic to clear debris, dead cells, and pathogens. They also play essential roles in synaptic pruning during development, modulating neuroinflammation, and can contribute to both repair and neurodegeneration in diseases.

Chromaffin cells are neuroendocrine cells found primarily in the adrenal medulla. They are derived from neural crest cells and function as modified postganglionic sympathetic neurons. They synthesize and store catecholamines (epinephrine ~80%, norepinephrine ~20%) in dense-core secretory granules. In response to stress signals (acetylcholine from preganglionic fibers), they release these hormones directly into the bloodstream to mediate the systemic "fight-or-flight" response.

Melanocytes are neural crest-derived cells located in the basal layer of the epidermis and in hair follicles. Their primary function is the production of melanin, a pigment that provides color to skin and hair and protects underlying cells from UV radiation damage. Melanin is synthesized in organelles called melanosomes, which are then transferred to neighboring keratinocytes via dendritic processes.

Neuronal cells (Neural cells) in species SP202. Single-cell UMAP atlas.

Neuronal/Neural cells (Neural cells) in species SP202. Single-cell UMAP atlas.

B cells are lymphocytes responsible for the humoral arm of the adaptive immune response. They develop in the bone marrow and, upon maturation, circulate in blood and lymph. When activated by antigen (often with T cell help), they proliferate and differentiate into antibody-secreting plasma cells or long-lived memory B cells. Their antibodies neutralize pathogens, opsonize them for phagocytosis, and activate the complement system.

Common lymphoid progenitors (CLPs) are bone marrow-derived progenitor cells committed exclusively to the lymphoid lineage. They arise from hematopoietic stem cells and give rise to all lymphocytes: B cells, T cells, Natural Killer (NK) cells, and some dendritic cell subsets (lymphoid DCs). The CLP represents the critical branch point in hematopoiesis where the lymphoid pathway is specified.

Common myeloid progenitors (CMPs) are bone marrow progenitors committed to the myeloid lineage. They are derived from hematopoietic stem cells and can generate all myeloid blood cells: erythrocytes (red blood cells), megakaryocytes (platelets), mast cells, and the granulocyte-monocyte lineage (neutrophils, eosinophils, basophils, monocytes, macrophages, and some dendritic cells). The CMP is a key intermediate in myeloid cell production.

Cycling B cells refer to B lymphocytes that are actively proliferating, progressing through the cell cycle (G1, S, G2, M phases). This occurs during immune activation following antigen encounter and T cell help, leading to clonal expansion within germinal centers of lymph nodes or in extrafollicular sites. This proliferation is essential to generate a large population of antigen-specific B cell clones for antibody production and memory formation.

Dendritic cells (DCs) are professional antigen-presenting cells (APCs) that act as sentinels linking innate and adaptive immunity. Immature DCs in tissues capture antigens, then mature and migrate to lymph nodes. There, they present processed antigens on MHC molecules to naive T cells, providing the critical "signal 1" and costimulatory "signal 2" required for T cell activation and differentiation, thereby initiating antigen-specific immune responses.

Erythroid cells represent the lineage of hematopoietic cells committed to becoming erythrocytes (red blood cells). This includes progenitors (BFU-E, CFU-E) and morphologically identifiable precursors: proerythroblasts, basophilic, polychromatophilic, and orthochromatic erythroblasts, which undergo hemoglobin synthesis, nuclear condensation, and finally enucleation to form reticulocytes and then mature RBCs. Their primary function is oxygen transport via hemoglobin.

Hematopoietic stem and progenitor cells (HSPCs) reside in the bone marrow and are responsible for lifelong blood cell production (hematopoiesis). Hematopoietic stem cells (HSCs) have long-term self-renewal and multipotent differentiation capacity. Progenitor cells (like CMPs, CLPs) are more restricted in potential but highly proliferative. Together, they give rise to all lineages of blood and immune cells.

Kupffer cells are specialized tissue-resident macrophages located within the sinusoids of the liver. They are the largest population of fixed macrophages in the body. They phagocytose pathogens, toxins, cellular debris, and aged red blood cells from the portal blood flow. They play crucial roles in liver immunity, iron recycling, lipid metabolism, and maintaining overall hepatic homeostasis. Their activation can contribute to liver inflammation and fibrosis.

