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BrightLine® single-band filter set, optimized for Cy3 and other like fluorophores

Semrock Set / Fluorophore Graphing

Part Number: Cy3-4040C-000

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Semrock Filter Set: Cy3-4040C

BrightLine® single-band filter set, optimized for Cy3 and other like fluorophores

This filter set is ideal for use with Cy3™ and a variety of other orange fluorophores (including DsRed fluorescent protein). It is optimized to provide the highest brightness, while maintaining a very high signal-to-noise ratio.
Are you co-labeling with YFP, GFP, or FITC? In order to substantially eliminate green-fluorophore bleedthrough we recommend using our TRITC-B filter set. For mercury (e.g., HBO) lamp users labeling with Cy3 the single-fluorophore signal-to-noise ratio will be slightly higher, and the brightness slightly lower, with the TRITC-A filter set. Xenon lamp users of the TRITC-A filter set who are labeling with Cy3 will enjoy a significantly enhanced signal-to-noise ratio and reduced photobleaching in exchange for brightness.

Individual filters and filter sets (no cube):
These filters sets contain individual filters. For filter sets already mounted in a holder/cube, scroll down to see complete mounted sets with cubes.
Part NumberPrice1Stock StatusQuantity
Click to expand/collapse details Cy3-4040C-000 (Standard size set, fits most microscopes2)$910Confirmed AROAdd To Cart
Filter RoleFilter SizePart NumberPrice1
Single Band Exciter25 mm x 5.0 mmFF01-531/40-25$355
Single Band Emitter25 mm x 3.5 mmFF01-593/40-25$355
Single Band Dichroic25.2 mm x 35.6 mm x 1.1 mmFF562-Di03-25x36$292
Click to expand/collapse details Cy3-4040C-000-ZERO (Standard size -ZERO pixel set)$1,019Confirmed AROAdd To Cart
Click to expand/collapse details Cy3-4040C-L01-ZERO (Leica 'Large' -ZERO pixel set)$1,019Confirmed AROAdd To Cart
Click to expand/collapse details Cy3-4040C-U02 (Olympus large-size (FX) set for U-M710I)$1,638Confirmed AROAdd To Cart

1) US domestic pricing only. If you are ordering from outside the US, please contact your nearest regional distributor for the correct list price.
2) Customers installing filters into their own Nikon Quadfluor cubes should contact us before ordering a filter set.

