Cellular Stains Selection Guides

Find the right dye for your application

Compare applications, fixability, cellular targets, and staining in different organisms at a glance.

For more detailed information, see our Cellular Stains Technology Page and Membrane & Cell Surface Stains Comparison. Download our Cellular Stains Brochure or visit our Brochure Library to browse our product flyers.

Nuclear Stains for Live, Dead, or Fixed Cells

Membrane & Organelle Stains for Live Cells

Stains for Fixed Cells & Tissue Sections

Dead Cell & Apoptosis Stains

Stains for Cell Cycle Analysis by Flow Cytometry

Stains for Spheroids, 3D Cultures, or Matrigel® Cultures

Cellular Stains in Different Organisms

Find stains that fit your workflow using our Cellular Stains Selection Guide! This resource features cellular stain comparison guides and a detailed cellular diagram to help you find stains for different applications, cellular targets, and organisms at a glance.

Nuclear Stains

Product	Stains live cells	Fix after staining	Permeabilize after staining	Fix before staining	Non- cytotoxic	Color (Ex/Em)¹	Applications / Notes
DAPI Hoechst 33342 Hoechst 33258	Yes	Yes	Yes	Yes	Yes	Blue (352/461 nm)	• Classic blue nuclear stains • No-wash, nontoxic, stable for several days • Use DAPI in antifade mounting medium
NucSpot® Live 488	Yes	Yes	Yes	Yes	Yes	Green (500/515 nm)	• Green nuclear stain for live or fixed cells • No-wash, nontoxic for real-time imaging
Thiazole Green (SYBR® Green I)	Yes	No²	No²	No²	No	Green (498/522 nm)	• Structurally identical to SYBR® Green I
Oxazole Gold (SYBR® Gold)	Yes	No²	No²	No²	No	Green (496/539 nm)	• Structurally identical to SYBR® Gold • Live cell staining of nuclei and mitochondrial DNA
NucSpot® 470	Dead cell- selective	No	No	Yes	Yes	Green (460/546 nm)	• No-wash green nuclear stain • Dead-cell selective in unfixed cells
NucSpot® 555/570	Dead cell- selective	No	No	Yes	Yes	Red (559/566 nm)	• Nuclear-specific red counterstain for fixed cells • Specifically stains dead cells in live cultures
NucSpot® 568/580	Dead cell- selective	No	No	Yes	Yes	Dark red (572/583 nm)	• Nuclear-specific red counterstain for fixed cells • Specifically stains dead cells in live cultures • Suitable for multi-day live cell imaging
NucSpot® 594/615	Dead cell- selective	No	No	Yes	Yes	Deep red (603/613 nm)	• Nuclear-specific red counterstain for fixed cells • Specifically stains dead cells in live cultures • Suitable for multi-day live cell imaging
NucSpot® 650/665	Dead cell- selective	No	No	Yes	Yes	Far-red (653/671 nm)	• Nuclear-specific far-red counterstain for fixed cells • Specifically stains dead cells in live cultures
NucSpot® Live 650	Yes	Yes	Yes	Yes	Yes	Far-red (650/675 nm)	• Far-red nuclear stain for live or fixed cells • No-wash, nontoxic for real-time imaging
RedDot™1 Far-Red Nuclear Stain	Yes	No	No	No²	No	Far-red (662/694 nm)	• No wash, far-red nuclear stain • Compare to Draq5™ • Endpoint only; toxic after several hours
RedDot™2 Far-Red Nuclear Stain	Dead cell- selective	No	No	Yes	Yes	Far-red (650/675 nm)	• No-wash, far-red nuclear stain • Dead cell-selective in unfixed cells • Compare to Draq7™
NucSpot® 680/700	Dead cell- selective	No	No	Yes	Yes	Near IR (683/707 nm)	• Nuclear-specific near-IR counterstain for fixed cells • Specifically stains dead cells in live cultures
NucSpot® 750/780	Dead cell- selective	No	No	Yes	Yes	Near IR (750/780 nm)	• Nuclear-specific near-IR counterstain for fixed cells • Specifically stains dead cells in live cultures • Suitable for multi-day live cell imaging
Cell-Membrane Impermeant Nucleic Acid Dyes	Dead cell- selective	No	No	No²	Yes	Multiple colors Blue to Far-Red	• PI, EthDIII, dimeric cyanine dyes, etc. • See Dead Cell & Apoptosis Stains • Nuclear staining in fixed cells requires RNase treatment

¹ With DNA
² Not nuclear-specific in fixed cells
SYBR is a registered trademark of Thermo Fisher Scientific