Macrophages are large, phagocytic cells of the innate immune system present in all tissues (where they have specific names like Kupffer cells, microglia). They derive from blood monocytes or local progenitors. They engulf and destroy pathogens and dead cells, secrete cytokines and chemokines to regulate inflammation, present antigens, and are key players in tissue repair, remodeling, and homeostasis. They exhibit remarkable functional plasticity (M1/M2 spectra).

Mast cells are tissue-resident granulocytes found near blood vessels and nerves, particularly in skin, lungs, and gut mucosa. They store pre-formed inflammatory mediators (histamine, tryptase, heparin) in their granules. They are central effectors in IgE-mediated allergic reactions (anaphylaxis, hay fever) and defense against parasites. Upon activation, they rapidly degranulate and also synthesize cytokines/chemokines, influencing inflammation, immunity, and even tissue remodeling.

Megakaryocyte erythrocyte progenitors (MEPs) are bipotent hematopoietic progenitor cells derived from the Common Myeloid Progenitor (CMP). MEPs are committed to producing two critical blood cell types: megakaryocytes (which fragment into platelets for clotting) and erythrocytes (red blood cells for oxygen transport). The MEP stage represents the final branch point before lineage-specific commitment to platelet or red cell production.

Monocytes are circulating white blood cells (agranulocytes) that serve as precursors for macrophages and dendritic cells. Produced in the bone marrow, they patrol the bloodstream for several days before migrating into tissues in response to inflammatory signals. In tissues, they differentiate into macrophages or dendritic cells. In blood, they can phagocytose pathogens and present antigens, acting as a bridge between innate and adaptive immunity.

Natural Killer (NK) cells are cytotoxic lymphocytes of the innate immune system. They provide rapid responses to virus-infected cells and tumor cells without prior sensitization. They use a balance of activating and inhibitory receptors to detect "missing self" (loss of MHC I) or "induced self" (stress ligands). They kill targets by releasing perforin and granzymes (cytotoxic granules) and through death receptor ligands like FasL.

Natural Killer T (NKT) cells are a unique subset of T lymphocytes that bridge innate and adaptive immunity. They express an invariant T cell receptor (TCR) that recognizes lipid antigens presented by the non-classical MHC molecule CD1d. Upon activation, they rapidly produce large quantities of cytokines (e.g., IFN-γ, IL-4), influencing the activity of many other immune cells and shaping immune responses to infection, cancer, and autoimmunity.

Neutrophils are the most abundant white blood cell and the first responders to sites of bacterial or fungal infection. They are highly motile phagocytic cells that engulf and destroy pathogens using antimicrobial granules (containing myeloperoxidase, defensins) and reactive oxygen species. They form neutrophil extracellular traps (NETs) to ensnare microbes. Their short lifespan and potent effector functions make them crucial for acute inflammation.

Plasma B cells (or plasma cells) are the terminal, fully differentiated effector state of activated B lymphocytes. They are antibody factories, specializing in the massive secretion of antibodies of a single specificity. They possess extensive endoplasmic reticulum and a prominent Golgi apparatus to support high-rate protein synthesis. Most are short-lived, but some become long-lived plasma cells that reside in the bone marrow, providing sustained antibody levels.

Platelets (thrombocytes) are small, anucleate cell fragments derived from megakaryocytes in the bone marrow. They circulate in blood and are essential for hemostasis: upon vascular injury, they adhere, activate, aggregate to form a plug, and provide a surface for coagulation factors. They also secrete growth factors and cytokines, playing roles in inflammation, immunity, and tissue repair.

T cells (T lymphocytes) are central players in cell-mediated adaptive immunity. They develop in the thymus and express T cell receptors (TCRs) that recognize peptide antigens presented by MHC molecules. Major subsets include: Helper T cells (CD4+, which secrete cytokines to help B cells and macrophages), Cytotoxic T cells (CD8+, which kill infected/cancerous cells), and Regulatory T cells (Tregs, which suppress immune responses to prevent autoimmunity).

