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CF® DYES FOR
SUPER-RESOLUTION MICROSCOPY

Superior Performance for Super-Resolution Imaging
CF® Dyes feature exceptional brightness and photoswitching properties ideal for several super-resolution applications
See below for a full list of publications of CF® Dyes being used for super-resolution applications
Get the most out of your STORM CF® Dye antibodies with specialized labeling kits and pre-labeled secondary antibodies with a low degree of labeling optimal for STORM
CF® Dye Spectrum:
CF®350 Dye

CF®350 is a blue fluorescent dye

300400500600700800900Wavelength (nm)CF350
Technical Summary

Abs/Em Maxima: 347/448 nm
Extinction coefficient: 18,000
Molecular weight: ~ 496
Excitation source: UV
Replaces: Alexa Fluor® 350, AMCA,
DyLight® 350

Features

Brighter and more photostable than AMCA
Direct replacement for Alexa Fluor® 350
Highly water soluble and pH-insensitive

CF®405S Dye

Improved brightness & photostability for the 405 nm laser line

300400500600700800900Wavelength (nm)CF405S
Technical Summary

Abs/Em Maxima: 404/431 nm
Extinction coefficient: 33,000
Molecular weight: ~ 1,169
Excitation laser line: 405 nm
Replaces: Alexa Fluor® 405, Cascade Blue®,
DyLight® 405

Features

Brighter than Alexa Fluor®  405
Validated for super-resolution imaging by SIM

CF®405M Dye

Improved brightness & photostability for the 405 nm laser line

300400500600700800900Wavelength (nm)CF405M
Technical Summary

Abs/Em Maxima: 408/452 nm
Extinction coefficient: 41,000
Molecular weight: ~ 503
Excitation laser line: 405 nm
Replaces: Pacific Blue®, BD Horizon™ V450

Features

More photostable than Pacific Blue®, with less spill-over in the green channel

An excellent choice for super-resolution imaging by SIM

CF®430 & CF®440 Dyes

Photostable 405 nm-excitable dyes with green fluorescence

300400500600700800900Wavelength (nm)CF430CF440
Technical Summary

CF®430
Abs/Em Maxima: 426/498 nm
Extinction coefficient: 40,000
Molecular weight: ~429
Excitation laser line: 405 nm
Replaces: Pacific Green®, BD Horizon™ V500,
Krome Orange™

CF®440
Abs/Em Maxima: 440/515 nm
Extinction coefficient: 40,000
Molecular weight: ~716
Excitation laser line: 405 nm
Replaces: Alexa Fluor® 430

Features

Photostable dyes suitable for microscopy
Perfect match for the CFP filter set
Highly water soluble and pH-insensitive
Suitable for flow cytometry in the AmCyan channel

CF®405L Dye

A 405 nm-excitable dye with green fluorescence emission

300400500600700800900Wavelength (nm)CF405L
Technical Summary

Abs/Em Maxima: 395/545 nm
Extinction coefficient: 24,000
Molecular weight: ~1573
Excitation laser line: 405 nm
Replaces: Pacific Orange®

Features

Expands potential detection channels for the 405 nm laser line

CF®450 Dye

A spectrally unique, 405 nm-excitable green dye

300400500600700800900Wavelength (nm)CF450
Technical Summary

Abs/Em Maxima: 450/538 nm
Extinction coefficient: 40,000
Molecular weight: ~689
Excitation laser line: 405 nm

Features

A spectrally unique, 405 nm-excitable green dye.

CF®488A Dye

A superior green fluorescent dye

300400500600700800900Wavelength (nm)CF488A
Technical Summary

Abs/Em Maxima: 490/515 nm
Extinction coefficient: 70,000
Molecular weight: ~914
Excitation laser line: 488 nm
Alternative for: Alexa Fluor® 488, DyLight® 488,
FITC, Cy®2

Features

Minimally charged, for less non-specific binding than Alexa Fluor® 488
Narrower emission spectrum for less bleed to red
Very photostable
Compatible with super-resolution imaging by TIRF
Highly water soluble and pH-insensitive

CF®503R Dye

A spectrally unique green dye ideal for spectral flow cytometry

300400500600700800900Wavelength (nm)CF503R
Technical Summary

Abs/Em maxima: 503/532 nm
Extinction coefficient: 90,000
Molecular weight: ~1100
Excitation laser line: 488 nm
Direct replacement for: ATTO 488

Features

A spectrally unique green dye ideal for spectral flow cytometry

CF®514 Dye

Alternative green fluorescent dye

300400500600700800900Wavelength (nm)CF514
Technical Summary

Abs/Em Maxima: 516/548 nm
Extinction coefficient: 105,000
Molecular weight: ~1216
Excitation laser line: 488 nm
Replaces: Alexa Fluor® 514

Features

Image using the same settings as FITC or CF®488A
Can be distinguished from CF®488A in the same specimen by spectral imaging and linear unmixing

CF®532 Dye

A bright green fluorescent dye for the 532 nm laser

300400500600700800900Wavelength (nm)CF532
Technical Summary

Abs/Em Maxima: 527/558 nm
Extinction coefficient: 96,000
Molecular weight: ~ 685
Excitation laser line: 532 nm
Direct replacement for: Alexa Fluor® 532, Atto 532

Features

Designed for the 532 nm laser
Brighter than Alexa Fluor® 532
Highly water-soluble and pH-insensitive

CF®543 Dye

An orange fluorescent dye ideal for the 543 nm laser

300400500600700800900Wavelength (nm)CF543
Technical Summary

Abs/Em Maxima: 541/560 nm
Extinction coefficient: 100,000
Molecular weight: ~ 870
Excitation laser line: 532 nm, 543 nm, or
546 nm
Direct replacement for: Alexa Fluor® 546,
TAMRA