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Live Cell Stains

Product	Localization	Fix after staining	Permeabilize after staining	Fix before staining	Non- cytotoxic	Staining stability¹	Colors	Applications / Notes
Hoechst 33342 Hoechst 33258	Nucleus	Yes	Yes	Yes	Yes	Days	Blue (352/461 nm)	• No-wash, nontoxic, stable for several days
NucSpot® Live Nuclear Stains	Nucleus	Yes	Yes	Yes	Yes	Days	Green (500/515 nm) Far-red (650/675 nm)	• No-wash, nontoxic for real-time imaging
Thiazole Green	Nucleus & cytoplasm	Yes	Yes	Yes	No	< 4 hours	Green (498/522 nm)	• Structurally identical to SYBR® Green I • Very bright, no-wash staining of DNA • Shows some mitochondrial & cytoplasmic staining • Toxic after several hours
RedDot™1 Far-Red Nuclear Stain	Nucleus	No	No	No	No	< 4 hours	Far-red (662/694 nm)	• Compare to Draq5™ • Toxic after several hours
ViaFluor® Live Cell Microtubule Stains	Microtubules	No	No	No	Possibly toxic	Days	Blue (408/452 nm) Green (500/515 nm) Far-red (650/675 nm)	• No-wash, live cell microtubule stains • Low toxicity, stain for 48 hours or longer
ViaFluor® SE Cell Proliferation Dyes	Cell interior	Yes	Yes	No	Yes	Days	Blue (408/452 nm) Green (493/532 nm)	• Stable, whole-cell labeling of live cells • Non-toxic for tracking multiple cell divisions • Excellent choice for cell tracing or co-cultures
Calcein-AM	Cell interior / Cell viability	No	No	No	Yes	≤ 24 h	Green (494/517 nm)	• Short-term, whole-cell labeling of live cells • For cell viability or dye efflux assays
Acridine Orange	Nucleus & Cytoplasm	Yes	Yes	Yes	Possibly toxic	Days	Green ( DNA) Red ( RNA)	• Membrane permeant nucleic acid dye • Stains DNA green (Ex/Em 500/526 nm), RNA red (Ex/Em 496/650 nm)
CellBrite® Steady Membrane Staining Kits	Membrane/ Cell Surface	No	No	No	Yes	Days	5 Colors Blue to Near-IR	• Image live cell surface for ≥24 hours • Optional Enhancer masks intracellular signal • Fast, even staining in complete medium • STORM-compatible options
CellBrite® Cytoplasmic Membrane Dyes CellBrite® NIR Cytoplasmic Membrane Stains	Membranes³	Yes²	No²	Yes²	Yes	Days to weeks³	8 Colors Blue to Near-IR	• Lipophilic carbocyanine membrane dyes • Fix before or after labeling² • Stable & non-toxic for cell tracking³
CellBrite® Fix Membrane Stains	Membrane/ Cell Surface³	Yes	Yes	No	Yes	Days³	Green (480/513 nm) Red (542/571 nm) Far-Red (638/667 nm)	• Covalent membrane labeling • More uniform staining than lipophilic dyes • Stain yeast and bacteria
MemBrite® Fix Cell Surface Stains	Cell surface³	Yes	Yes	No	Yes	Days³	8 colors Blue to Near-IR	• Covalent labeling of surface proteins • Rapid, uniform cell surface staining • STORM-compatible dye options • Stain yeast and gram-positive bacteria
SynaptoGreen™ & SynaptoRed™ Nerve Terminal Dyes	Vesicles	Yes⁴	Yes⁴	No	Yes	Minutes to hours	Green (~480/600 nm) Red (~510/750 nm)	• Cationic styryl membrane dyes • Track vesicle trafficking & release • Dye options with fixable amine group • Equivalent to FMÂ® dyes
CF® Dye Cholera Toxin Conjugates	Lipid rafts	Yes	Yes	Yes	Yes	≤ 24 h	6 colors Green to Near-IR	• Binds GM1 ganglioside in lipid rafts • For cell surface labeling or neuronal tracing • Staining can be heterogeneous in cultured cells
CF® Dye Transferrin Conjugates	Endocytic tracer	Yes	Yes	No	Yes	≤ 24 h	7 colors Green to Near-IR	• Transferrin receptor ligand • Traffics to recycling endosomes
CF® Dye Dextrans	Fluid phase tracer	Yes	No	No	Yes	≤ 24 h	Wide selection Green to Near-IR	• Fluid phase endocytosis & permeability tracers • Range of molecular weights
WGA Conjugates ConA Conjugates PNA Conjugates	Glycoproteins	Yes	Yes	Yes	Possibly toxic	≤ 24 h	Wide selection UV to Near-IR	• Bind to cell surface glycoproteins³ • Binding/biological effects vary by cell type • See Stains in Different Organisms for bacteria/yeast • Wide choice of CFÂ® dye colors
LipidSpot™ Lipid Droplet Stains	Lipid droplets / Neutral lipids	Yes	Yes	Yes	Yes	≥24 h	Green (427/585 nm) Far-red (610/663 nm)	• No wash, live or fixed cell staining • Tolerates permeabilization
LysoView™ Dyes	Lysosomes	No	No	No	Yes	Days	Blue, Green, Orange, Far-Red	• No wash, live cell staining of lysosomes
MitoView™ Dyes	Mitochondria/ Cell viability	No⁵	No	No⁵	Yes	Days	Blue, Green, Far-Red, Near-IR	• No wash, live cell staining of mitochondria • MitoView™ 633 is potential-dependent
MitoView™ Fix 640	Mitochondria/ Cell viability	Yes	Yes	No	Yes	Days	Far-red (644/665 nm)	• No wash, non-toxic mitochondria staining • Stable for several days • Tolerates fixation and permeabilization
Aquaphile™ JC-1 JC-1, Iodide JC-1, Chloride JC-1 Mitochondrial Membrane Kit	Mitochondria/ Cell viability	No	No	No	Yes	Days	Green (510/527 nm, cytoplasm), Red (585/590 nm, healthy mitochondria)	• No wash, live cell staining of mitochondria • Measure mitochondrial potential/cell health • Green fluorescence in cytoplasm, red fluorescence in polarized mitochondria
TMRM TMRE	Mitochondria/ Cell viability	No	No	No	Yes	Days	Red (548/573 nm)	• No wash, live cell staining of mitochondria • Preferred dyes for quantitative mitochondrial membrane potential measurement
Annexin V Conjugates	Apoptotic cell membranes	Yes	No	No	Yes	Days	Wide selection UV to Near-IR	• Stain cell surface of apoptotic cells • Washing is optional • Azide-free options for real-time imaging
NucView® Caspase-3 Substrates	Apoptotic cell nuclei	Yes	Yes	No	Yes	Days	Blue (429/469 nm) Green (500/530 nm) Orange (528/563 nm)	• Detect caspase-3 activity in intact cells • No-wash assay for endpoint or real-time analysis • NucView® 488 tested in >100 cell types & 200 papers
Cell-Membrane- Impermeant Nucleic Acid Dyes	Necrotic cells⁶	No	No	No⁶	Yes	Days	Wide selection Green to Far-Red	• No wash staining for real-time imaging • See Dead Cell & Apoptosis Stains