T/NKT cells encompass T lymphocyte populations together with natural killer T (NKT) cells, which recognize lipid antigens presented by the non-polymorphic CD1d molecule. NKT cells bridge innate and adaptive immunity by rapidly releasing large amounts of cytokines upon activation. They are implicated in tumor surveillance, autoimmunity, and antimicrobial responses.

Club cells (formerly Clara cells) are non-ciliated secretory cells found in the bronchiolar epithelium of the lungs. They secrete surfactant proteins and components of the airway lining fluid. They possess cytochrome P450 enzymes for detoxification. Importantly, they function as progenitor cells for both themselves and ciliated cells in the bronchioles, contributing to the repair and maintenance of the distal airway epithelium.

Goblet cells are specialized unicellular mucus-secreting glands found within simple columnar epithelia of the respiratory and intestinal tracts. They have a characteristic goblet shape, with a basal nucleus and an apical region packed with mucin granules. They secrete mucins, which hydrate and form the protective mucus layer that traps particles, lubricates surfaces, and protects the epithelium from pathogens and damage.

Pancreatic islet (islets of Langerhans) cells are the endocrine cells of the pancreas, organized into clusters scattered throughout the exocrine tissue. Major types include: Alpha cells (secrete glucagon, raises blood sugar), Beta cells (secrete insulin, lowers blood sugar), Delta cells (secrete somatostatin, inhibits other islet cells), and PP cells (secrete pancreatic polypeptide). They precisely regulate glucose homeostasis.

Photoreceptor cells (Immune cells) in species SP202. Single-cell UMAP atlas.

Cycling T_NKT cells (Immune cells) in species SP202. Single-cell UMAP atlas.

Cycling immune cells (Immune cells) in species SP202. Single-cell UMAP atlas.

Cycling immune progenitor cells (Immune cells) in species SP202. Single-cell UMAP atlas.

Immune cells (Immune cells) in species SP202. Single-cell UMAP atlas.

Acinar cells are the exocrine secretory cells of glands like the salivary glands and pancreas. In the pancreas, they are organized into acini and synthesize, store, and secrete digestive pro-enzymes (zymogens) into a ductal network. They have a highly developed rough ER and abundant secretory (zymogen) granules. When stimulated (e.g., by cholecystokinin), they release their contents into the pancreatic duct, which empties into the duodenum.

Alveolar type 2 (AT2) cells are cuboidal epithelial cells found in the alveolar corners. They have three critical functions: (1) They synthesize and secrete pulmonary surfactant, a phospholipid-protein mixture that reduces surface tension and prevents alveolar collapse. (2) They serve as progenitor cells for both AT1 and AT2 cells, repairing the alveolar epithelium after injury. (3) They contribute to innate immune defense in the alveoli.

Cells of the thick ascending limb (TAL) of the loop of Henle in the kidney nephron. They are impermeable to water but actively reabsorb sodium, potassium, and chloride via the Na-K-2Cl cotransporter (NKCC2) on their apical membrane. This transport is critical for generating the hypertonic medullary interstitium necessary for water reabsorption in the collecting duct. They also contribute to magnesium and calcium reabsorption.

Basal cells are a layer of mitotically active epithelial progenitor/stem cells found attached to the basement membrane in stratified and pseudostratified epithelia (e.g., skin, airways, prostate). They divide to give rise to cells that differentiate and move upward to replenish the superficial layers. In the airway, they are major stem cells capable of regenerating both ciliated and secretory cells after injury.

Cholangiocytes are the epithelial cells that line the intrahepatic and extrahepatic bile ducts. They modify the composition of bile (through secretion and absorption of water, ions, and bicarbonate), form a protective barrier, and respond to hormonal signals. They express receptors and channels (e.g., CFTR) critical for bile flow. Their proliferation and dysfunction are central to cholangiopathies like primary sclerosing cholangitis (PSC).

