Table 1 Reporter systems to track different immune cells and their functions by single-cell imaging.

This list serves as a general survey of intravital imaging labeling strategies across cell types; however, numerous Cre strains can additionally be incorporated into useable reporter systems. CFP, cyan fluorescent protein; DsRed, Discosoma sp. red fluorescent protein; FOXP3, forkhead box P3; TBX21, T-box 21; eGFP, enhanced GFP; Bcl6, B cell lymphoma 6; pDCs, plasmacytoid DCs; Zbtb46, zinc finger and BTB domain containing 46; Csf-1, colony-stimulating factor 1; AID, activation-induced cytidine deaminase; DTR, diphtheria toxin receptor.

T cells
GFP, CFP, DsRedRequires adoptive cell transfer(29)
PA-GFPPhotoactivatable fluorescent reporter useful for cell tracking; requires adoptive
cell transfer
DPE -GFPA pan T cell marker; can also label pDCs(25)
NFAT-GFP, NFAT-YFP;H2B-mCherryReadout of TCR signaling(43)
IFN-γ–YFPSubset of activated T cells; can also be produced by NK cells(25)
IL-10–GFPSubset of T cells; can also be expressed by macrophages(43)
FOXP3-GFP, FOXP3-mRFPLabels Treg cells; FOXP3 is on the X chromosome, be aware of X chromosome
inactivation in females
Nur77-GFPLabels T cells and also B cells upon antigen receptor engagement(110)
Granzyme B–TdTomatoA marker of granule exocytosis in cytolytic T cells and NK cells(111)
Tbx21-ZsGreenFor assessing TH1 responses in T cells(112)
CD2-eGFPLabels peripheral T cells and some NK subsets(113)
IL-17F–CreeYFPMany variants exist for studying TH17 cells in vivo(114)
IL-4–eGFPUsed to assess TH2 immunity(115)
IL-21–GFPUsed to study the role of TFH cells(116)
B cells
GFP, CFP, DsRedRequires adoptive cell transfer(117)
PA-GFPPhotoactivatable fluorescent reporter useful for cell tracking; requires adoptive
cell transfer
CD19-tdRFPExpressed by numerous B cells, adoptive transfer may be necessary if tissues are
densely infiltrated by B cells
Bcl6-YFPA B cell marker already validated for two-photon microscopy; also labels TFH cells(118)
Blimp-1–YFPExpressed by B cells and highly expressed in plasma cells(119)
Activation-induced cytidine deaminase (AID)–GFPSubset of B cells(120)
CD11c(ITGAX)-YFP, CD11c-mCherryCells other than DCs can express CD11c(121)
XCR1-Venus/+Homozygous mice are null for XCR1(55)
XCR1-KIKGR/+Xcr1 replaced with photoconvertible fluorescent protein Kikume
Green-Red (KikGR)
CXCL9-RFP, CXCL10-BFPThese chemokines can also be expressed by other cell types, including monocytes,
macrophages, granulocytes, and nonimmune cells
SIGLEC-H–GFPExpressed by pDCs(54)
Flt3-BFP2This construct has also been incorporated into a genetic model used to visualize
DCs, macrophages, and CD4+ and CD8+ T cells simultaneously (Flt3-BFP2,
Mertk-GFP–diphtheria toxin receptor, Cd4-tdTomato, Cd8a-tdTomato)
Zbtb46-GFPA cDC marker that may be expressed in erythroid and endothelial populations(122)
CX3CR1-GFP/+This chemokine receptor can also be expressed by T cells, NK, DC, and
macrophages. Homozygous mice are null for CX3CR1
CCR2-RFP/+Homozygous mice are null for CCR2(61)
CX3CR1-GFP/+;CCR2-RFP/+Homozygous mice are null for CX3CR1 and/or CCR2(61)
Mertk-GFP-DTRHomozygous mice are null for MerTK(11)
c-fms–GFPc-fms is also known as Csf-1 receptor(60)
MacBlueA gal4-responsive UAS-ECFP cassette also under the Csf-1 receptor promoter(124)
Dye-conjugated ferumoxytolAdministered to mice several hours before imaging(25)
Dye-conjugated dextrans and dextran nanoparticlesAdministered to mice several hours before imaging; can be used to label blood
vessels in short term after administration
Dye-conjugated anti-CD169 mAbUsed to label SCS macrophages(125)
Dye-conjugated anti-F4/80 mAbA pan macrophage marker in mice(61)
Dye-conjugated anti–Ly-6G mAbImaging is performed shortly after administration (~15 min)(126)
Dye-conjugated anti–Gr-1 mAbImaging is performed shortly after administration (~15 min)(126)
LysM-GFPCan also be expressed by macrophages(77)
Dye-conjugated anti-neutrophil elastase mAbImaging is performed shortly after administration (~15 min)(85)
CXCL12-mRFPCan also be expressed by stromal cells(80)
SYTOX GreenUsed to visualize NETs (extracellular DNA labeling); also demarcates cell death(85)
Innate lymphocytes
GFP, CFP, DsRedRequires adoptive cell transfer(92)
CXCR6-GFPCan be used to track ILCs and iNKT cells but is also expressed by some T cells(89)
Megakaryocytes and platelets
PF4-cre tdTomatoLabels megakaryocytes as well as platelets, which are defined based on their
smaller size
Dye-conjugated anti-CD49b mAbLabels all platelets(85)
CD41-YFPki/+Labels a fraction of platelets(85)
HSC-derived cells
GFP, CFP, DsRedRequires adoptive cell transfer and is used to track HSCs and their progeny(84)
Nonimmune components
Dye-conjugated anti–Lyve-1 mAbLabels lymphatics(45)
AngioSPARKLabels blood vessels(71)
Second-harmonic generationApplicable to multiphoton (not confocal) microscopy; enables visualization of
collagen fibers
IL-7–eCFPExpressed by stromal cells in thymus and bone marrow(44)
GCaMP6sSensor of calcium flux; relevant in the context of, for example, virus-infected cells(39)
qDotsBright, highly tunable fluorophores surface-engineered to maximize circulation(127)
IsolectinUsed to label endothelial wall of blood vessels(128)
Hoechst33342 and CellTracker dyesIndiscriminately labels cell nuclei or cytosol; often used for adoptive cell transfer(41)