Features

Optimized for the 543 nm laser
Yields the brightest conjugates among spectrally similar dyes
Highly water-soluble and pH-insensitive

CF®535ST Dye

A red fluorescent dye designed for STORM super-resolution imaging

300400500600700800900Wavelength (nm)CF535ST
Technical Summary

Abs/Em Maxima: 535/568 nm
Extinction coefficient: 95,000
Molecular weight: ~728
Excitation laser line: 532 nm

Features

Designed specifically for super-resolution imaging by STORM

CF®550R Dye

A spectrally unique orange/red dye ideal for spectral flow cytometry

300400500600700800900Wavelength (nm)CF550R
Technical Summary

Abs/Em maxima: 551/577 nm
Extinction coefficient: 100,000
Molecular weight: ~686
Excitation laser line: 532 nm or 568 nm

Features

A spectrally unique orange/red dye ideal for spectral flow cytometry

CF®555 Dye

A bright and photostable orange-red dye

300400500600700800900Wavelength (nm)CF555
Technical Summary

Abs/Em Maxima: 555/565 nm
Extinction coefficient: 150,000
Molecular weight: ~ 901
Excitation laser line: 532 nm or 568 nm
Alternative for: Alexa Fluor®
555, ATTO 550, Cy®3, DyLight® 549,
Rhodamine

Features

Brighter than Cy®3
Highly water-soluble
Validated in multicolor STORM super-resolution imaging

CF®568 Dye

Outshines Alexa Fluor®568

300400500600700800900Wavelength (nm)CF568
Technical Summary

Abs/Em Maxima: 562/584 nm
Extinction coefficient: 100,000
Molecular weight: ~ 714
Excitation laser line: 532 nm or 568 nm
Direct replacement for: Alexa Fluor® 568,
ATTO 565, Rhodamine Red

Features

Yields much brighter antibody conjugates than Alexa
Fluor® 568
Extremely photostable
Excellent choice for multi-color imaging with CF®488A and CF®640R
Compatible with TIRF and multicolor STORM super resolution imaging

CF®570

Bright red fluorescent dye

300400500600700800900Wavelength (nm)CF570
Technical Summary

Abs/Em maxima: 568/591 nm
Extinction coefficient: 150,000
Molecular weight: ~2998
Excitation laser line: 561 to 568 nm
Replaces: Alexa Fluor® 568, ATTO 565, DY-560, Rhodamine Red

Features

Produces antibody conjugates with brighter fluorescence compared to spectrally similar dyes

CF®583 & CF®583R Dyes

Bright red fluorescent dyes

300400500600700800900Wavelength (nm)CF583CF583R
Technical Summary

CF®583 Technical Summary
Abs/Em maxima: 583/606 nm
Extinction coefficient: 150,000
Molecular weight: ~3127
Excitation laser line: 561 to 568 nm
Alternative for: Cy®3.5

CF®583R Technical Summary
Abs/Em maxima: 586/609 nm
Extinction coefficient: 100,000
Molecular weight: ~773
Excitation laser line: 561 to 568 nm
Alternative for: Cy®3.5, Texas Red®

Features

Spectrally similar red fluorescent dyes with exceptional brightness
Serves as an alternative for Cy®3.5 and Texas Red®
Rhodamine-based CF®583R can be used as an excellent energy acceptor for FRET when paired with R-PE

CF®594 Dye

Truly the brightest deep red dye

300400500600700800900Wavelength (nm)CF594
Technical Summary

Abs/Em Maxima: 593/614 nm
Extinction coefficient: 115,000
Molecular weight: ~730
Excitation laser line: 561 to 568 nm
Replaces: Alexa Fluor® 594, DyLight® 594,
Texas Red®

Features

Yields the brightest antibody conjugates among spectrally
similar dyes.
Excellent choice for multicolor imaging with green dyes like CF®488A
Extremely photostable
Also see CF®594ST, a version of CF®594 engineered specifically for STORM microcopy

CF®594ST Dye

Deep red dye for STORM

300400500600700800900Wavelength (nm)CF594ST
Technical Summary

Abs/Em maxima: 593/620 nm
Extinction coefficient: 115,000
Molecular weight: ~868
Excitation laser line: 561 to 568 nm

Features

Designed specifically for super-resolution imaging by STORM

CF®597R Dye

Unique green-excited dye for STORM

4006008001,000Wavelength (nm)CF597R
Technical Summary

Abs/Em Maxima: 597/619 nm
Extinction coefficient: 115,000
Molecular weight: ~800
Excitation laser line: 561 to 568 nm
Replaces: Alexa Fluor® 594, DyLight® 594, ATTO 594

Features

Unique green-excited dye for STORM
Excellent solubility and photochemical switching properties
Validated for multicolor STORM with red-excited dyes

RPE-Astral™616

Novel long Stokes shift tandem dye for flow cytometry multiplexing

3004005006007008009001,000Wavelength (nm)RPE-Astral616
Technical Summary

Abs/Em maxima: 496, 546, 566/617 nm
Laser line: 488, 532, and 561 nm
Spectrally similar to: PE/Dazzle™ 594, PE-CF®594, and PE-DyLight® 594

Features

Exceptional signal-to-noise for flow cytometry
Designed for enhanced FRET performance
Available with flow validated primary antibodies

CF®620R Dye

A bright and photostable far-red dye

300400500600700800900Wavelength (nm)CF620R
Technical Summary

Abs/Em Maxima: 620/643 nm
Extinction coefficient: 115,000
Molecular weight: ~ 738
Excitation laser line: 633 nm or 635 nm
Replaces: LightCycler® Red 640