Ciliated cells are epithelial cells characterized by the presence of motile cilia (hair-like projections) on their apical surface. They are found in the respiratory tract, oviducts, and ventricles of the brain (ependymal cells). Coordinated, rhythmic beating of cilia moves fluid or mucus over the epithelial surface. In the airways, this "mucociliary escalator" traps and propels inhaled particles and pathogens out of the lungs, a key defense mechanism.

Corticotropes are endocrine cells in the anterior pituitary gland (adenohypophysis) that produce and secrete adrenocorticotropic hormone (ACTH). ACTH is derived from the precursor pro-opiomelanocortin (POMC). In response to corticotropin-releasing hormone (CRH) from the hypothalamus, corticotropes release ACTH into the bloodstream, which then stimulates the adrenal cortex to produce glucocorticoids (like cortisol), key stress hormones.

A broad categorization for any epithelial cell (from various tissues) that is captured in an active phase of the cell cycle. This label is used in genomic datasets to distinguish proliferating cells from quiescent or terminally differentiated ones. It highlights the dynamic nature of epithelia, where constant renewal and repair are driven by these cycling populations.

Refers to secretory epithelial cells within glands (e.g., gastric glands, salivary glands, prostate glands) that are actively dividing. These cells may be progenitor cells within the gland that will give rise to new secretory cells, or they could be mature secretory cells that retain some proliferative capacity to maintain the glandular population.

In tissues with stratified epithelia (e.g., skin, esophagus), intermediate cells (also called transit-amplifying cells) are partially differentiated cells between basal and superficial layers. "Cycling" indicates that these cells are actively proliferating, serving to amplify the number of cells produced by the stem cell (basal cell) division before they terminally differentiate into the outer layer cells.

Cells of the distal convoluted tubule (DCT) in the nephron. They are responsible for fine-tuning electrolyte balance. They actively reabsorb sodium and chloride (via the Na-Cl cotransporter, NCC) and are a major site for parathyroid hormone (PTH)-regulated calcium reabsorption. Their activity is crucial for maintaining blood pressure, potassium, calcium, and magnesium homeostasis.

Enterocytes are the principal absorptive columnar epithelial cells lining the small intestine villi. Their apical surface is covered with microvilli, forming a "brush border" that dramatically increases surface area for nutrient absorption. They digest and absorb carbohydrates, peptides, amino acids, and lipids. They also secrete water and ions and form a crucial barrier between the gut lumen and the internal environment.

Ependymal cells are ciliated epithelial-like glial cells that line the ventricles of the brain and the central canal of the spinal cord. Their coordinated ciliary beating helps circulate cerebrospinal fluid (CSF). They contribute to the blood-CSF barrier, secrete factors into the CSF, and in certain niches (like the lateral ventricles), some can act as neural stem cells (radial glia-like cells).

Epithelial cells form continuous sheets (epithelia) that cover external body surfaces and line internal cavities and tubes. They are polarized, with distinct apical, lateral, and basal domains. Functions include protection (skin), absorption (intestine), secretion (glands), filtration (kidney), and sensation (taste buds). They are classified by shape (squamous, cuboidal, columnar) and layering (simple, stratified).

Fasciculata cells are steroidogenic endocrine cells that constitute the zona fasciculata, the middle and largest layer of the adrenal cortex. Their primary function is the production of glucocorticoids (mainly cortisol in humans), stimulated by ACTH from the pituitary. They contain abundant lipid droplets with cholesterol esters (giving a "foamy" appearance) and smooth endoplasmic reticulum for steroid hormone synthesis.

In the thyroid gland, follicular cells (thyrocytes) are the principal epithelial cells that form spherical follicles. They synthesize thyroglobulin and, upon stimulation by TSH, take up iodine to produce the thyroid hormones thyroxine (T4) and triiodothyronine (T3), which are stored in the colloid-filled follicle lumen and released into the blood to regulate metabolism, growth, and development.

Glandular cells are specialized epithelial cells that constitute the secretory units of exocrine and endocrine glands. They synthesize and release specific products. Exocrine glandular cells (e.g., in salivary, sweat glands) secrete via ducts. Endocrine glandular cells (e.g., in thyroid, pituitary) secrete hormones directly into the bloodstream. Their morphology is adapted for secretion, with abundant rough ER and secretory granules.