¹ Stability of staining is a general guideline only, actual stability may depend on cell type/experimental system.
² Formaldehyde fixation only, dyes do not tolerate alcohol/solvent treatment; dyes have poor tolerance for detergent, but cells can be stained after fixation/permeabilization with good results.
³ Surface staining is internalized by endocytosis, becoming mostly intracellular after several hours.
⁴ Dye options with formaldehyde-fixable amine groups; can be used with a low-detergent permeabilization protocol.
⁵ Cells can be fixed before or after MitoView™ Green staining, but dye localization will not be as specific as in live cells. We recommend mitochondrial marker antibodies for fixed cell staining.
⁶ Necrotic cell stains also stain late apoptotic cells with leaky membranes; staining is not dead cell-selective in fixed samples.

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Stains for Fixed Cells or Tissue Sections

Product	Target	Also stains live cells?	Color (Ex/Em)	Applications / Notes
Phalloidin Conjugates	F-actin	No	Wide selection UV to Near-IR	• Widely used stain for actin filaments • Formaldehyde-fixation only (no methanol fixation)
CF® Dye α-Bungarotoxin Conjugates	Nicotinic acetylcholine receptor	Yes	Wide selection UV to Near-IR	• Labels neuromuscular junctions
CytoLiner™ Fixed Cell Membrane Stains	Cell Membrane	Yes¹	5 colors Blue to Near-IR	• Novel lipophilic dyes for bright & uniform membrane staining in fixed cells
CellBrite® Cytoplasmic Membrane Dyes CellBrite® NIR Cytoplasmic Membrane Stains	Cell Membrane	Yes	8 colors Blue to Near-IR	• Lipophilic dyes for stable, non-toxic membrane labeling • Fix before or after labeling²
CF® Dye WGA Conjugates CF® Dye ConA Conjugates CF® Dye PNA Conjugates	Glycoproteins	Yes	Wide selection UV to Near-IR	• Bind to cell surface glycoproteins • May stain intracellular targets in permeabilized cells • Staining is tissue- and cell-type dependent
CF® Dye Cholera Toxin Conjugates	GM1 ganglioside in lipid rafts	Yes	6 colors Green to Near-IR	• For cell surface labeling or neuronal tracing • Expression/staining can be heterogeneous in cultured cells
LipidSpot™ Lipid Droplet Stains	Lipid droplets / Neutral lipids	Yes	Green (427/585 nm) and Far-red (610/663 nm in vegetable oil, ~592/638 nm in cells)	• Stain before or after fixation • Tolerates permeabilization after fixation
Organelle marker antibodies	Mitochondria, nuclear envelope, nucleoli, Golgi and more	No	Wide selection Blue to Near-IR	• Best options for fixed cell organelle staining
MitoView™ Green	Mitochondria	Yes	Green	• Can be used if suitable mitochondria antibody not available • Staining not as specific as in live cells

¹ CytoLiner™ Fixed Cell Membrane Stains may have higher background if used to stain live cells before fixation than when used to stain cells after fixation.
² Formaldehyde fixation only, dyes do not tolerate alcohol/solvent treatment; dyes have poor tolerance for detergent, but cells can be stained after fixation/permeabilization with good results.