Features

Highly water-soluble
Highly fluorescent and extremely photostable
Can be used as an excellent energy acceptor for FRET when paired with R-PE

CF®633 Dye

The best dye for 633/635 laser lines

300400500600700800900Wavelength (nm)CF633
Technical Summary

Abs/Em Maxima: 630/650 nm
Extinction coefficient: 100,000
Molecular weight: ~820
Excitation laser line: 633 nm or 635 nm
Alternative for: Alexa Fluor® 633, Alexa Fluor®
647, Cy®5, DyLight® 633, DyLight® 649

Features

Yields the brightest antibody conjugates among spectrally similar dyes
Far more photostable than Alexa Fluor® 647
Compatible with TIRF, FIONA, and gSHRImP super-resolution imaging methods

CF®640R Dye

A highly photostable far-red dye

4006008001,000Wavelength (nm)CF640R
Technical Summary

Abs/Em Maxima: 642/662 nm
Extinction coefficient: 105,000
Molecular weight: ~ 832
Excitation laser line: 633 nm, 635 nm or
640 nm
Alternative for Alexa Fluor® 647, ATTO 647N,
Cy®5, DyLight® 649

Features

Best photostability among Cy®5-like dyes
Yields highly fluorescent protein conjugates
Compatible with TIRF and FLIMP super-resolution microscopy

CF®647 Dye

A highly fluorescent far-red dye

300400500600700800900Wavelength (nm)CF647
Technical Summary

Abs/Em Maxima: 650/665 nm
Extinction coefficient: 240,000
Molecular weight: ~ 1058
Excitation laser line: 633 nm, 635 nm or
640 nm
Alternative for: Cy®5, Alexa Fluor® 647,
DyLight® 649

Features

Brighter than Cy®5
Highly water soluble and pH insensitive
Validated in multi-color super-resolution imaging by STORM

CF®660C & CF®660R

Superior alternatives to Alexa Fluor® 660

300400500600700800900Wavelength (nm)CF660CCF660R
Technical Summary

CF®660C
Abs/Em Maxima: 667/685 nm
Extinction coefficient: 200,000
Molecular weight: ~ 3112
Excitation laser line: 633 nm, 635 nm or 640 nm
Replaces: Alexa Fluor® 660, APC

CF®660R
Abs/Em Maxima: 663/682 nm
Extinction coefficient: 100,000
Molecular weight: ~ 888
Excitation laser line: 633 nm, 635 nm or 640 nm
Replaces: Alexa Fluor® 660, APC

Features

CF®660C Features
Much brighter and more photostable than Alexa Fluor® 660
Compatible with multicolor super-resolution imaging by STORM

CF®660R Features
Brighter than Alexa Fluor® 660
Unrivaled photostability among spectrally similar dyes

CF®680 & CF®680R

Two outstanding 680 nm-excitable dyes

300400500600700800900Wavelength (nm)CF680CF680R
Technical Summary

CF®680
Abs/Em Maxima: 681/698 nm
Extinction coefficient: 210,000
Molecular weight: ~ 3241
Excitation laser line: 680 nm or 685 nm
Alternative for: Alexa Fluor® 680, Cy®5.5, IR®Dye 680

CF®680R
Abs/Em Maxima: 680/701 nm
Extinction coefficient: 140,000
Molecular weight: ~ 912
Excitation laser line: 680 nm or 685 nm
Alternative for: Alexa Fluor® 680, Cy®5.5, IR®Dye 680

Features

CF®680 Features
The brightest among spectrally similar dyes
Validated in multicolor STORM and 3D super-resolution
microscopy
Compatible with LI-COR® Odyssey®

CF®680R Features
Unrivaled photostability among spectrally similar dyes
Compatible with STED and single molecule spectroscopy super-resolution imaging (see pp. 20-21)
Molecular weight compatible with nucleic acid labeling
Compatible with LI-COR® Odyssey®

CF®700 Dye

Near-infrared CF® Dye

4006008001,000Wavelength (nm)CF700
Technical Summary

Abs/Em Maxima: 695/720 nm
Extinction coefficient: 240,000
Molecular weight: ~ 2315
Excitation laser line: 633, 635, 680 or 685 nm
Replaces: Alexa Fluor® 700, DyLight® 700

Features

Exceptionally bright and stable
Ideal for in vivo imaging
Compatible with LI-COR® Odyssey®
Superior signal-to-noise for bioconjugates
Dye options for STORM & photoacoustic imaging

CF®740 Dye

Near-infrared CF® Dye with exceptional photostability

3004005006007008009001,000Wavelength (nm)CF740
Technical Summary

Abs/Em Maxima: 742/767 nm
Extinction coefficient: 105,000
Molecular weight: ~ 900
Excitation laser line: 633 to 685 nm
Replaces: Alexa Fluor® 750, Cy®7, DyLight® 750

Features

Superior photostability for microscopy and chemical stability for TSA

CF®750 Dye

Near-infrared CF® Dye

4006008001,000Wavelength (nm)CF750
Technical Summary

Abs/Em Maxima: 755/777 nm
Extinction coefficient: 250,000
Molecular weight: ~ 3009
Excitation laser line: 633, 635, 680 or 685 nm
Alternative for: Alexa Fluor® 750, Cy®7, DyLight® 750

Features

Exceptionally bright and stable
Ideal for in vivo imaging
Compatible with LI-COR® Odyssey®
Superior signal-to-noise for bioconjugates
Dye options for STORM & photoacoustic imaging

CF®770 Dye

Near-infrared CF® Dye

4006008001,000Wavelength (nm)CF770
Technical Summary

Abs/Em Maxima: 770/797 nm
Extinction coefficient: 220,000
Molecular weight: ~ 3138
Excitation laser line: 785 nm
Replaces: DyLight™ 800, IRDye 800CW