Gonadotropes are endocrine cells in the anterior pituitary gland that produce and secrete the gonadotropins: follicle-stimulating hormone (FSH) and luteinizing hormone (LH). In response to gonadotropin-releasing hormone (GnRH) from the hypothalamus, they release these hormones into the bloodstream. FSH and LH then act on the gonads (ovaries and testes) to regulate gametogenesis and sex steroid hormone production.

Hepatocytes are the principal parenchymal cells of the liver, making up about 80% of its mass. They are metabolic powerhouses with functions including: protein synthesis (albumin, clotting factors), bile production, detoxification and metabolism of drugs/toxins, glycogen storage and glucose homeostasis, lipid metabolism, and cholesterol synthesis. They are arranged in plates radiating from central veins, with polarized faces facing sinusoids and bile canaliculi.

Keratinocytes are the predominant cell type in the epidermis (the outermost skin layer). They originate from basal layer stem cells and undergo a process of terminal differentiation as they move outward, producing keratin intermediate filaments. In the stratum corneum, they become anucleate corneocytes, forming a tough, waterproof barrier that protects against mechanical injury, water loss, and microbial invasion.

Lactotropes (or mammotropes) are endocrine cells in the anterior pituitary gland that produce and secrete prolactin (PRL). Prolactin's primary role is to stimulate milk production (lactation) in the mammary glands after childbirth. Its secretion is primarily under inhibitory control by dopamine from the hypothalamus. Lactotropes can increase in number during pregnancy and lactation.

Melanotropes are endocrine cells found in the intermediate lobe of the pituitary gland (well-developed in some vertebrates, rudimentary in humans). They produce and secrete melanocyte-stimulating hormone (MSH), which is cleaved from the POMC precursor. MSH stimulates melanocytes to produce melanin, leading to skin darkening. In humans, its role is less prominent compared to other POMC-derived hormones like ACTH.

Mucous cells are specialized secretory epithelial cells that produce and secrete mucus (mucins). They are found in the surface epithelium of the stomach, in salivary glands (as mucous acinar cells), and elsewhere. Their secretions serve to lubricate, protect, and hydrate epithelial surfaces. The mucin granules often stain lightly with H&E, giving the cytoplasm a clear or foamy appearance.

Neuroendocrine cells are specialized cells that possess properties of both neurons (they receive neural input and may contain dense-core vesicles) and endocrine cells (they secrete hormones or peptides into the bloodstream). They are found scattered in various epithelia (e.g., lungs, GI tract) and in dedicated glands (adrenal medulla, pituitary). They release substances like serotonin, gastrin, or catecholamines in response to neuronal or chemical stimuli.

Pancreatic ductal cells form the lining of the ductal network that transports digestive enzymes from the acini and bicarbonate-rich fluid from the centroacinar cells to the duodenum. They modify the pancreatic juice by secreting bicarbonate ions (HCO3-) to neutralize gastric acid. They express CFTR, and mutations here cause cystic fibrosis-related pancreatic disease. They can also act as progenitor cells in certain contexts.

Podocytes are highly specialized epithelial cells in the Bowman's capsule of the kidney glomerulus. They wrap around capillaries with primary and secondary foot processes. The slits between these foot processes, covered by the slit diaphragm, form the final filtration barrier preventing proteins from entering the urine. Podocyte injury or loss leads to proteinuria and glomerular diseases like focal segmental glomerulosclerosis (FSGS).

In the kidney's collecting duct, principal cells are the most abundant cell type. They are responsible for the final regulation of water, sodium, and potassium balance. They express aquaporin-2 channels on their apical membrane (inserted in response to vasopressin/ADH) for water reabsorption. They also reabsorb sodium via ENaC channels and secrete potassium, processes regulated by aldosterone.

These cells line the proximal convoluted tubule (PCT) of the nephron, the first and longest segment. They are responsible for the bulk reabsorption of filtered nutrients (glucose, amino acids), ions (sodium, chloride, bicarbonate), and water (~65%). Their apical surface has a dense brush border of microvilli to increase surface area. They also actively secrete organic acids and bases into the filtrate.