Complete filter sets mounted in microscope holders/cubes:
These sets are delivered already mounted in microscope filter holders, often called 'cubes', ready to be dropped into your microscope.
Nikon Quadfluor for microscopes: E200, E400, E600, E800, E1000, TS100, TS100F, TE200, TE300, ME600L, L150A, and some Labophot, Optiphot, and Diaphot series
Click to expand/collapse details Cy3-4040C-NQF (set mounted in cube)$1,309Confirmed AROAdd To Cart
Click to expand/collapse details Cy3-4040C-NQF-ZERO (-ZERO pixel set mounted in cube)$1,418Confirmed AROAdd To Cart
Nikon TE 2000 for microscopes: TE 2000, 50i, 55i, 80i, 90i, Eclipse Ti, Ni, and Ci series, and any using the Epi-fluor Illuminator
Click to expand/collapse details Cy3-4040C-NTE (set mounted in cube)$1,309Confirmed AROAdd To Cart
Click to expand/collapse details Cy3-4040C-NTE-ZERO (-ZERO pixel set mounted in cube)$1,418Confirmed AROAdd To Cart
Olympus U-MF2 for microscopes: AX70, BX, BX41, BX50, BX51, BX60, BX61, BX50/51WI, BX60/61WI, IX50, IX51, IX70, IX71, IX81
Click to expand/collapse details Cy3-4040C-OMF (set mounted in cube)$1,359Confirmed AROAdd To Cart
Click to expand/collapse details Cy3-4040C-OMF-ZERO (-ZERO pixel set mounted in cube)$1,468Confirmed AROAdd To Cart
Olympus U-FF for microscopes: BX53, BX63
Click to expand/collapse details Cy3-4040C-OFF (set mounted in cube)$1,359Confirmed AROAdd To Cart
Click to expand/collapse details Cy3-4040C-OFF-ZERO (-ZERO pixel set mounted in cube)$1,468Confirmed AROAdd To Cart
Olympus U-M710I for microscopes: Requires a 32mm emitter & exciter and 32x44mm dichroic beamsplitter. For IX53, IX73, & IX83 model microscopes
Click to expand/collapse details Cy3-4040C-OFX (set mounted in cube)$1,609Confirmed AROAdd To Cart
Zeiss FL Cube EC P+C for microscopes: Axio Imager, Axiostar Plus, Axioskop 40, Axioskop 2 (post-2001), Axioplan 2i, Axioplan 2ie, Axiovert 200, Axiovert 40, Axio Observer, Axio Examiner and Axio Scope A1
Click to expand/collapse details Cy3-4040C-ZHE (set mounted in cube)$1,199Confirmed AROAdd To Cart
Click to expand/collapse details Cy3-4040C-ZHE-ZERO (-ZERO pixel set mounted in cube)$1,308Confirmed AROAdd To Cart
Leica DM-K for microscopes: DM-2000, DM-2500, DM-3000, DMI3000 B, DM-4000, DMI4000 B, DM-5000, DM-5500, DM-6000, DMI6000 B, DM4 and DM6
Click to expand/collapse details Cy3-4040C-LDMK-ZERO (-ZERO pixel set mounted in cube)$1,378Confirmed AROAdd To Cart
Leica DMi8 (P-Cube) for microscopes: DMi8
Click to expand/collapse details Cy3-4040C-LDMP-ZERO (-ZERO pixel set mounted in cube)$1,468Confirmed AROAdd To Cart
Aperio AMF for microscopes: ScanScope FL
Click to expand/collapse details Cy3-4040C-AMF-ZERO (-ZERO pixel set mounted in cube)$1,488Confirmed AROAdd To Cart

1) US domestic pricing only. If you are ordering from outside the US, please contact your nearest regional distributor for the correct list price.
Optical Specifications
BlockingBrightLine filters have blocking far exceeding OD 6 as needed to ensure a black background, even when using modern low-noise CCD cameras. The blocking is optimized for microscopy applications using our exclusive SpecMaker™ fluorescence filter design.

General Filter Specifications
Microscope CompatibilityBrightLine filters are available to fit Leica, Nikon, Olympus, Zeiss, and Aperio microscopes.
Optical Damage RatingTesting has proven to show no signs of degradation when exposed to at least 6.0 W of power from an unfiltered xenon arc lamp over a 25 mm diameter (corresponding to 1.2 W/cm2) for over 500 hours.

Physical Filter Specifications
Exciter/Emitter OrientationArrow on ring indicates preferred direction of propagation of light.
Dichroic Orientation"Reflective coating side" should face toward light source and sample.

