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Which dyes are best for tracing neurons?
Posted January 16, 2020
Neuronal tracingfunctional imaging of neuronsFM dyesRH dyesDiIDiDDiODiRDiS
Answer
Fluorescent styryl dyes (also referred to as FM or RH dyes) are principally used in neuronal tracing and functional imaging applications.
The table below shows the range of available neuronal tracers, their excitation and emission maxima, and their staining properties to assist you in selecting the best tracer for imaging neurons.

Product NameEx/Em (nm)Standard Filter SetChroma Filter1Omega Filter2Unit SizePriceCat#
DiOC2(3) iodide [3,3-Diethyloxacarbocyanine iodide]482/500FITC Filter Set31001-ChromaXF23-Omega25 mg$7922038
DiOC3(3) iodide [3,3-Dipropyloxacarbocyanine iodide]482/500FITC Filter Set31001-ChromaXF23-Omega25 mg$7922039
DiOC7(3) iodide [3,3-Diheptyloxacarbocyanine iodide]482/500FITC Filter Set31001-ChromaXF23-Omega25 mg$7922040
DiOC16(3) perchlorate [3,3-Dihexadecyloxacarbocyanine perchlorate]482/500FITC Filter Set31001-ChromaXF23-Omega25 mg$7922042
DiOC5(3) iodide [3,3-Dipentyloxacarbocyanine iodide]482/500FITC Filter Set31001-ChromaXF23-Omega25 mg$7922045
DiOC6(3) iodide [3,3-Dihexyloxacarbocyanine iodide]482/500FITC Filter Set31001-ChromaXF23-Omega25 mg$7922046
DiO perchlorate [3,3-Dioctadecyloxacarbocyanine perchlorate]482/500FITC Filter Set31001-ChromaXF23-Omega25 mg$7922066
MM 1-43 [N-(3-Triethylammoniumpropyl)-4-(4-(dibutylamino)styryl)pyridinium dibromide]473/579TRITC Filter Set31002-ChromaXF32-Omega1 mg$10021483
DiIC12(3) perchlorate [1,1-Didodecyl-3,3,3,3-tetramethylindocarbocyanine perchlorate]549/563TRITC Filter Set31002-ChromaXF32-Omega25 mg$7922035
DiIC16(3) perchlorate [1,1-Dihexadecyl-3,3,3,3-tetramethylindocarbocyanine perchlorate]549/563TRITC Filter Set31002-ChromaXF32-Omega25 mg$7922044
DiIC12(3)-DS [1,1-Diododecyl-3,3,3,3-tetramethylindocarbocyanine-5,5-disulfonic acid]549/563TRITC Filter Set31002-ChromaXF32-Omega5 mg$10022050
DiIC18(3)-DS [1,1-Dioctadecyl-3,3,3,3-tetramethylindocarbocyanine-5,5-disulfonic acid]549/563TRITC Filter Set31002-ChromaXF32-Omega5 mg$10022052
DiSC2(3) [3,3-Diethylthiacarbocyanine iodide]560/571TRITC Filter Set31002-ChromaXF32-Omega25 mg$10022073
DiI iodide [1,1-Dioctadecyl-3,3,3,3- tetramethylindocarbocyanine iodide]549/563TRITC Filter Set31002-ChromaXF32-Omega100 mg$7922101
DiI perchlorate [1,1-Dioctadecyl-3,3,3,3-tetramethylindocarbocyanine perchlorate] CAS 41085-99-8549/563TRITC Filter Set31002-ChromaXF32-Omega100 mg$7922102
DiI triflate [1,1-Dioctadecyl-3,3,3,3-tetramethylindocarbocyanine triflate]549/563TRITC Filter Set31002-ChromaXF32-Omega100 mg$20522103
MM 2-10 [N-(3-Triethylammoniumpropyl)-4-(4-(diethylamino)styryl)pyridinium dibromide]506/620Texas Red Filter Set31024-ChromaXF21-Omega1 mg$10021489
DiA [4-(4-(Dihexadecylamino)styryl)-N-methylpyridinium iodide]491/611Texas Red Filter Set31024-ChromaXF21-Omega25 mg$7922030
DiD labeling solution [1,1-Dioctadecyl-3,3,3,3-tetramethylindodicarbocyanine] 5 mM DMSO solution645/663Cy5 Filter Set31023-ChromaXF47-Omega10 mL$20522033
DiIC12(5)-DS [1,1-Diododecyl-3,3,3,3-tetramethylindodicarbocyanine-5,5-disulfonic acid]650/670Cy5 Filter Set31023-ChromaXF47-Omega5 mg$10022051
DiIC18(5)-DS [1,1-Dioctadecyl-3,3,3,3-tetramethylindodicarbocyanine-5,5-disulfonic acid]652/668Cy5 Filter Set31023-ChromaXF47-Omega5 mg$10022054
DiIC1(5) iodide [1,1,3,3,3,3-Hexamethylindodicarbocyanine iodide]640/657Cy5 Filter Set31023-ChromaXF47-Omega25 mg$7922056
DiSC3(5) [3,3-Dipropylthiadicarbocyanine iodide]660/675Cy5 Filter Set31023-ChromaXF47-Omega25 mg$10022076
MM 4-64 [N-(3-Triethylammoniumpropyl)-4-(6-(4-(diethylamino)phenyl)hexatrienyl)pyridinium dibromide]558/734Cy5.5® Filter SetN/AN/A1 mg$20521487
DiR iodide [1,1-dioctadecyl-3,3,3,3-tetramethylindotricarbocyanine iodide]754/778Cy7 Filter Set41009-ChromaXF112-Omega25 mg$79220703
Note:
  1. Chroma filters are supplied by Chroma TechnologyCorp. (www.chroma.com).
  2. Omega filters are supplied by Omega Optical, Inc. (www.omegafilters.com).
  3. Fluorescence emission of DiR iodide is invisible to human eyes and must be detected using a CCD camera or other infrared-sensitive detector.
Additional resources
DiIC18(3)-DS Product PageDiI perchlorate Product PageMM 1-43 Product PageMM 4-64 Product Page

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