Retinal pigment epithelium (RPE) cells form a monolayer between the neural retina and the choroid. They are crucial for photoreceptor health: they phagocytose shed photoreceptor outer segments, recycle visual pigments, absorb scattered light (melanin), transport nutrients, and form the outer blood-retinal barrier. RPE dysfunction leads to age-related macular degeneration and other retinal diseases.

Serous cells are protein-secreting epithelial cells found in exocrine glands like the salivary glands (parotid) and pancreatic acini. Their secretory granules contain enzymes (e.g., amylase in saliva, digestive enzymes in pancreas). The granules often stain darkly with H&E. They typically have a round nucleus and basophilic cytoplasm due to abundant rough ER for protein synthesis.

Somatotropes are endocrine cells in the anterior pituitary gland that produce and secrete growth hormone (GH or somatotropin). GH secretion is stimulated by growth hormone-releasing hormone (GHRH) and inhibited by somatostatin from the hypothalamus. GH promotes growth in children by stimulating liver production of insulin-like growth factor 1 (IGF-1) and has metabolic effects in adults (e.g., lipolysis).

Squamous cells are thin, flat, scale-like epithelial cells. Simple squamous epithelium (e.g., endothelium, alveolar lining) facilitates diffusion and filtration. Stratified squamous epithelium (e.g., skin epidermis, oral mucosa, esophagus) provides protection against abrasion and pathogens. The outermost cells may be keratinized (skin) or non-keratinized (esophagus). Their shape minimizes friction and allows for easy sloughing and replacement.

Thyrotropes are endocrine cells in the anterior pituitary gland that produce and secrete thyroid-stimulating hormone (TSH or thyrotropin). TSH secretion is stimulated by thyrotropin-releasing hormone (TRH) from the hypothalamus. TSH acts on the thyroid gland to stimulate the synthesis and release of thyroid hormones (T3 and T4), which are critical for regulating metabolism, growth, and development.

Urothelial cells (transitional epithelial cells) line the urinary tract from renal pelvis to urethra. They form a distensible, impermeable barrier. The superficial umbrella cells have a unique apical plaque of uroplakin proteins and can change shape (from cuboidal to squamous) as the bladder fills and stretches, preventing urine from leaking into underlying tissues. This epithelium also protects against toxic substances in urine.

Peritubular myoid cells are smooth muscle-like cells that surround the seminiferous tubules in the testes. They contract rhythmically to help move sperm and testicular fluid through the tubules. They also secrete extracellular matrix components and growth factors, providing structural support and contributing to the microenvironment necessary for spermatogenesis within the tubules.

Sertoli cells are the "nurse" or sustentacular cells within the seminiferous tubules of the testes. They create the blood-testis barrier, provide structural and nutritional support to developing sperm cells (spermatogenesis), phagocytose residual bodies, and secrete fluid, androgen-binding protein (ABP), and hormones like inhibin and anti-Müllerian hormone (AMH). They are essential for male fertility.

Leydig cells (or interstitial cells) are steroidogenic cells located in the connective tissue between the seminiferous tubules of the testes. Their primary function is the production and secretion of testosterone, stimulated by LH from the pituitary. Testosterone is essential for male sexual differentiation, development of secondary sexual characteristics, spermatogenesis, and maintenance of libido and muscle mass.

Adipocytes (fat cells) are the primary cells of adipose tissue, specialized in storing energy as triglycerides within a large, single lipid droplet (white adipocytes) or in dissipating energy as heat via uncoupling protein 1 (UCP1) in numerous smaller droplets (brown/beige adipocytes). White adipocytes also secrete hormones (leptin, adiponectin) and cytokines, making adipose tissue an important endocrine organ involved in metabolism and inflammation.

Endoneurial cells are fibroblasts and other stromal cells found within the endoneurium, the delicate connective tissue surrounding individual nerve fibers (axons and their Schwann cells) within a peripheral nerve fascicle. They produce and maintain the extracellular matrix of the endoneurial space, providing structural support and contributing to the microenvironment that supports axonal health and regeneration.