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Dead Cell & Apoptosis Stains

Product	Target	Nuclear- specific	Fix after staining	Permeabilize after staining	Color (Ex/Em)	Applications / Notes
Oxazole Blue	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Blue (434/457 nm)²	• Cell-impermeant monomeric nucleic acid dye • Reported to selectively stain early apoptotic cells • Equivalent to PO-PRO™-1
Oxazole Blue Homodimer	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Blue (433/457 nm)²	• Cell-impermeant monomeric nucleic acid dye • Equivalent to POPO™-1
NucView® Caspase-3 Substrates	Apoptotic cells Caspase activity	Yes	Yes	Yes	Blue (429/469 nm)² Green (500/530 nm)² Orange (528/563 nm)²	• Detect caspase-3 activity in intact cells • No-wash assay for endpoint assay or real-time analysis • NucView® 488 validated in >100 cell types & 200 papers
CF® Dye Annexin Conjugates	Apoptotic cells Phosphatidylserine	No	Yes	No	Wide selection UV to Near-IR	• Annexin V with CF® dyes & other labels • Available preservative-free for real-time cell imaging
Live-or-Dye™ Fixable Viability Stains	Necrotic cells¹ Cell-impermeant reactive dyes	No	Yes	Yes	8 Colors UV to Near-IR	• Covalent labeling of dead cell cytoplasm • Excellent tolerance for fixation/permeabilization • Wash required after staining
NucSpot® Nuclear Stains	Necrotic cells¹ Cell-impermeant DNA dyes	Yes	No	No	7 Colors Green to Near-IR	• Nuclear-specific counterstains or dead cell stains • No-wash staining, compatible with real-time imaging
Oxazole Yellow	Early apoptotic cells Cell-impermeant DNA/RNA dye	No	No	No	Green (491/506 nm)²	• Equivalent to YO-PRO®-1 Iodide • Reported to selectively stain early apoptotic cells • No-wash staining, compatible with real-time imaging
Oxazole Yellow Homodimer	Early apoptotic cells Cell-impermeant DNA/RNA dye	No	No	No	Green (491/508 nm)²	• Equivalent to YOYO®-1 Iodide • No-wash staining, compatible with real-time imaging
TO Iodide	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Green (515/531 nm)²	• Equivalent to TO-PRO®-1 Iodide • No-wash staining, compatible with real-time imaging
Thiazole Orange Homodimer	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Green (514/531 nm)²	• High-affinity dimeric cyanine DNA/RNA dye • Equivalent to TOTO®-1 Iodide • No-wash staining, compatible with real-time imaging
PathoGreen™ Histofluorescent Stain	Degenerating neurons	No	N/A	N/A	Green (497/520 nm)	• For fixed neuronal cells/tissue sections
CF® Dye TUNEL Assay	Apoptotic cells DNA strand breaks	Yes	N/A	N/A	Green (490/515 nm) Red (593/614 nm) Far-red (642/662 nm)	• Label dsDNA breaks with bright, photostable CF® dyes • For fixed cells or tissue sections
Live-or-Dye NucFix™ Red	Necrotic cells¹ Cell-impermeant DNA/RNA dye	Yes³	Yes	Yes	Red (520/610 nm)²	• Covalent, red fluorescent dead cell nuclear stain • The only fixable dead cell nuclear stain • Wash after staining required
Ethidium Homodimer III	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Red (530/620 nm)²	• Developed at Biotium as an alternative to EthDI • 45% brighter than EthDI when bound to DNA
Ethidium Homodimer I	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Red (528/616 nm)²	• High-affinity membrane-impermeant DNA/RNA stain • >30-fold fluorescence enhancement upon binding DNA
Propidium Iodide	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Red (535/617 nm)²	• Can be excited at 488 nm for the PE channel • Useful for cell cycle analysis in fixed cells (with RNase)
RedDot™2 Far-Red Nuclear Stain	Necrotic cells¹ Cell-impermeant DNA/RNA dye	Yes	No	No	Far-red (662/694 nm)²	• Far-red nuclear counterstain or dead cell stain • Compare to Draq7™ • No-wash staining, compatible with real-time imaging
Thiazole Red Homodimer	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Far-red (642/661 nm)²	• High-affinity dimeric cyanine DNA/RNA dye • Equivalent to TOTO®-3 Iodide • No-wash staining, compatible with real-time imaging
Thiazole Red	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Far-red (642/657 nm)²	• Equivalent to TO-PRO®-1 Iodide • No-wash staining, compatible with real-time imaging
7-AAD	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Far-Red (546/647 nm)²	• Far-red dye for the PE-Cy®5 flow cytometry channel • Can be excited by the 488 nm or 532 nm laser line • Useful for cell cycle analysis in fixed cells
NucSpot® Far-Red	Necrotic cells¹ Cell-impermeant DNA/RNA dye	No	No	No	Far-Red (597/667 nm)²	• Designed as improved replacement for 7-AAD • For flow cytometry in the PE-Cy®5 or APC channel • Less bleed into the PE-Texas Red® channel • Useful for cell cycle analysis in fixed cells