Features

Exceptionally bright and stable
Ideal for in vivo imaging
Compatible with LI-COR® Odyssey®
Superior signal-to-noise for bioconjugates
Dye options for STORM & photoacoustic imaging

CF®790 Dye

Near-infrared CF® Dye

4006008001,000Wavelength (nm)CF790
Technical Summary

Abs/Em Maxima: 784/806 nm
Extinction coefficient: 210,000
Molecular weight: ~ 3267
Excitation laser line: 785 nm
Replaces: Alexa Fluor® 790

Features

Exceptionally bright and stable
Ideal for in vivo imaging
Compatible with LI-COR® Odyssey®
Superior signal-to-noise for bioconjugates
Dye options for STORM & photoacoustic imaging

APC-Astral™813

Novel long Stokes shift tandem dye for flow cytometry multiplexing

3004005006007008009001,000Wavelength (nm)APC-Astral813
Technical Summary

Abs/Em maxima: 633, 638/813 nm
Laser line: 633 -640 nm
Spectrally similar to: APC/Fire™ 813, cFluor®R840

Features

Exceptional signal-to-noise for flow cytometry
Designed for enhanced FRET performance
Available with flow validated primary antibodies

CF®800 Dye

Near-infrared CF® Dye

4006008001,000Wavelength (nm)CF800
Technical Summary

Abs/Em Maxima: 797/816 nm
Extinction coefficient: 210,000
Molecular weight: ~3334
Excitation laser line: 785 nm
Spectrally similar to: Indocyanine Green

Features

Exceptionally bright and stable
Ideal for in vivo imaging
Compatible with LI-COR® Odyssey®
Superior signal-to-noise for bioconjugates
Dye options for STORM & photoacoustic imaging

CF®820 Dye

Near-infrared CF® Dye

4006008001,000Wavelength (nm)CF820
Technical Summary

Abs/EmMaxima: 822/835 nm
Extinction coefficient: 253,000
Molecular weight: ~2553
Excitation laser line: 785 nm

Features

Exceptionally bright and stable
Ideal for in vivo imaging
Compatible with LI-COR® Odyssey®
Superior signal-to-noise for bioconjugates
Dye options for STORM & photoacoustic imaging

CF®850 Dye

Near-infrared CF® Dye

4006008001,000Wavelength (nm)CF850
Technical Summary

Abs/EmMaxima: 852/870 nm
Molecular weight: ~2787
Excitation laser line: 808 nm

Features

Exceptionally bright and stable
Ideal for in vivo imaging
Compatible with LI-COR® Odyssey®
Superior signal-to-noise for bioconjugates
Optimal for the 808 nm laser for flow cytometry

CF®870 Dye

Near-infrared CF® Dye

4006008001,000Wavelength (nm)CF870
Technical Summary

Abs/EmMaxima: 876/896 nm
Molecular weight: ~2773
Excitation laser line: 808 nm

Features

Exceptionally bright and stable
Ideal for in vivo imaging
Compatible with LI-COR® Odyssey®
Superior signal-to-noise for bioconjugates
Optimal for the 808 nm laser for flow cytometry

CF® Dyes for Multi-Color Super-Resolution Microscopy

Technical Summary

Features

CF Dyes validated in SIM, STORM, STED, TIRF, and more
Superior brightness, photostability, and photochemical switching
Single label antibody conjugates for STORM
Growing list of publications

The Best Probes for Super-Resolution

Super-resolution microscopy encompasses a broad family of imaging techniques that push beyond the diffraction limit of traditional light microscopy, revealing the finer details of biological structures. These techniques rely on extremely precise control over the excitation, emission, and image acquisition of fluorescently labeled cells and tissues. Consequently, the quality and efficiency of super-resolution imaging relies heavily on the fluorescent properties of the probe. Biotium’s CF® Dyes have met this demand with industry-leading brightness and photochemical switching properties over other commercially available fluorescent probes. Moreover, CF® Dyes have been published in dozens of studies for a wide range of super-resolution applications.

Superior Performance for STORM Imaging

Several CF® Dyes are specifically developed and validated for optimal performance in Stochastic Optical Reconstruction Microscopy (STORM). This includes Biotium’s red-excited CF® Dyes such as CF®647, CF®660C, and CF®680 which display superior brightness and unique photoswitching properties that are ideal for STORM. However, while STORM imaging commonly relies on photoswitchable red-excited dyes, finding comparable dyes for other excitation sources to produce quality multi-color STORM images remains a challenge. In response, Biotium has developed several green-excited dyes developed for optimal performance in STORM. Specifically, green-excited CF®583R and CF®597R were developed in collaboration with UC Berkeley and STORM scientist Ke Xu, PhD for exceptional performance in multi-color STORM imaging (Figures 1 and 2). In addition, green-excited CF®568 has also demonstrated better performance than Cy3b (Figure 3). CF®594ST is Biotium’s unique version of CF®594 developed specifically for STORM. See below for a full list of validated CF® Dyes for STORM and available products.