Epineurial cells are fibroblasts and other connective tissue cells that constitute the epineurium, the outermost and toughest connective tissue sheath of a peripheral nerve. It surrounds the entire nerve trunk, binding together the nerve fascicles. Its cells produce dense collagen, providing mechanical strength and protection for the nerve against stretching and compression injuries.

Fibroblasts are the most common cells of connective tissue. They synthesize and secrete the extracellular matrix (ECM) components, including collagen, elastin, and fibronectin, providing structural and biochemical support to surrounding cells. They are key players in wound healing, where they proliferate, migrate to the injury site, and differentiate into contractile myofibroblasts to close wounds. They also communicate with immune and epithelial cells.

Chondrocytes found in fibrocartilage, a tough tissue in intervertebral discs, menisci, and tendon-bone junctions. These cells produce an extracellular matrix rich in type I collagen (in addition to type II) and proteoglycans, giving the tissue great tensile strength and resistance to compression and shear forces. Their phenotype is distinct from that of hyaline cartilage chondrocytes.

Folliculostellate cells are non-endocrine, sustentacular-like cells found in the anterior pituitary gland. They form a network surrounding the hormone-producing endocrine cells. They produce growth factors and cytokines, regulate blood flow and the local microenvironment, phagocytose debris, and may coordinate the activity of pituitary endocrine cells through gap junctions and paracrine signaling.

Chondrocytes in a healthy, steady-state articular cartilage. They maintain a careful balance between anabolic (synthesizing collagen type II, aggrecan) and catabolic activities to preserve the structural and functional integrity of the cartilage matrix. They are typically quiescent, embedded in lacunae, and rely on diffusion from synovial fluid for nutrients.

Mesenchymal cells are a broad category of cells derived from the mesoderm. They include fibroblasts, adipocytes, osteoblasts, chondrocytes, and muscle cells. In development, they give rise to connective tissues, bone, cartilage, and blood vessels. Mesenchymal stem/stromal cells (MSCs) are multipotent adult cells that can differentiate into these lineages and have immunomodulatory properties, holding potential for regenerative medicine.

Pericytes are contractile mesenchymal cells that wrap around the endothelial cells of capillaries and venules. They are embedded in the basement membrane and are crucial for vascular stability, regulating blood flow, promoting endothelial survival, and participating in the formation and maintenance of the blood-brain barrier. They also have stem cell properties and can differentiate into other mesenchymal cells during tissue repair.

Chondrocytes attempting to repair damaged cartilage matrix. They may increase anabolic activity, upregulating synthesis of collagen and proteoglycans in response to injury or mild degradation signals. However, in adult articular cartilage, this reparative capacity is very limited and often insufficient to counteract the catabolic processes in degenerative joint disease.

In the liver, hepatic stellate cells (HSCs) reside in the space of Disse. In their quiescent state, they store vitamin A. Upon liver injury, they activate, proliferate, and transform into myofibroblast-like cells that produce large amounts of extracellular matrix, driving liver fibrosis and cirrhosis. Pancreatic stellate cells play a similar fibrogenic role in pancreatitis and pancreatic cancer.

Stromal cells in human. 101,901 cells across 16 tissues.

Cardiomyocytes are the striated muscle cells that constitute the cardiac muscle of the heart. They are responsible for generating the contractile force that pumps blood. They are connected end-to-end by intercalated discs containing gap junctions for electrical coupling and desmosomes for mechanical attachment. Unlike skeletal muscle, they are mononucleated or binucleated and have intrinsic automaticity (pacemaker cells).

Satellite cells are the resident stem cells of skeletal muscle, located between the basal lamina and the sarcolemma of muscle fibers. They are normally quiescent but activate, proliferate, and differentiate into myoblasts in response to injury or exercise. They fuse with existing fibers or with each other to form new myofibers, enabling muscle growth and repair.