¹ Necrotic cell stains also stain late apoptotic cells with leaky cell membranes.
² With DNA.
² Not nuclear-specific in yeast.
Cy Dye is a registered trademark of Cytiva; POPO, TOTO, YOYO, TO-PRO, PO-PRO, and YO-PRO are trademarks or registered trademarks of Thermo Fisher Scientific; Draq5 and Draq7 are trademarks of Biostatus, Ltd.

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Stains for Cell Cycle Analysis by Flow Cytometry

Product	Live or Fixed Cells?	RNase treatment required?	Color (Ex/Em)¹	Applications / Notes
NucSpot® 470	Fixed	No	Green (460/546 nm)	• Nuclear-specific green counterstain for fixed cells • Selectively stains dead cells in live cultures • Excellent match for blue LED excitation sources
Propidium Iodide	Fixed	Yes	Red (535/617 nm)	• Widely used dead cell stain • Can be excited by 488 nm laser line for detection in the PE channel
7-AAD	Fixed	No	Far-Red (546/647 nm)	• Far-red dye for detection in the PE-Cy®5 channel • Can be excited by the 488 nm or 532 nm laser line
NucSpot® Far-Red	Fixed	No	Far-Red (597/667 nm)	• Designed as improved replacement for 7-AAD • For the PE-Cy®5 or APC channel • Less bleed into the PE-Texas Red® channel
RedDot™1 Far-Red Nuclear Stain	Live	No	Far-red (662/694 nm)	• For short-term live cell staining (≤4 hours) • Useful for cell number normalization for In Cell Western® • Can be excited at wavelengths between 488 and 647 nm • Detect in Cy®5 or APC channel

¹ With DNA
Cy Dye is a registered trademark of Cytiva. In Cell Western is a registered trademarks of LI-COR Inc.

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Stains for Spheroids, 3D Cultures, or Matrigel® Cultures

Product	Target	Fixable?	Tolerates optical clearing?	Applications / Notes
Hoechst 33342 Hoechst 33258	All cell nuclei	Yes	Yes	• See Nuclear Stains
NucSpot® Live Nuclear Stains	All cell nuclei	Yes	ND	• See Nuclear Stains
CellBrite® Cytoplasmic Membrane Dyes CellBrite® NIR Cytoplasmic Membrane Stains	Cell membranes	Yes¹	No	• Lipophilic carbocyanine dye have been used for labeling cells before or after spheroid formation • See Live Cell Stains
MitoView™ Dyes	Mitochondria	No	No	• See Live Cell Stains
NucView® 488 Caspase-3 Substrate	Apoptotic cells	Yes	Yes	• See Dead Cell & Apoptosis Stains
Calcein-AM	Viable cells (whole cell interior)	No	No	• Commonly used to stain cells in Matrigel® or spheroids • See Live Cell Stains
Cell-Membrane Impermeant Nucleic Acid Dyes	Necrotic cells²	No	No	• See Dead Cell & Apoptosis Stains
ViaFluor® SE Cell Proliferation Dyes	Whole cell interior	Yes	Yes	• Can be used to label cells before seeding in Matrigel® or spheroids • See Live Cell Stains
LipidSpot™ Lipid Droplet Stains	Lipid droplets	Yes¹	ND	• LipidSpot™ 488 has been validated for staining 3D cell spheroids
ViaFluor® Live Cell Microtubule Stains CellBrite® Steady Membrane Staining Kits LysoView™ Dyes	Membrane and various organelles	No	ND	• May be suitable for staining spheroids, 3D cultures, or Matrigel® cultures, but have not yet been validated

¹ Formaldehyde fixation only, dyes do not tolerate alcohol/solvent treatment; dyes have poor tolerance for detergent, but cells can be stained after fixation/permeabilization with good results.
² Necrotic cell stains also stain late apoptotic cells with leaky membranes; staining is not dead cell-selective in fixed samples.
Matrigel is a registered trademark of Corning, Inc.

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Cellular Stains in Different Organisms

The table below lists the application of several cellular stains for various organisms. A “Yes” indicates the stain is validated for the organism and may be used for reliable analysis. A “No” indicates that we do not recommend this stain for that organism; however some staining may still occur. See our FAQ for more information.

