Excitation filters are always recommended when using pE-Series LED illumination systems for fluorescence microscopy. Successful fluorescence microscopy depends on matching filters with the source of illumination and the stain to be excited. These filters are commonly included within filter cubes in the microscope.

optical_imgBenefits of excitation filters

CoolLED specialize in LED illumination systems for microscopy. We know that to get the best results from your microscope you need to match the right filters to your illumination system and samples.

Although LEDs produce a narrow spectral peak of light, there are often regions of shorter and longer wavelength illumination which may lead to increased background in the image or interfere with the excitation of another stain if no excitation filter is used.

When selecting an LED illumination system which is based on a single, or few wavelength peaks, it is essential that care is taken to match these with the excitation filter in the microscope. Alternatively, a new filter can be fitted which is matched to the illumination system and the stain.

Broad spectrum illumination systems are less sensitive to this optimisation requirement but it is still beneficial to check the filters. With modular LED systems, CoolLED’s wide range of LED wavelengths (LAMs) means that an LED wavelength can be specified which matches with the existing filters in the microscope.

Our products will work with most filter sets out there, but for optimum results we have made some suggestions below. There is never a definite right answer as depending on the demands of your setup you may want more brightness, more contrast or to satisfy some other requirement.

Below are suggested filter sets from Chroma and Semrock for popular fluorophores. In most cases performance is similar, but those looking for particular brightness or contrast are urged to examine the manufacturer’s specifications further or ask CoolLED for help.


pE-300 Series      Semrock Chroma  
  DAPI DAPI-5060C 49000-et-dapi SB Version
  DAPI LED-DAPI-A 49028-et-dapi MB Version
  FITC/GFP LED-FITC-A 49002-et-egfp-fitc-cy2  
  TRITC/Cy3/dsRed/rfp Cy3-4040C 49004-et-cy3-tritc  
  mCherry/TxRed mCherry-C 49008-et-mcherry-texas-red  
  Cy5 LED-Cy5-A 49009-et-cy5  
  DAPI/FITC/TRITC/Cy5 LED-DA/FI/TR/Cy5-A 89401-et-dapi-fitc-tritc-cy5-quad MB Version Only
  DAPI/FITC/TRITC As above 69013v2-ET MB Version Only
  DAPI/FITC/TxRED As above 69013v2-ET MB Version Only


pE-4000                  Semrock LED Chroma LED
  DAPI LED-DAPI-A 385 49028-et-dapi 400
  FITC/GFP LED-FITCA 470 49002-et-egfp-fitc-cy2 460
  TRITC/Cy3/dsRed/rfp Cy3-4040C 550 49004-et-cy3-tritc 550
  mCherry/TxRed mCherry-C 550 49008-et-mcherry-texas-red 550
  Cy5 LED-Cy5-A   49009-et-cy5 635
  DAPI/FITC/TRITC DA/FI/TR-A 385/470/550 69013v2-ET 400/470/550
  DAPI/FITC/TxRED DA/FI/TX-B 385/470/550 69013v2-ET 400/490/580
  DAPI/FITC/TRITC/Cy5 LED-DA/FI/TR/Cy5-A 385/470/550/635 89402 – ET 400/490/550/635
  CFP LED-CFP-A 435 ET – ECFP 435
  YFP YFP-2427B 500 49003 – ET – EYFP 500
  CFP/YFP CFP/YFP-A 435/500 59017 – ET – ECFP/EYFP 435/500
  CFP/YFP/RFP/Cy7     89403 – ET 435/500/580/740
  For NIR dyes and other multi band combinations please ask for advice from CoolLED