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Short answer: BODIPY is a family of fluorescent dyes built on a boron-containing core, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene. The name is a registered trademark. Most variants fluoresce green, such as BODIPY FL (about 503/512 nm excitation/emission) and BODIPY 493/503; BODIPY 581/591 is red until oxidised, then shifts to green. This page is general reference for lab staff, not a protocol.
What does BODIPY stand for, and what is the dye?
The Thermo Fisher Molecular Probes Handbook describes BODIPY dyes as a series sharing one core structure, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene, and notes that the dyes are identified with the registered trademark BODIPY. PubMed’s own term mapping also links “BODIPY” to the same chemical name. The sources cited here give the chemical name rather than an expansion of the letters, so the chemical name is the one to quote.
Two properties from the handbook explain its popularity: a narrow emission bandwidth giving higher peak intensity than fluorescein, and greater photostability than fluorescein in some environments. The handbook also says the low polarity of the fluorophore makes BODIPY-containing probes “excellent analogs of biological lipids”.
What color is BODIPY?
It depends on the variant. The table uses values from the Thermo Fisher handbook (BODIPY FL from its text; the other two from its data table, measured in methanol).
| Variant | Excitation / emission (nm) | Color | Use named by the source |
|---|---|---|---|
| BODIPY FL | about 503 / 512 | Green | Green-fluorescent label with a fluorescein-like spectrum |
| BODIPY 493/503 | about 500 / 509 (methanol) | Green | Lipid droplets in fixed and unfixed cells (Spangenburg et al., 2011) |
| BODIPY 581/591 | about 581 / 591 (methanol) | Red, shifting to green on peroxidation | Ratiometric lipid oxidation readout in live cells (handbook) |
Which BODIPY for which question? A decision aid
- Where is the neutral lipid? This is the BODIPY 493/503 use documented by Spangenburg et al. (J Biomed Biotechnol 2011; PMC3180081), who visualised lipid droplets in sectioned skeletal muscle and cultured single fibers. They report it works in fixed and nonfixed cells, with staining that seemed unaffected by permeabilisation, and call it an acceptable alternative and, under certain conditions, a simpler method. For the classic non-fluorescent stain see Oil Red O staining.
- Is lipid oxidation happening? This is the BODIPY 581/591 question. The handbook states that its red fluorescence shifts to green upon peroxidation, so oxidation appears as a fall in red signal (about 590 nm) and a rise in green (about 510 nm).
- I need a general green label. BODIPY FL has fluorescein-like spectra; for the older dye it is compared with, see FITC: spectra, labeling and limits.
What is BODIPY C11?
“C11 BODIPY 581/591” is the name used in the literature for the lipid-peroxidation sensor built on the 581/591 fluorophore. Huang et al. (Int J Mol Sci 2024; PMC10889550) used the “C11 BODIPY 581/591 Lipid Peroxidation Sensor” to show that a treatment reduced lipid peroxidation in erastin-induced cells, and Pham et al. (Clin Mol Hepatol 2026; PMC12835794) compared a new near-infrared probe against “BODIPY 581/591 C11” for lipid peroxidation in ferroptotic hepatocytes. Because lipid peroxidation is central to ferroptosis, the reagent turns up often in that literature; see ferroptosis for the cell-death context.
BODIPY staining: what this page does and does not give
“BODIPY staining” in the lipid-droplet sense means using BODIPY 493/503 as a neutral-lipid stain, as in the muscle study above. Dye concentrations, incubation times and fixation steps vary by tissue and vendor and should come from the instructions for use of the product in hand and the methods section of the paper being reproduced; they are intentionally not listed here.
Common misunderstandings
- BODIPY is one dye. It is a series; color, and what it reports, change with the variant. Match the variant to the question.
- BODIPY stains the cell membrane. The documented use of BODIPY 493/503 in the work cited here is lipid droplets, not plasma-membrane labeling. Where a given conjugate localises depends on the product, so check that product’s documentation.
- Red 581/591 signal alone shows oxidation state. The shift from red to green is the readout, so both channels matter.
- BODIPY and FITC are interchangeable. FITC is the reference green label; BODIPY FL is spectrally similar, but the handbook cites narrower emission and, in some environments, better photostability than fluorescein.
Where it matters in the lab
BODIPY 493/503 emits green (about 509 nm), and oxidised BODIPY 581/591 also emits green (about 510 nm), so the two cannot be told apart in one green detector. Check filter sets and instrument channels against the maxima in the table before combining reagents. This follows from the spectra above rather than from a vendor rule.
FAQ
What does the acronym BODIPY stand for?
BODIPY is a registered trademark for dyes with a 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene core; the Thermo Fisher handbook gives the chemical name rather than spelling out the letters.
What is BODIPY C11?
It is the literature name for the BODIPY 581/591 lipid-peroxidation sensor, whose red fluorescence shifts to green when oxidised.
Does BODIPY stain the cell membrane?
The cited lipid-droplet work with BODIPY 493/503 does not describe membrane staining; localisation depends on the specific conjugate.
What color is BODIPY?
BODIPY FL and BODIPY 493/503 are green (about 512 and 509 nm emission); BODIPY 581/591 is red (about 591 nm) until peroxidised.
Sources
- Thermo Fisher Scientific, Molecular Probes Handbook, BODIPY Dye Series (Section 1.4), read 2026-11-07.
- Spangenburg EE et al., “Use of BODIPY (493/503) to visualize intramuscular lipid droplets in skeletal muscle,” J Biomed Biotechnol 2011;2011:598358, doi:10.1155/2011/598358, PMID 21960738, read 2026-11-07.
- Huang YX et al., Int J Mol Sci 2024;25(4):2315, doi:10.3390/ijms25042315, PMID 38397002, read 2026-11-07.
- Pham LBH et al., Clin Mol Hepatol 2026;32(1):318-338, doi:10.3350/cmh.2025.0779, PMID 41248896, read 2026-11-07.