Localization	Product	Mammalian Cells	Yeast	Gram+ Bacteria	Gram- Bacteria	Notes / Applications
Cell Surface	CytoLiner™ Fixed Cell Membrane Stains	Yes	N/A	N/A	N/A	• See Stains for Fixed Cells & Tissue Sections
	CellBrite® Cytoplasmic Membrane Dyes	Yes	No	No	No	• See Live Cell Stains • See Stains for Fixed Cells & Tissue Sections
	CellBrite® Steady Membrane Dyes	Yes	No	No	No	• See Live Cell Stains
	CellBrite® Fix Membrane Stains	Yes	Yes	Yes	Yes	• See Live Cell Stains
	MemBrite® Fix Membrane Stains	Yes	Yes	Yes	No	• See Live Cell Stains
	BactoSpore™ 485/500 Membrane Stain	Yes¹	Yes¹	Yes	Yes	• see Microbiology Stains
	SynaptoGreen™ C4 (FM®1-43)	Yes	Yes²	Yes	Yes	• See Live Cell Stains
	SynaptoRed™ C2 (FM®4-64)	Yes	Yes²	Yes	Yes	• See Live Cell Stains
	CF® Dye WGA Conjugates	Yes	Yes³	Yes	No	• See Live Cell Stains • See Stains for Fixed Cells & Tissue Sections
	CF® Dye ConA Conjugates	Yes	Yes	No	No	• See Live Cell Stains • See Stains for Fixed Cells & Tissue Sections
	Calcofluor White	No	Yes	Yes	No	• Stains cell walls of fungi, algae, and plants
DNA	Hoechst	Yes	No⁴	Yes	Yes	• See Nuclear Stains
	DAPI	Yes	No⁴	Yes	Yes	• See Nuclear Stains
	NucSpot® Live Cell Nuclear Stains	Yes	No	Yes	No	• See Nuclear Stains
	BactoSpore™ 488/540 Nuclear Stain	No data	No data	Yes	Yes	• see Microbiology Stains
	RedDot™1 Far-Red Nuclear Stain	Yes	No⁴	Yes	Yes	• See Nuclear Stains
	DMAO	Yes⁵	No⁴	Yes	Yes	• Green fluorescent nucleic acid dye for live bacteria
	BactoView™ Live Green	Yes	No⁴	Yes	Yes	• Green and red fluorescent nucleic acid dyes for live & dead bacteria
	BactoView™ Live Red	No⁵	No⁴	Yes	Yes
	Thiazole Orange	Yes⁶	Yes¹²	Yes	Yes	• See Nuclear Stains
Dead Cells (Yes indicates dead cell selectivity)	Propidium Iodide	Yes	Yes	Yes	Yes	• See Nuclear Stains
	Ethidium Homodimer I (EthD-I)	Yes	Yes	Yes	Yes	• See Nuclear Stains
	Ethidium Homodimer III (EthD-III)	Yes	Yes	Yes	Yes	• See Nuclear Stains
	RedDot™2	Yes	Yes	Yes	Yes	• See Nuclear Stains
	Live-or-Dye™ NucFix Red	Yes	Yes⁷	No⁸	Yes	• See Nuclear Stains
	Live-or-Dye™ Fixable Viability Stains	Yes	Yes	Yes	Yes	• See Nuclear Stains
	NucSpot® Nuclear Stains	Yes	Yes	No⁸	Yes	• See Nuclear Stains
	BactoView™ Dead Stains	Yes	No data	Yes	Yes	• see Microbiology Stains
Cytoplasm	ViaFluor® 405 SE Cell Proliferation Dye	Yes	No⁹	Yes	No	• See Live Cell Stains
	ViaFluor® 488 SE Cell Proliferation Dye	Yes	No⁹	Yes	No	• See Live Cell Stains
	ViaFluor® CFSE Cell Proliferation Dye	Yes	Yes	Yes	No	• See Live Cell Stains
Intracellular Structures	MitoView™ 405	Yes	Yes	Yes	Yes	• See Live Cell Stains
	MitoView™ Green	Yes	Yes	Yes	Yes	• See Live Cell Stains
	MitoView™ 633	Yes	Yes	Yes	Yes	• See Live Cell Stains
	MitoView™ 650	Yes	Yes	Yes	Yes	• See Live Cell Stains
	MitoView™ 720	Yes	Yes	Yes	Yes	• See Live Cell Stains
	LysoView™ 405	Yes	No¹⁰	Yes	Yes	• See Live Cell Stains
	LysoView™ 488	Yes	No	Yes	No	• See Live Cell Stains
	LysoView™ 540	Yes	Yes	No	No	• See Live Cell Stains
	LysoView™ 633	Yes	Yes	No	No	• See Live Cell Stains
	LysoView™ 650	Yes	No	No	No	• See Live Cell Stains
	LipidSpot™ 488 Lipid Droplet Stain	Yes	Yes	Yes	No	• See Live Cell Stains
	LipidSpot™ 610 Lipid Droplet Stain	Yes	No	Yes	No	• See Live Cell Stains
	Phalloidin Conjugates	Yes	Yes	No	No	• See Stains for Fixed Cells & Tissue Sections
	ViaFluor® Live Cell Microtubule Stains	Yes	No¹¹	No¹¹	No¹¹	• See Live Cell Stains
	ViaVac™ Red/Green	No	Yes	No data	No data	• Stains vacuoles in healthy yeast red; stains cytoplasm of all yeast green • Equivalent to FUN®1

