Theory of Confocal Microscopy

Fluorochrome Data Table

As a guide to fluorophores for confocal and widefield fluorescence microscopy, the table presented below lists many commonly-used fluorochromes, with their respective peak absorption and emission wavelengths and suggested laser illumination sources. While the authors assume responsibility for the accurate reporting of the data as published in various reliable sources, several caveats must be given. Fluorochrome dyes are environmentally sensitive and different results will be obtained with different solvents and applications. In reviewing the literature, one will frequently find somewhat different data supplied for the identical fluorochrome. There are also, in many instances, several sub-varieties of a fluorochrome.

The Handbook of Fluorescent Probes and Research Chemicals, published by Molecular Probes, Inc. in Eugene, Oregon is a rich source of information about fluorochrome dyes. Also, consult the publications of Omega Optical and Chroma Technology.

Fluorochrome Peak Absorption and Emission Wavelengths

Fluorochrome Absorption Wavelength Emission Wavelength Suggested Laser Acid Fuchsin 540 630 Green He-Ne ACMA (Aminochloromethoxyacridine) 430 474 Blue Diode Acridine Orange (Bound to DNA) 502 526 Argon-Ion Acridine Red 455-600 560-680 Argon-Ion Acridine Yellow 470 550 Argon-Ion Acriflavin 436 520 Blue Diode AFA (Acriflavin Feulgen SITSA) 355-425 460 Blue Diode Alexa Fluor 350 346 442 Helium-Cadmium Alexa Fluor 405 401 421 Blue Diode Alexa Fluor 430 433 541 Blue Diode Alexa Fluor 488 495 519 Argon-Ion Alexa Fluor 500 503 525 Argon-Ion Alexa Fluor 514 518 540 Argon-Ion Alexa Fluor 532 532 553 Krypton-Argon Alexa Fluor 546 556 573 Green He-Ne Alexa Fluor 555 555 565 Krypton-Argon Alexa Fluor 568 578 603 Krypton-Argon Alexa Fluor 594 590 617 Orange He-Ne Alexa Fluor 610 612 628 Orange He-Ne Alexa Fluor 633 632 647 Red He-Ne Alexa Fluor 647 650 665 Krypton-Argon Alexa Fluor 660 663 690 Red Diode Alexa Fluor 680 679 702 Red Diode Alizarin Complexon 530-560 580 Green He-Ne Alizarin Red 530-560 580 Green He-Ne AMCA 350 445 Helium-Cadmium Aminoactinomycin D 555 655 Krypton-Argon 6-Aminoquinoline 355 550 Helium-Cadmium Aniline Blue 370 509 Argon-Ion ANS (Anilinonaphthalene Sulfonic Acid) 385 485 Blue Diode Anthroyl Stearate 361-381 446 Argon-Ion APC (Allophycocyanin) 650 661 Krypton-Argon Astrazon Brilliant Red 4G 500 585 Argon-Ion Astrazon Orange R 470 540 Argon-Ion Astrazon Red 6B 520 595 Argon-Ion Astrazon Yellow 7 GLL 450 480 Argon-Ion Atabrine 436 490 Blue Diode ATTO-TAG CBQ 465 560 Argon-Ion ATTO-TAG FQ 486 591 Argon-Ion Auramine O 460 550 Argon-Ion Aurophosphine 450-490 515 Argon-Ion Aurophosphine