Figure 1. Typical (d)STORM image of the actin cytoskeleton in a fixed COS-7 cell labeled by phalloidin-CF®583R. (d)STORM was performed under standard conditions using a standard tris-based (d)STORM imaging buffer containing 100 mM cysteamine and an oxygen scavenger. Image courtesy of Bowen Wang, Michael Xiong, and Professor Ke Xu, College of Chemistry, University of California, Berkeley.
Figure 2. Comparison of typical (d)STORM images obtained in fixed COS-7 cells for microtubules immunolabeled by different dyes. (d)STORM was performed under standard conditions using a standard tris-based (d)STORM imaging buffer containing 100 mM cysteamine and an oxygen scavenger. (a) CF®583R. (b) CF®597R. (c) Alexa Fluor® 532. (d) Cy3B. (e) CF®568. Localization distributions are further given for single CF®583R and CF®597R molecules in the sample, in the X (in-plane; top) and Z (depth; bottom) directions, respectively. Gaussian fits (red curves) give standard deviations of ~10 and ~20 nm in the two directions, respectively. Color denotes depth (Z) values. Images and figures courtesy of Bowen Wang, Michael Xiong, and Professor Ke Xu, College of Chemistry, University of California, Berkeley.
Figure 3. CF®568 (left) produces better images than Cy®3b (right) in 3-D STORM microscopy. Images courtesy of Sam Kenny and Professor Ke Xu, College of Chemistry, University of California, Berkeley

CF® Dyes Validated for STED and FLIM Imaging by STELLARIS 8 STED Confocal Microscope

CF® Dyes were validated for high-quality super-resolution imaging of microtubules by Leica’s STELLARIS 8 STED FALCON platform. See the table on the right for fluorescent lifetime data for several CF® Dyes.

STED imaging of microtubules in U2OS cells. Microtubules were labeled with mouse anti-tubulin (DM1a) and anti-mouse CF®640R secondary antibody. Image acquired on a STELLARIS 8 STED FALCON confocal microscope, courtesy Leica Microsystems GmbH, Germany.

CF® Dye Fluorescence Lifetime Data

Dyeτ (ns) /free acid in PBS pH 7.4, ε (ns)τ (ns) /S.Ab§
CF®405S 3.88 ± 0.05
CF®488A 4.11 ± 0.051.705
CF®568 3.66 ± 0.05 1.539
CF®594 1.746
CF®633 3.39* (in water)3*
CF®640R 2.38 ± 0.05 1.557
CF®647 1.07 ± 0.05 1.195
CF®680 1.23 ± 0.05 1.277
CF®680R 1.22 ± 0.051.6
CF®750 0.58 ± 0.050.636
CF®790 0.39 ± 0.050.54

Measurements were made on a Stellaris 8 STED FALCON microscope courtesy Leica Microsystems, Germany. § Fluorescence lifetime measurements of CF® Dye labeled anti-mouse secondary antibodies used for immunostaining microtubules in U2OS using mouse anti-tubulin (DM1a) and mounted in ProLong™ Diamond. *Lifetime data obtained via customer communication under different experimental conditions and imaging setup.

 

 

Don’t Just Take Our Word for It!

Check Out More Publications Validating CF® Dyes for STORM

Sign up to our e-newsletter to download our Literature Digest: CF® Dyes for STORM Super-Resolution Microscopy.

CF® Dye Products Useful for Super-Resolution Microscopy

Antibody Labeling Kits

Our Mix-n-Stain™ STORM CF® Dye Antibody Labeling Kits allow you to label 50 ug of your antibody with one of Biotium’s STORM CF® Dyes to produce an antibody conjugate with a low 1-2.5 DOL (degree of labeling) optimal for super-resolution STORM (Stochastic Optical Reconstruction Microscopy). Labeling takes just 30 minutes, with minimal hands-on time and no purification. Click here to learn more about Biotium’s antibody labeling kits.

  • Choice of 8 CF® Dye colors ideal for STORM
  • CF®583R and CF®597R are novel green-excited STORM dyes
  • Labeling optimized to provide low 1-2.5 DOL
  • Less than 30 seconds of hands-on time
  • 30 minutes total reaction time
  • No purification, 100% recovery

Reactive CF® Dyes

Developing a custom probe for super-resolution applications? Biotium offers CF® Dyes in a wide array of reactive chemistries to suit your research needs.

Single-Label Secondary Antibody Conjugates for STORM

Secondary antibodies with a low degree of labeling (DOL, or number of dye molecules per antibody molecule) have been reported to be optimal for STORM (Bittel et al. 2015). Biotium offers single-label secondary antibody conjugates with an average DOL of one for STORM applications.

Probes for Cytoskeleton and Other Cellular Structures

Biotium offers a wide variety of CF® Dye bioconjugates used for labeling specific cellular structures.

  • Phalloidin conjugates for F-actin labeling available in 16 CF® Dyes. CF®647 and CF®680 phalloidins ideal for STORM imaging.
  • Con A, WGA, and PNA lectin CF® Dye conjugates for labeling glycoproteins and cellular surfaces
  • Streptavidin & biotinylated CF® Dye conjugates
  • CF® Dye nucleotides and probes for apoptosis, endocytosis, and other cellular processes also available.

Learn more about CF® Dyes for Super-Resolution Imaging:

CF® Dyes Validated for Super-Resolution Microscopy

DyeAbs/Em (nm)STORMSTEDSIM2-PhotonTIRFOther ApplicationsFeatures
CF®405S411/431• Brighter than Alexa Fluor® 405
CF®405M416/452• More photostable than Pacific Blue™
• Excellent choice for SIM imaging
CF®440433/512• More photostable than spectrally similar dyes
CF®488A490/516DNA-PAINT• Less non-specific binding than Alexa Fluor® 488
CF®505505/519• Identical to ATTO 488
CF®535ST535/569• Orange dye designed specifically for STORM imaging
CF®555554/56811• Brighter and more photostable than Cy®3
• Less non-specific binding than Alexa Fluor® 555
CF®568562/5841• Yields much brighter conjugates than Alexa Fluor® 568
• Outperforms Cy®3b in STORM
• Pairs well with CF®647 and CF®680 for multi-color STORM – see publication
CF®583R585/6091• One of two top-performing dyes specifically designed for STORM
with green laser (also see CF®597R) – see publication
CF®594593/615• Significantly brighter than Alexa Fluor® 594 and Texas Red®
• Extremely photostable
CF®597R597/6191• Deep-red fluorescent dye designed specifically for STORM
• Top-performing dye specifically designed for STORM
with green laser (also see CF®583R) – see publication
CF®633629/650FIONA, gSHRImp, SMT• Significantly brighter than spectrally similar far-red dyes
• Far more photostable than Alexa Fluor® 647
CF®640R642/663FLImP• Offers improved brightness and photostability over ATTO 647N
and spectrally similar dyes
CF®647652/6681• Spectrally similar to Cy®5 and Alexa Fluor® 647
• Pairs well with CF®568 for multi-color STORM
• The best far-red dye for demixing-based multi-color
(d)STORM imaging when paired with CF®680 – see publication
CF®660R662/682SMLM, DNA-PAINT• Much brighter than Alexa Fluor® 660
• The most photostable 660 nm dye
• Validated for use with DNA-PAINT SMLM – see publication
CF®660C667/6851MINFLUX• Much brighter and more photostable than Alexa Fluor® 660
• Ideal for long high-intensity 3D (d)STORM image acquisitions
with minimal photobleaching – see publication
CF®680681/6981Dual-color 3D SMLM, MINFLUX• The brightest among spectrally similar 680 nm dyes
• Pairs well with CF®568 for multi-color STORM
• The best near-IR dye for demixing-based multi-color
(d)STORM imaging when paired with CF®647 – see publication
CF®680R680/7011Single-molecule spectroscopy, SMT• The most photostable 680 nm dye
• Suitable for labeling nucleic acids and small biomolecules
CF®750755/779• Exceptionally bright and photostable near-IR dye
• Patented pegylated dye for superior performance
A check mark indicates the respective dye has been published and/or validated for the application. Please contact techsupport@biotium.com for more information.

1 Dye was validated in multi-color STORM experiments

FLImP: Fluorophore localization imaging with photobleaching; SIM: Structured illumination microscopy; STED: Stimulated emission depletion; STORM: Stochastical optical reconstruction microscopy; TIRF: Total internal reflection fluorescence; FIONA: Fluorescence imaging with one-nanometer accuracy; ExM: Expansion microscopy; SMT: Single-molecule tracking; SMLM: Single-molecule localization microscopy.

References for CF® Dyes in Super-Resolution Microscopy and Other Specialized Applications

DyeAbs/Em (nm)ApplicationsReferences
CF®405S404/431SIMDemmerle, J. et al. (2017). Strategic and practical guidelines for successful structured illumination microscopy. Nature Protocols 12, 988–1010. (SIM)

Essig, K. et al. (2017). Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells. Volume 47, Issue 6, p1067–1082.e12 (SIM)
CF®405M408/452SIM
STED
2-photon
Demmerle, J. et al. (2017). Strategic and practical guidelines for successful structured illumination microscopy. Nature Protocols 12, 988–1010. (SIM)

Kraus, F. et al. (2017) Quantitative 3D structured illumination microscopy of nuclear structures.Nat Protoc 12, 1011-1028, doi:nprot.2017.020 [pii] (SIM)

Markaki, Y. et al. (2013). Fluorescence In Situ Hybridization Applications for Super-Resolution 3D Structured Illumination Microscopy. Methods Mol Biol 950, 43-64. (SIM)

Miron, E. et. al. (2016). In Vivo and In Situ Replication Labeling Methods for Super-resolution Structured Illumination Microscopy of Chromosome Territories and Chromatin Domains. in Mark C. Leake (ed.), Chromosome Architecture: Methods and Protocols, Methods in Molecular Biology, vol. 1431, 127-140. (SIM)

Ohgomori, T. et al. (2017). Differential activation of neuronal and glial STAT3 in the spinal cord of the SOD1G93A mouse model of amyotrophic lateral sclerosis.Eur J Neurosci 46, 2001-2014, doi:10.1111/ejn.13650 (SIM)

Zhang, R. et al. (2019). The mechanisms of dynamin-actin interaction. bioRxiv doi: https://doi.org/10.1101/586461 (STED)

Kim, YR et al. (2020). Neutrophils Return to Bloodstream Through the Brain Blood Vessel After Crosstalk With Microglia During LPS-Induced Neuroinflammation. Front. Cell Dev. Biol. (2-photon)
CF®488A490/515STED
STORM
TIRF
2-photon
Angelov, B. & Angelova, A. (2017). Nanoscale clustering of the neurotrophin receptor TrkB revealed by super-resolution STED microscopy. Nanoscale 9, 9797-9804, doi:10.1039/c7nr03454g. (STED)

Mercier, L. et al. (2016). In vivo imaging of skeletal muscle in mice highlights muscle defects in a model of myotubular myopathy. Intravital. 5(1), e1168553. (2-photon)

Zanetti-Domingues, L.C. et al. (2013). Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule Tracking Experiments Due to Non-Specific Binding. PLoS ONE 8(9): e74200. (TIRF)

Collaborator communication (CF®488A for STORM using OxEA buffer); for more information contact Tech Support.
CF®535ST535/568STORMCollaborator communication; for more information contact Tech Support.
CF®555555/565Multicolor STORMLehmann, M. et al. (2015). Novel organic dyes for multicolor localization-based super-resolution microscopy. J Biophotonics DOI 10.1002/jbio.201500119
CF®568562/583Multicolor STORM
SIM
TIRF
STED
Gong, Y.-N. et al. (2017). Biological events and molecular signaling following MLKL activation during necroptosis. Cell Cycle, 1-13. doi:10.1080/15384101.2017.1371889 (STORM)