¹ Stains intracellular membranes
² Internalizes to vacuolar membranes
³ Stains bud scars of budding yeast
⁴ Weak staining and not nuclear
⁵ Staining is not nuclear
⁶ Initially stains mitochondria, then redistributes to nucleus & cytoplasm
⁷ Dead cell specific but not nuclear
⁸ Stains live and dead cells
⁹ Not cytoplasmic, stains cell periphery
¹⁰ Staining is not lysosomal
¹¹ Not predicted to bind yeast/bacteria cytoskeleton
¹² Staining is both nuclear and cytoplasmic
FUN1 is a registered trademark of Thermo Fisher Scientific

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Related categories

Cell Surface & Membrane Dyes

Cytoskeletal Stains

Dyes for Mitochondria & Other Organelles

Nuclear Stains & DNA/RNA Dyes

Related downloads

Faq

CellBrite® & MemBrite® Membrane & Cell Surface Stains

What is the difference between CellBrite®, CellBrite® NIR, CellBrite® Fix, and MemBrite® Fix?

CellBrite® Cytoplasmic Membrane Stains are lipophilic dyes for simple, non-toxic, stable labeling of membranes in live or fixed cells. Cells can be fixed with formaldehyde before or after CellBrite® staining. But the staining has poor tolerance for permeabilization or methanol fixation, so CellBrite® staining is not easily combined with intracellular immunofluorescence (IF) staining. The dyes also do not stain bacteria or yeast. CellBrite® NIR dyes are CellBrite® dyes with near-infrared fluorescence compatible with small animal NIR imaging systems. CellBrite® Fix and MemBrite® Fix stains were developed to overcome some of these shortcomings. They are novel covalent stains that can be fixed and permeabilized for IF staining. CellBrite® Fix Membrane Stains are fluorogenic reactive membrane dyes that rapidly accumulate at the plasma membrane. When they incorporate into lipids, they become fluorescent, and at the same time react covalently with membrane proteins for stable labeling. Staining takes only 15 minutes in a single step with no wash. CellBrite® Fix stains mammalian cells, yeast, and bacteria. MemBrite® Fix Cell Surface Stains do not bind lipids, but label cell surface proteins. MemBrite® Fix requires a two-step staining protocol with washing, but offers a more extensive choice of dye colors than CellBrite® Fix. MemBrite® Fix also can be used to stain yeast. But unlike original CellBrite® dyes and lectins, CellBrite® Fix and MemBrite® Fix cannot be used on cells that are already fixed. To select a dye that’s right for your application, see our Membrane and Cell Surface Stains Comparison, or download our Membrane & Surface Stains Brochure.

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Can CellBrite® or MemBrite® Stains be used to stain exosomes/extracellular vesicles?

CellBrite® Cytoplasmic Membrane Dyes do not efficiently stain EVs. Some of the CellBrite® Fix, MemBrite® Fix, and CellBrite® Steady dye options can be used for this application. However, for optimal staining of exosome membranes we recommend our ExoBrite™ True EV Membrane Stains, which are novel lipophilic membrane dyes specifically designed and optimized for efficient staining of EV membranes with minimal dye aggregation. See our Extracellular Vesicle Research page for more information about our complete line of EV stains and antibodies

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What is the difference between CellBrite® dyes and PKH dyes?

Biotium’s CellBrite® Cytoplasmic Membrane Dyes are dye delivery solutions that can be added directly to normal culture media to uniformly label suspended or adherent cells in culture. The PKH dyes are structurally related dyes for cell membrane labeling. But unlike CellBrite®, labeling with PKH dyes requires multiple steps and subjects cells to an iso-osmotic mannitol loading medium that can negatively affect cell membrane integrity and viability. CellBrite® Fix dyes also feature rapid and simple labeling in isotonic buffer. Cells can be fixed and permeabilized after labeling with CellBrite® Fix, unlike original CellBrite® dyes or PKH dyes, which don’t tolerate detergent.

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Microbiology: Dyes for bacteria and yeast

What stain can I use to differentiate bacterial cells from mammalian cells in a co-culture or infection model?

To date, we have not identified a fluorescent cellular stain that will detect bacteria but not mammalian cells with high specificity, or vice versa. While some mammalian cell stains show weak staining of bacteria, they usually do show some signal, and will frequently stain dead bacteria more intensely than live bacteria. We offer a selection of antibodies for specific bacterial antigens, which potentially have applications for differential staining of bacteria vs. mammalian cells, but we have not validated them in co-culture models. Also see our Viability PCR Technology Page to learn about how PMA dye can be used for highly specific detection of microbial cell viability in complex samples.