G 450 580 Argon-Ion BAO 9-(Bisaminophenyloxadiazole) 365 395 Argon-Ion BCECF 505 530 Argon-Ion Berberine Sulphate 430 550 Blue Diode Bisbenzamide 360 600-610 Helium-Cadmium BOBO-1, BO-PRO-1 462 481 Argon-Ion BOBO-3, BO-PRO-3 570 604 Krypton-Argon Blancophor FFG Solution 390 470 Blue Diode Blancophor SV 370 435 Argon-Ion BODIPY FL 503 512 Argon-Ion BODIPY TMR 542 574 Green He-Ne BODIPY TR 589 617 Yellow He-Ne BODIPY 492/515 490 515 Argon-Ion BODIPY 493/503 500 506 Argon-Ion BODIPY 500/510 509 515 Argon-Ion BODIPY 505/515 502 510 Argon-Ion BODIPY 530/550 533 550 Krypton-Argon BODIPY 558/568 558 568 Krypton-Argon BODIPY 564/570 564 570 Krypton-Argon BODIPY 581/591 582 590 Yellow He-Ne BODIPY 630/650 625 640 Red He-Ne BODIPY 650/665 647 665 Red He-Ne BODIPY 665/676 665 676 Red Diode Brilliant Sulphoflavin FF 430 520 Blue Diode BTC (Benzothiazole Calcium Indicator) 401, 464 529 Blue Diode Calcein 494 517 Argon-Ion Calcein Blue 370 435 Argon-Ion Calcium Crimson 590 611 Yellow He-Ne Calcium Green 505 532 Argon-Ion Calcium Orange 549 576 Green He-Ne Calcofluor (RW Solution) 370 440 Argon-Ion Calcofluor White 440 500-520 Blue Diode Calcofluor White (ABT Solution) 380 475 Argon-Ion Calcofluor White (Standard Solution) 365 435 Argon-Ion Carbocyanine LDL 520 560 Argon-Ion 5-(and 6-)-Carboxy SNARF-1 Indicator 548 (Low pH) 576 (High pH) 587 (Low pH) 635 (High pH) Krypton-Argon 5-Carboxynaphthofluorescein 598 668 Yellow He-Ne 6-Carboxyrhodamine 6G 525 555 Argon-Ion Cascade Blue 400 425 Blue Diode Cascade Yellow 402 545 Blue Diode Catecholamine 410 470 Blue Diode CCF2 (GeneBLAzer) 402 520 Blue Diode CellTracker Blue 353 466 Helium-Cadmium CellTracker Green BODIPY 522 529 Argon-Ion CFDA (Carboxyfluorescein Diacetate) 495 520 Argon-Ion Chinacrine 450-490 515 Argon-Ion Chromomycin A3 450 570 Argon-Ion CL-NERF 504 (Low pH) 514 (High pH) 587 (Low pH) 540 (High pH) Argon-Ion Coriphosphine O 460 575 Argon-Ion Coumarin-Phalloidin 387 470 Blue Diode CPM (Coumarin-Maleimide) 385 465 Blue Diode CTC Formazan 450 630 Argon-Ion Cy2 489 506 Argon-Ion Cy3 548 562 Green He-Ne Cy3.1.8 554 568 Krypton-Argon Cy3.5 581 596 Krypton-Argon Cy5 650 670 Krypton-Argon Cy5.1.8 649 666 Krypton-Argon Cy5.5 675 695 Red Diode Cy7 710 805 Near-Infrared DANS 340 525 Helium-Cadmium DANSA 340-380 430 Helium-Cadmium Dansyl Cadaverine 335 518 Helium-Cadmium Dansyl Chloride 335 500 Helium-Cadmium Dansyl Hydrazine 336 531 Helium-Cadmium DAO (Diaminophenyloxydiazole) 280 460 Helium-Cadmium DAPI 350 470 Helium-Cadmium Dapoxyl 373 574 Argon-Ion Di-4-ANEPPS 496 705 Argon-Ion Di-8-ANEPPS 488 605 Argon-Ion DiA 456 590 Argon-Ion DiD (DilC18(5)) 644 665 Krypton-Argon DIDS 341 414 Helium-Cadmium DiI-C18(3) 549 565 