What fluorescent dyes, labels, and proteins are compatible with the SLICE microscope?

Light Sheet Microscopy
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Fluorescent dyes and antibody–dye conjugates compatible with the SLICE microscope are widely available from commercial life-science suppliers. Achieving optimal performance, however, requires careful selection of fluorescent dyes tailored to the system’s excitation laser and emission filters. For the most up-to-date list on fluorescence channel configurations and compatible dyes/ labels, visit the SLICE-compatible fluorescent dyes and proteins page in the user guide.

The table below lists commonly used dyes and links to vendor websites, including Abcam, Jackson ImmunoResearch, and Thermo Fisher Scientific, where users can search for antibody–dye conjugates. These links are provided for convenience only. Product availability, specifications, and compatibility may vary by antibody type, host species, and conjugation format. Users should review the vendor documentation to confirm suitability for their specific experiment.

Conjugated Antibodies

SLICE Filter Dye Ex. (nm) Em. (nm) Abcam Jackson ImmunoResearch Thermo Fisher Scientific
Blue narrow/ Blue Alexa Fluor 488 493 519 View product View product View product
Blue narrow/ Blue Cy2 492 510 View product View product –
Blue narrow/ Blue FITC 492 520 View product View product View product
Green Alexa Fluor 555 552 572 View product View product View product
Green Alexa Fluor 568 578 603 View product View product View product
Green Cy3 550 570 View product View product View product
Green PE-Texas Red 565 578 View product View product (R-PE) View product
Red Alexa Fluor 647 650 668 View product View product View product
Red Alexa Fluor 680 679 702 View product View product View product
Red Cy5 650 670 View product View product View product

For experiments requiring genetically encoded fluorescence, fluorescent reporter mouse lines can be obtained from repositories such as The Jackson Laboratory, and equivalent reagents may be available from other providers.

Fluorescent Reporter Mouse Lines

SLICE Filter Dye Ex. (nm) Em. (nm)
Blue narrow/ Blue ECFP 433 475
Blue narrow/ Blue EGFP 488 507
Blue narrow/ Blue mNeonGreen 506 517
Blue narrow/ Blue mTurquoise 434 474
Green DsRed 553 584
Green EYFP 513 527
Green mCherry 587 610
Green mRuby 558 605
Green RFP 555 584
Green tdTomato 554 581
Green Venus 515 528
Red iRFP670 643 670

To review the detection efficiency of fluorophores on the SLICE microscope, please refer to SLICE-compatible fluorescent dyes and proteins. For other fluorophores of interest, you can use external fluorescence spectra tools (e.g. FPbase Fluorescence Spectra Viewer and Fluorescence SpectraViewer) to evaluate how effectively a specific dye will perform with the SLICE optical configuration. These tools calculate theoretical signal yield by modeling how the dye interacts with the system’s lasers and bandpass filters as:

  • Excitation efficiency: The fraction that an incident photon at a given wavelength will be absorbed by the fluorophore as image, where image is molar extinction coefficient of the dye at wavelength image.
  • Emission efficiency: The fraction of the dye’s emission spectrum that passes through the detection filter as image, where image is normalized emission spectrum of the dye at wavelength image and image is transmission of the bandpass filter at wavelength image.
  • Detection efficiency: The fraction of incident excitation photons that ultimately produce detectable fluorescence photons within the detection filter bandwidth as multiplication of excitation efficiency and emission efficiency.