Skeletal myonuclei are the multiple nuclei contained within a single, multinucleated skeletal muscle fiber (myofiber). They are post-mitotic and are responsible for gene expression to maintain the massive cytoplasmic volume of the myofiber. They are evenly distributed, but in some muscle types, they may be clustered near the neuromuscular junction or myotendinous junction.

Smooth muscle cells (SMCs) are involuntary, non-striated muscle cells found in the walls of hollow organs (e.g., blood vessels, gut, bladder, uterus). They are spindle-shaped with a single central nucleus. They contract slowly and can maintain tension for long periods (tonus). Contraction is regulated by the autonomic nervous system, hormones, and local factors (e.g., nitric oxide, endothelin).

In skeletal muscle, myonuclei within slow-twitch (Type I) muscle fibers. These fibers are oxidative, fatigue-resistant, and suited for endurance. Their myonuclei govern the expression of genes for mitochondrial proteins, myosin heavy chain I, and other components defining the slow, aerobic metabolic phenotype of the fiber.

In skeletal muscle, myonuclei within fast-twitch (Type II) muscle fibers. These fibers are glycolytic, generate more force but fatigue quickly. Type II myonuclei (subtypes IIa, IIx/d) govern the expression of genes for glycolytic enzymes, fast myosin heavy chains, and other components defining the fast, anaerobic metabolic phenotype of the fiber.

Vascular Smooth Muscle Cells (Muscle cells) in species SP202. Single-cell UMAP atlas.

Endothelial cells form a single layer (the endothelium) lining the interior surface of all blood and lymphatic vessels. They are more than a passive barrier; they actively regulate vascular tone, blood clotting (hemostasis), inflammation, immune cell trafficking, and angiogenesis. They produce key molecules like nitric oxide (vasodilation), endothelin-1 (vasoconstriction), and von Willebrand factor. Dysfunction is central to cardiovascular diseases.

Spermatocytes are developing male germ cells that undergo meiosis. Primary spermatocytes (diploid, 4N DNA) result from spermatogonial mitosis. They undergo Meiosis I to form two secondary spermatocytes (haploid, 2N DNA). Secondary spermatocytes rapidly undergo Meiosis II to produce four spermatids (haploid, 1N DNA). This process occurs within the seminiferous tubules, supported by Sertoli cells.

Spermatogonia are the undifferentiated germ stem cells located on the basement membrane of the seminiferous tubules. They undergo mitotic divisions to self-renew and produce a population of cells committed to differentiation (primary spermatocytes). Type A spermatogonia are the stem cell reservoir, while Type B spermatogonia are committed progenitors. They are the foundation of lifelong sperm production.

Intercalated cells are specialized cells found in the collecting ducts of the kidney nephron. They are critical for regulating systemic acid-base balance. There are two main types: Type A (alpha) cells secrete protons (H+) via H+-ATPase pumps and reabsorb bicarbonate, correcting acidosis. Type B (beta) cells secrete bicarbonate and reabsorb protons, correcting alkalosis. They also play a role in potassium balance.

Mesothelial cells form a monolayer (the mesothelium) that lines the body's serous cavities (pleural, pericardial, peritoneal) and covers the outer surface of internal organs. They produce a lubricating serous fluid that allows organs to move smoothly. They also provide a protective barrier, participate in immune surveillance and inflammation, and can undergo transition to a fibroblast-like phenotype (mesothelial-to-mesenchymal transition) in pathology.

Ribosomal protein-enriched cells in human. 2,198 cells across 1 tissues.

Translation machinery-rich cells (Other) in species SP202. Single-cell UMAP atlas.

Mitochondrial-rich cells (Other) in species SP202. Single-cell UMAP atlas.

Salivary gland cells (Other) in species SP202. Single-cell UMAP atlas.

Cycling cells are cells actively progressing through the cell cycle (G1, S, G2, and M phases), typically identified by expression of proliferation markers such as MKI67 and TOP2A. In single-cell atlases they represent a transient proliferative state rather than a fixed lineage and can arise from multiple progenitor or stem cell populations within a tissue. Their abundance reflects the turnover and regenerative activity of the tissue sampled.

Salivary gland secretory cells (Other) in species SP202. Single-cell UMAP atlas.