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Is staining with the Viability/Cytotoxicity Assay Kit for Bacteria Live & Dead Cells (cat. # 30027) compatible with subsequent fixation with paraformaldehyde (PFA)?

Fixation is not recommended after staining with the Viability/Cytotoxicity Assay Kit (cat. # 30027) as the dead cell dye, EthD-III will transfer to all cells and not maintain dead cell-specific staining. Our Live-or-Dye™ NucFix™ Red (cat. # 32010) is a formaldehyde-fixable dead cell dye that can be used in bacteria. Viability qPCR (vPCR) can be an alternative strategy for quantitating live and dead bacteria. Using dead cell-specific dyes, PMA (cat. # 40019) or PMAxx (cat. # 40069) that covalently modify DNA (of only dead cells) after photo-crosslinking, a simple quantitative PCR (qPCR) amplification is used to selectively amplify live-cell DNA. Learn more about the vPCR technology.

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Can I use CellBrite® or MemBrite® Stains with non-mammalian cells or organisms?

CellBrite® and MemBrite® Stains were originally developed for staining mammalian cells in culture, but some of the stains also have been validated for other organisms and applications. For dyes to stain yeast or bacteria membranes, see Cellular Stains in Different Organisms. For information on staining other organisms or cell types, please see our Tech Tip: Researching Applications for Membrane Dyes.

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Organelle & Cytoskeleton Stains

What is the staining mechanism of MitoView™ and other mitochondrial dyes? Where do they localize in the organelle?

Cationic dyes are widely used as mitochondrial probes. They accumulate within the cell and preferentially localize in the mitochondrial matrix, induced by the greater negative membrane potential of mitochondria in live cells compared to the plasma membrane potential. Membrane potential plays a direct role in governing the distribution of the dyes across the plasma membrane: the more negative the potential, the greater the accumulation of the positively charged dyes. MitoView™ 633 is a cationic lipophilic dye that is potential-dependent and accumulates in mitochondria in proportion to the electron gradient similar to classic dyes like TMRM, TMRE and Rhodamine-123. Ratiometric dyes like JC-1 constitute another class of potential-dependent mitochondrial dyes. In normal healthy cells, JC‐1 accumulates in the mitochondria and undergoes aggregation in a potential‐dependent manner, whereas in unhealthy, apoptotic or dying cells with dissipated mitochondrial potential, the dye delocalizes to the cytosol where it dissociates to the monomeric state. The aggregated dyes (J-aggregates) fluoresce red, while the monomeric dyes fluoresce green. Some mitochondrial‐specific dyes are considered “structural” dyes, as opposed to “functional” dyes, because they are capable of staining mitochondria regardless of their polarization status. The fluorescence of cells stained with these dyes is directly proportional to their mitochondrial content or “mitochondrial mass.” MitoView™ Green is a potential-independent dye that accumulates in the mitochondria and interacts with the mitochondrial matrix via hydrophobic interactions. It can be used to stain mitochondria in live as well as formaldehyde-fixed cells. MitoView™ Green staining is not compatible with solvent-based fixatives or permeabilization. Nonyl Acridine Orange (NAO) is another potential-independent mitochondrial dye that binds specifically to cardiolipin in the inner mitochondrial membrane. However, mitochondrial dye staining of fixed cells generally is less specific compared to live cell staining. For fixed cell staining, we recommend using one our CF® Dye conjugated mitochondrial marker antibodies.

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What is the mechanism of RedDot™ 1 or RedDot™ 2 binding to DNA? Are the dyes intercalators, or minor groove binders?

The mechanism of binding for RedDot™ 1 and RedDot™ 2 to DNA has not been characterized. However, based on the dye structure, it may bind by a similar mechanism as DRAQ®5, which has been reported in the literature to be a concentration-dependent intercalator and minor groove binder. DRAQ is a registered trademark of Biostatus, Ltd.

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Are TrueBlack® or TrueBlack® Plus lipofuscin autofluorescence quenchers compatible with lipid droplet stains like BODIPY or LipidSpot®?

TrueBlack® and TrueBlack® Plus are hydrophobic in nature and quench lipofuscin autofluorescence mainly through hydrophobic interactions. They could therefore stain/bind to lipid structures and quench the fluorescence signal of BODIPY and other lipid droplet stains. Also, original TrueBlack® #23007 is used in 70% EtOH, which could interfere with lipid droplet morphology and affect staining. TrueBlack® Plus #23014, on the other hand, can be used in buffer instead of 70% ethanol, and may be more suitable for combining with lipid droplet staining. However, since the binding of TrueBlack® Plus is also dependent on hydrophobic interactions, we recommend testing TrueBlack® pre-treatment and post-treatment for compatibility with lipid droplet staining in your sample type.

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CellBrite® & MemBrite® Membrane & Cell Surface Stains

Microbiology: Dyes for bacteria and yeast

Organelle & Cytoskeleton Stains