Gorur, A. et al. (2017). COPII-coated membranes function as transport carriers of intracellular procollagen I. J Cell Biol 216, 1745-1759. doi:10.1083/jcb.201702135 (STORM)

Haas, K. et al. (2018). Single-molecule localization microscopy reveals molecular transactions during RAD51 filament assembly at cellular DNA damage sites. Nucleic Acids Research, Volume 46(5), 2398–2416. (STORM)

Heller, J. (2017). Exploring Nanoscale Organisation of Synapses with Super-Resolution Microscopy. OM&P 3, 48-58, doi:doi:10.20388/omp2017.002.0045 (STORM)

Jorgans, D.M. et al. (2017). Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture. J Cell Sci 2017 130: 177-189. doi: 10.1242/jcs.190967 (STORM)

Karanasios, E. et al. (2016). Autophagy initiation by ULK complex assembly on ER tubulovesicular regions marked by ATG9 vesicles.Nature Communications 7: 12420. DOI: 10.1038/ncomms12420 (STORM)

Kraus, F. et al. (2017) Quantitative 3D structured illumination microscopy of nuclear structures.Nat Protoc 12, 1011-1028, doi:nprot.2017.020 [pii] (SIM)

Lehmann, M. et al. (2015). Novel organic dyes for multicolor localization-based super-resolution microscopy.J Biophotonics DOI 10.1002/jbio.201500119 (STORM)

Lim, A. et al. (2017). Two kinesins drive anterograde neuropeptide transport.Mol Biol Cell, doi:mbc.E16-12-0820 [pii] (SIM)

Turkowyd, B. et al. (2016). From single molecules to life: microscopy at the nanoscale. Anal Bioanal Chem DOI 10.1007/s00216-016-9781-8 (STORM)

Zanetti-Domingues, L.C. et al. (2013). Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule Tracking Experiments Due to Non-Specific Binding. PLoS ONE 8(9): e74200. (TIRF)

Zhang, M. et al. (2015).Translocation of interleukin-1β into a vesicle intermediate in autophagy-mediated secretion. eLife 2015;10.7554/eLife.11205 (STORM)

Catsburg, L. A. et al. (2021) Dynamics and nanoscale organization of the postsynaptic endocytic zone at 1 excitatory synapses. BioRxiv 2021.02.18.431766 (STED)
CF®583R585/609Multicolor STORMWang, B. et al. (2021). Transforming Rhodamine Dyes for (d)STORM Super-Resolution Microscopy via 1,3-Disubstituted Imidazolium Substitution. Angewandte Chemie International Edition, e202113612.
CF®594593/6142-photon
STED
Wagner, M.C. et al. (2016). Mechanism of increased clearance of glycated albumin by proximal tubule cells. Am J Physiol Renal Physiol 310, F1089–F1102. (2-photon)

Collaboration with Leica using the STELLARIS STED microscope (STED); for more information contact Tech Support.
CF®594ST593/614STORMCollaborator communication; for more information contact Tech Support.

Please note: CF®594ST is a unique dye designed specifically for STORM. Our original CF®594 dye is not suitable for STORM.
CF®597R597/619Multicolor STORMWang, B. et al. (2021). Transforming Rhodamine Dyes for (d)STORM Super-Resolution Microscopy via 1,3-Disubstituted Imidazolium Substitution. Angewandte Chemie International Edition, e202113612.
CF®633630/650FIONA
gSHRImP
Single-molecule tracking (SMT)
TIRF
Bosch, P.J. et al. (2014).Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-molecule tracking microscopy in live cells. Biophys J 107, 803-814. (TIRF)

Huang, T. et al. (2018). Simultaneous Multicolor Single-Molecule Tracking with Single-Laser Excitation via Spectral Imaging. Biophysical Journal 114, 301–310. (SMT)

Kim, H.J., and Selvin, P.R. (2013). Fluorescence Imaging with One Nanometer Accuracy.SpringerReference Encyclopedia of Biophysics. (FIONA)

Simonson, P. D. et al. (2011). Single-molecule-based super-resolution images in the presence of multiple fluorophores.Nano Lett 11, 5090-5096. DOI:10.1021/nl203560r (gSHRImP)


Zanetti-Domingues, L.C. et al. (2013). Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule Tracking Experiments Due to Non-Specific Binding. PLoS ONE 8(9): e74200. (TIRF)
CF®640R642/662FLImP
SIM
TIRF
STED
Bosch, P. J. et al. (2014).Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-molecule tracking microscopy in live cells. Biophys J 107, 803-814. (TIRF)

Loh, L. N. (2017). Dissecting Bacterial Cell Wall Entry and Signaling in Eukaryotic Cells: an Actin-Dependent Pathway Parallels Platelet-Activating Factor Receptor-Mediated Endocytosis.MBio 8, doi:mBio.02030-16 [pii] (SIM)

Martin-Fernandez, M. L. et al. (2013). A ‘pocket guide’ to total internal reflection fluorescence.J Microsc 252, 16-22. (TIRF)

Needham, S.R. et al. (2015). Determining the geometry of oligomers of the human epidermal growth factor family on cells with <10 nm resolution. Biochem Soc Trans 43, 309-314. (FLImP)

Needham, S.R. et al. (2016). EGFR oligomerization organizes kinase-active dimers into competent signalling platforms. Nat Commun 7, 13307. doi:ncomms13307 (FLImP)

Zanetti-Domingues, L.C. et al. (2013). Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule Tracking Experiments Due to Non-Specific Binding.PLoS ONE 8(9): e74200. (TIRF)

Zanetti-Domingues, L.C. et al. (2015). Determining the geometry of oligomers of the human epidermal growth factor family on cells with 7 nm resolution. Prog Biophys Mol Biol 118, 139-152, doi:S0079-6107(15)00047-4 (FLImP)

Zhang, R. et al. (2017). Structural insight into TPX2-stimulated microtubule assembly. eLife 2017;6:e30959. (TIRF)

Collaboration with Leica using the STELLARIS STED microscope (STED); for more information contact Tech Support.
CF®647650/665Multicolor STORMGong, Y.-N. et al. (2017). Biological events and molecular signaling following MLKL activation during necroptosis. Cell Cycle, 1-13. doi:10.1080/15384101.2017.1371889

Lehmann, M. et al. (2015). Novel organic dyes for multicolor localization-based super-resolution microscopy.J Biophotonics DOI 10.1002/jbio.201500119

Olivier, N. et al. (2013). Simple buffers for 3D STORM microscopy.Biomed Opt Express 4, 885-899.