Green He-Ne Dimethylamino-5-Sulphonic Acid 310-370 520 Helium-Cadmium DiO-C18(3) 484 501 Argon-Ion Diphenyl Brilliant Flavine 7GFF 430 520 Blue Diode DM-NERF 497 (Low pH) 510 (High pH) 527 (Low pH) 536 (High pH) Argon-Ion DPH (Diphenylhexatriene) 351 430 Helium-Cadmium Dopamine 340 490-520 Helium-Cadmium DsRFP (Ds Red Fluorescent Protein) 558 583 Green He-Ne ELF-97 Alcohol 345 530 Helium-Cadmium EBFP (Enhanced Blue FP) 380 440 Blue Diode ECFP (Enhanced Cyan FP) 433, 453 475, 501 Blue Diode EGFP (Enhanced GFP) 488 507 Argon-Ion ERTracker Blue/White DPX 374 575 Argon-Ion EYFP (Enhanced Yellow FP) 513 527 Argon-Ion Eosin 525 545 Argon-Ion Erythrosin Isothiocyanate 530 558 Argon-Ion Ethidium Bromide 510 595 Argon-Ion Ethidium Homodimer 528 617 Argon-Ion Euchrysin 430 540 Blue Diode Evans Blue 550 610 Green He-Ne FAM (5-Carboxyfluorescein) 492 518 Argon-Ion Fast Blue 360 410 Helium-Cadmium FDA (Fluorescein Diacetate) 495 520 Blue Diode Flazo Orange 375-530 612 Argon-Ion Fluorescamine 390 460 Blue Diode Fluorescein 494 518 Argon-Ion Fluorescein Isothiocyanate (FITC) 490 525 Argon-Ion Fluo-3 485 503 Argon-Ion Fluo-4 494 516 Argon-Ion FluoroEmerald 494 520 Argon-Ion FluoroGold (Hydroxystilbamidine) 323 (Low pH) 368 (High pH) 408 (Low pH) 565 (High pH) Helium-Cadmium FluoroJade 425 510 Blue Diode FluoroRuby 555 582 Krypton-Argon FluorX 494 520 Argon-Ion FM1-43 479 598 Argon-Ion FM4-64 515 640 Argon-Ion Formaldehyde Induced Fluorescence 405 435 Blue Diode Fura-2 363 (Low [Ca]) 335 (High [Ca]) 512 (Low [Ca]) 505 (High [Ca]) Helium-Cadmium Fura Red 472 (Low [Ca]) 436 (High [Ca]) 657 (Low [Ca]) 637 (High [Ca]) Argon-Ion Genacryl Brilliant Red B 520 590 Argon-Ion Genacryl Brilliant Yellow 10GF 430 485 Blue Diode Genacryl Pink 3G 470 583 Argon-Ion Genacryl Yellow 5GF 430 475 Blue Diode GFP (Green Fluorescent Protein) 395, 475 510 Blue Diode Gloxalic Acid 405 460 Blue Diode Granular Blue 355 425 Helium-Cadmium Haematoporphyrin 530-560 580 Green He-Ne Hoechst 33258, 33342 (Bound to DNA) 352 461 Helium-Cadmium 3-Hydroxypyrene-5,8,10-TriSulfonic Acid 403 513 Blue Diode 7-Hydroxy-4-methylcoumarin 360 455 Helium-Cadmium 5-Hydroxy-Tryptamine (5-HT) 380-415 520-530 Blue Diode 1,5-IAEDANS 336 482 Helium-Cadmium Indo-1 350 405-482 Helium-Cadmium Indodicarbocyanine 644 665 Krypton-Argon Intrawhite Cf (Liquid) 360 430 Helium-Cadmium JC-1 514 529 Argon-Ion 6-JOE 525 555 Argon-Ion JOJO-1, JO-PRO-1 529 545 Argon-Ion Leucophor PAF 370 430 Argon-Ion Leucophor SF 380 465 Argon-Ion Leucophor WS 395 465 Blue Diode Lissamine Rhodamine B200 (RD200) 575 595 Krypton-Argon LOLO-1, LO-PRO-1 565 579 Krypton-Argon Lucifer Yellow CH 425 528 Blue Diode Lucifer Yellow VS 430 535 Blue Diode LysoSensor