5-Star Optimized – Filter set is specifically optimized for that fluorophore.
3-Star Compatible – Should result in nearly ideal performance in most situations.
1-Star Acceptable – Actual performance is dependent on specific experimental conditions.
FluorophorePeak Excitation
Wavelength (nm)
Peak Emission
Wavelength (nm)
CompatibilityDisplay on
Plot above
5-TAMRA (5-carboxytetramethylrhodamine, pH 7.0)5425685-Star
Alexa Fluor® 5325345531-Star
Alexa Fluor® 5465565721-Star
Alexa Fluor® 5555535655-Star
Amplex UltraRed peroxidation product (pH 7.5)5685811-Star
AsRed 25765921-Star
ATTO 5325015451-Star
ATTO 5505535763-Star
ATTO 5655635921-Star
BODIPY TMR-X5445733-Star
BODIPY TR-X (MeOH)5445733-Star
Calcium Orange5896095-Star
Dendra2 (Red)5545693-Star
DyLight 5495535693-Star
Ethidium bromide5186033-Star
Ethidium homodimer5276171-Star
FluoSpheres Orange fluorescent microspheres5405591-Star
FluoSpheres Red fluorescent microspheres5776071-Star
Gold 5505515641-Star
HCS LipidTOX Red phospholipidosis5846081-Star
HiLyte Fluor™ 5555505661-Star
LysoTracker Red5735921-Star
LysoTracker Yellow HCK-1234885653-Star
Magnesium Orange5505743-Star
Merocyanine 5405595791-Star
MitoTracker™ Orange5515755-Star
Nile red-triglyceride5105833-Star
Orange 5525525743-Star
pHrodo™, succinimidyl ester5605871-Star
Phycoerythrin (PE)5655753-Star
Propidium Iodide (PI)3056171-Star
Pro-Q Diamond5565833-Star
Qdot® 585 Nanocrystals3005881-Star
Qdot® 605 Nanocrystals3006021-Star
Rhodamine phalloidin5585755-Star
R-phycoerythrin (PE)5655761-Star
SNARF-1 488nm (ph 6.0)5485863-Star
SNARF-1 514nm (ph 6.0)5495873-Star
SYTO 825405591-Star
SYTOX Orange5475703-Star
Tetramethylrhodamine dextran5545823-Star
Texas Red DHPE5846081-Star
TRITC (Tetramethylrhodamine)5525783-Star
Vybrant DyeCycle Orange5195631-Star

Tech Note
Cleaning Optical FiltersInstructions for cleaning hard coated optical filters
Cube Assembly InstructionsPDF and video instruction for installing filters into popular filter cubes
Filter ReliabilityCompares the performance and reliability of hard coated filters to traditional soft-coated filters and provides information about the testing standards for Semrock filters
Introduction to Fluorescence FiltersShows how optical filters are used in a traditional fluorescence microscope and describes important factors to consider when choosing optical filters.
Orientation of Filters in a MicroscopeA guide to properly orienting Semrock filters based on the filter markings.
What is Pixel Shift?Explains how filter wedge angle causes pixel shift and describesthe impact of pixel shift on image fidelity
Journal Article
Achieving the Best Alignment for Fluorescent ImagesTuran Erdogan, PhD, and Atul Pradhan, PhD, Semrock Inc., BioPhotonics, August 2005
Semrock's BrightLine ZERO filter sets eliminate the beam deviation that can cause pixel shift when combining single-color images to create a multicolor image
White Paper
Spectral Modeling in Fluorescence MicroscopyDiscusses various sources of noise in fluorescence microscopy and how to maximize signal-to-noise ratios using software, sample preparation and optical filter selection
High Performance MicroscopyAn overview of high performance microscopy, including solutions from Semrock and additional learning resources.

Cy3-4040C Cy3 531/40 593/40 562 Single-Band FF01-531/40 FF01-593/40 FF562-Di03 FF562 5-TAMRA Alexa-Fluor-555 AF555 Alexa555 ATTO-550 BODIPY-TMR-X Calcium-Orange Dendra2-(Red) DiI DsRed dTomato DyLight-549 Ethidium-bromide Magnesium-Orange MitoTracker-Orange mRFP mRuby Nile-red-triglyceride OFP Orange-552 Phycoerythrin PE POPO-3 PO-PRO-3 Pro-Q-Diamond Rhod-2 Rhodamine-phalloidin SpectrumOrange SYTOX-Orange TRITC TurboRFP Cy3-4040C-000 Cy3-4040C-000-ZERO Cy3-4040C-L01-ZERO Cy3-4040C-U02 Cy3-4040C-NQF Cy3-4040C-NQF-ZERO Cy3-4040C-NTE Cy3-4040C-NTE-ZERO Cy3-4040C-OMF Cy3-4040C-OMF-ZERO Cy3-4040C-OFF Cy3-4040C-OFF-ZERO Cy3-4040C-OFX Cy3-4040C-ZHE Cy3-4040C-ZHE-ZERO Cy3-4040C-LDMP-ZERO Cy3-4040C-LDMK-ZERO Cy3-4040C-AMF-ZERO

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