Turkowyd, B. et al. (2016). From single molecules to life: microscopy at the nanoscale.Anal Bioanal Chem DOI 10.1007/s00216-016-9781-8
CF®660C667/685Multicolor STORMGu, L., Li, Y., Zhang, S. et al. Molecular-scale axial localization by repetitive optical selective exposure. Nat Methods 18, 369–373 (2021). https://doi.org/10.1038/s41592-021-01099-2

Turkowyd, B. et al. (2016). From single molecules to life: microscopy at the nanoscale. Anal Bioanal Chem DOI 10.1007/s00216-016-9781-8

Zhang, Z. et al. (2015). Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy. Nature Methods doi:10.1038/nmeth.3528

CF®680681/698Dual-color 3D SMLM
Multicolor STORM
Früh, S.M. et al. (2015). Molecular architecture of native fibronectin fibrils. Nature Communications 6, 7275. (STORM)

Glebov, O. O. et al. (2017).Nanoscale Structural Plasticity of the Active Zone Matrix Modulates Presynaptic Function. Cell Rep 18, 2715-2728. doi:S2211-1247(17)30279-6 [pii] (STORM)

Gorur, A. et al. (2017). COPII-coated membranes function as transport carriers of intracellular procollagen I. J Cell Biol 216, 1745-1759. doi:10.1083/jcb.201702135 (STORM)

Lehmann, M. et al. (2015). Novel organic dyes for multicolor localization-based super-resolution microscopy.J Biophotonics DOI 10.1002/jbio.201500119 (STORM)

Platonova, E. et al. (2015). A Simple Method for GFP- and RFP-based Dual Color Single-Molecule Localization Microscopy. ACS Chem. Biol.10(6),1411-1416. (STORM)

Platonova, E. et al. (2015). Single-molecule microscopy of molecules tagged with GFP or mRFP derivatives in mammalian cells using nanobody binders.Methods doi: http://dx.doi.org/10.1016/j.ymeth.2015.06.018 (STORM)

Salvador-Gallego, R. et al. (2016). Bax assembly into rings and arcs in apoptotic mitochondria is linked to membrane pores. EMBO J 35, 389-401. doi:embj.201593384 (STORM)

Shrestha, R. L. et al. (2017). Aurora-B kinase pathway controls the lateral to end-on conversion of kinetochore-microtubule attachments in human cells. Nat Commun 8, 150. doi:10.1038/s41467-017-00209-z (STORM)

Thiele, J. C. et al. (2022). Isotropic three-dimensional dual-color super-resolution microscopy with metal-induced energy transfer. Sci. Adv. 8, eabo2506, doi:10.1126/sciadv.abo2506 (MIET-SMLM)

Turkowyd, B. et al. (2016). From single molecules to life: microscopy at the nanoscale.Anal Bioanal Chem DOI 10.1007/s00216-016-9781-8 (SMLM)

Winterflood, C.M. et al. (2015). Dual-Color 3D Superresolution Microscopy by Combined Spectral-Demixing and Biplane Imaging. Biophys J. 109, 3-6. (SMLM)

Zhang, Z. et al. (2015). Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy.Nature Methods doi:10.1038/nmeth.3528 (STORM)
CF®680R680/701Multicolor STORM
Single-molecule spectroscopy
Single-molecule tracking (SMT)
STED
2-photon
Conley, G. et al. (2017). Jamming and overpacking fuzzy microgels: Deformation, interpenetration, and compression. Science Advances 3(10), e1700969 DOI:10.1126/sciadv.1700969 (STORM)

Görlitz, F. et al. (2014). A STED Microscope Designed for Routine Biomedical Applications. Progress Electromagnetics Res 147, 57-68. (STED)

Huang, T. et al. (2018). Simultaneous Multicolor Single-Molecule Tracking with Single-Laser Excitation via Spectral Imaging. Biophysical Journal 114, 301–310. (SMT)

König, I. et al. (2015). Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells. Nature Methods doi:10.1038/nmeth.3475 (Single molecule spec)

Moran, I. et al. (2018). Memory B cells are reactivated in subcapsular proliferative foci of lymph nodes. Nature Communications 9:3372. (2-photon)

Winter, F. R. et al. (2017). Multicolour nanoscopy of fixed and living cells with a single STED beam and hyperspectral detection.Sci Rep 7, 46492. doi:srep46492 [pii]10.1038/srep46492 (STED)
CF®750755/777STORMCollaborator communication; for more information contact Tech Support.
FIONA: Fluorescence Imaging with One Nanometer Accuracy; FLImP: Fluorophore localization imaging with photobleaching; SHRImP: Single-molecule high-resolution imaging with photobleaching; SIM: Structured illumination microscopy; SMLM: Single molecule localization microscopy; STED: Stimulated emission depletion; STORM: Stochastical optical reconstruction microscopy; TIRF: Total internal reflection fluorescence

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