Blue DND-192, DND-167 374 425 Argon-Ion LysoSensor Green DND-153, DND-189 442 505 Argon-Ion LysoSensor Yellow/Blue 384 (Low pH) 329 (High pH) 540 (Low pH) 440 (High pH) Helium-Cadmium LysoTracker Blue 373 422 Argon-Ion LysoTracker Blue/White 466 536 Argon-Ion LysoTracker Green 504 511 Argon-Ion LysoTracker Red 577 590 Krypton-Argon LysoTracker Yellow HCK-123 465 535 Green He-Ne Magdala Red 524 600 Argon-Ion Magnesium Green 506 531 Argon-Ion Magnesium Orange 550 575 Green He-Ne Marina Blue 362 459 Argon-Ion Maxilon Brilliant Flavin 10 GFF 450 495 Argon-Ion Maxilon Brilliant Flavin 8 GFF 460 495 Argon-Ion Merocyanine 540 500 572 Argon-Ion 4-Methylumbelliferone 360 449 Helium-Cadmium Mithramycin 450 570 Argon-Ion MitoFluor Green 490 516 Argon-Ion MitoFluor Red 589 588 622 Yellow He-Ne MitoFluor Red 594 598 630 Orange He-Ne MitoFluor Far Red 680 680 >700 Red Diode MitoTracker Green FM 490 516 Argon-Ion MitoTracker Orange CMTMRos 554 576 Krypton-Argon MitoTracker Red CMXRos 579 599 Krypton-Argon MitoTracker Red 580 581 644 Krypton-Argon MitoTracker Deep Red 633 644 665 Krypton-Argon MPS (Methyl Green Pyronine Stilbene) 364 395 Argon-Ion Monochlorobimane 380 461 Blue Diode Nano Orange 485 590 Argon-Ion NBD 450 530 Argon-Ion Nile Red 515-530 525-605 Argon-Ion Nitrobenzoxadidole 460-470 510-650 Argon-Ion Noradrenaline 340 490-520 Helium-Cadmium Nuclear Fast Red 289-530 580 Argon-Ion Nuclear Yellow 365 495 Argon-Ion Nylosan Brilliant Flavin E8G 460 510 Argon-Ion Olivomycin 430 545 Blue Diode OPT (o-Phthalaldehyde) 340 455 Helium-Cadmium Oregon Green 488 496 524 Argon-Ion Oregon Green 500 503 522 Argon-Ion Oregon Green 514 511 530 Argon-Ion Pacific Blue 410 455 Blue Diode Pararosaniline (Feulgen) 570 625 Krypton-Argon PE-B (Phycoerythrin B) 545 576 Green He-Ne PE-R (Phycoerythrin R) 490, 565 578 Argon-Ion Phorwite AR (Solution) 360 430 Helium-Cadmium Phorwite BKL 370 430 Argon-Ion Phorwite Rev 380 430 Argon-Ion Phorwite RPA 375 430 Argon-Ion Phosphine 3R 465 565 Argon-Ion Phosphine R 480-565 578 Argon-Ion Phycocyanin C 620 648 Orange He-Ne Phycocyanin R 618 642 Orange He-Ne PKH26 551 567 Green He-Ne Pontochrome Blue Black 535-553 605 Green He-Ne POPO-1, PO-PRO-1 434 456 Blue Diode POPO-3, PO-PRO-3 534 572 Green He-Ne Primuline O 410 550 Blue Diode Procion Yellow 470 600 Argon-Ion Propidium Iodide 536 617 Green He-Ne PyMPO 415 570 Blue Diode Pyrene 345 378 Helium-Cadmium Pyronin Y 540 570 Green He-Ne Pyronine 410 540 Blue Diode Pyronine B 540-590 560-650 Krypton-Argon Pyrozal Brilliant Flavin 7GF 365 495 Argon-Ion Qdot 525 350-450 525 Blue Diode Qdot 525 350-525 565 Blue Diode Qdot 585 350-550 585 Blue Diode Qdot 605 350-575 605 Blue Diode Qdot 655 350-600 655 Blue Diode Quinacrine Mustard 423 503 Blue Diode Resorufin 570 585 Krypton-Argon RH 414 532 716 Argon-Ion Rhod-2 550 571 Green He-Ne Rhodamine 110 496 520 Argon-Ion Rhodamine 123 511 534 Argon-Ion Rhodamine 5 GLD 470 565 Argon-Ion Rhodamine 6G 526 555 Argon-Ion Rhodamine B 540 625 Green He-Ne Rhodamine B 200 523-557 595 Green He-Ne Rhodamine B Extra 550 605 Green He-Ne Rhodamine BB 540 580 Green He-Ne Rhodamine BG 540 572 Green He-Ne Rhodamine Green 502 527 Argon-Ion Rhodamine Red 570 590 Krypton-Argon Rhodamine WT 530 555 Argon-Ion Rhodol Green 499 525 Argon-Ion RITC (Rhodamine B Isothiocyanate) 570 595 Krypton-Argon Rose Bengal 540 550-600 Green He-Ne ROX (Carboxy-X-Rhodamine) 574 602 Krypton-Argon SBFI 334 525 Helium-Cadmium Serotonin 365 520-540 Argon-Ion Sevron Brilliant Red 2B 520 595 Argon-Ion Sevron Brilliant Red 4G 500 583 Argon-Ion Sevron Brilliant Red B 530 590 Argon-Ion Sevron Orange 440 530 Blue Diode Sevron Yellow L 430 490 Blue Diode SITS (Stilbeneisothiosulphonic Acid) 337 436 Helium-Cadmium Sodium Green 507 535 Argon-Ion Spectrum Aqua 433 480 Blue Diode Spectrum Green 497 524 Argon-Ion Spectrum Orange 559 588 Krypton-Argon Spectrum Red 604 624 Orange He-Ne Stilbene 335 440 Helium-Cadmium Sulforhodamine 101 586 605 Yellow He-Ne Sulforhodamine B 565 586 Krypton-Argon Sulforhodamine G 529 548 Argon-Ion SYTOX Blue 444 480 Blue Diode SYTOX Green 504 523 Argon-Ion SYTOX Orange 547 570 Green He-Ne TAMRA (Carboxytetramethylrhodamine) 542 568 Green He-Ne Tetracycline 390 560 Blue Diode Texas Red 596 615 Yellow He-Ne Thiazine Red R 510 580 Argon-Ion Thiazole Orange 453 480 Argon-Ion Thioflavin S 430 550 Blue Diode Thioflavin TCN 350 460 Helium-Cadmium Thiolyte 370-385 477-484 Argon-Ion Tinopol CBS 390 430 Blue Diode TOTO 1, TO-RRO-1 514 533 Argon-Ion TOTO 3, TO-PRO-3 642 661 Krypton-Argon TRITC 557 576 Krypton-Argon True Blue 365 420-430 Argon-Ion Ultralite 656 678 Krypton-Argon Uranine B 420 520 Blue Diode Uvitex SFC 365 435 Argon-Ion X-Rhodamine 580 605 Krypton-Argon Xylenol Orange 546 580 Green He-Ne XRITC (X-Rhodamine Isothiocyanate) 582 601 Krypton-Argon YOYO-1, YO-PRO-1 491 509 Argon-Ion YOYO-3, YO-PRO-3 612 631 Orange He-Ne

Although the data presented in this table have been checked for accuracy, it is strongly urged that the properties for a particular fluorophore be confirmed by first consulting the dye manufacturer to secure a full specification of the spectral profiles for absorption and emission prior to launching experiments. In addition, the suggested lasers are intended as a reference guide only, and in many cases, alternative illumination sources may produce superior results.

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