Fluorescent Proteins: In Vivo Imaging
Fluorescence microscopy is a powerful tool to study proteins and cells, but imaging in deep-tissue organs or whole animals presents unique challenges. Genetically-encoded fluorescent proteins most suitable for stable imaging in live animals are those with emission near or above 650 nm (far-red or near-infrared), as signals below 650 nm are highly absorbed by hemoglobin and cause undesirable background signals.
Many near-infrared fluorescent proteins are derived from bacterial phytochrome photoreceptors. Spectrally distinct fluorescent iRFP variants have been shown to have high brightness and allow for single or multicolor imaging. Photoactivatable iRFPs can be turned on by non-phototoxic far-red light and can be used for spatially selective imaging of tissues in living animals. Learn more about in vivo imaging tools in this blog post.
Far-Red
| Protein | Excitation (nm) | Emission (nm) | Brightness | Plasmids |
|---|---|---|---|---|
| mCardinal | 604 | 659 | 18 | pcDNA3-mCardinal |
| mNeptune2 | 600 | 650 | 21 | pcDNA3-mNeptune2 mNeptune2-N1 |
| E2-Crimson | 611 | 646 | 29 | pEF.myc.ER-E2-Crimson pAAV-CAG-E2-Crimson |
Near-Infrared
| Protein | Excitation (nm) | Emission (nm) | Brightness | Plasmids |
|---|---|---|---|---|
| emiRFP670 | 642 | 670 | 12 | pemiRFP670-N1 |
| miRFP670 | 642 | 670 | 12 | pmiRFP670-N1 |
| iRFP670 | 643 | 670 | 12.7 | piRFP670-N1 |
| miRFP670nano3 | 645 | 670 | 24 | pcDNA-miRFP670nano3 |
| miRFP680 | 661 | 680 | 14 | pmiRFP680-N1 |
| iRFP682 | 663 | 682 | 10.2 | piRFP682-N1 |
| emiRFP703 | 674 | 703 | 8 | pemiRFP703-N1 |
| iRFP702 | 673 | 702 | 7.6 | piRFP702-N1 |
| miRFP703 | 673 | 703 | 8 | pmiRFP703-N1 |
| miRFP709 | 683 | 709 | 4 | pmiRFP709-N1 |
| miRFP713 | 690 | 713 | 7 | pmiRFP713-N1 |
| iRFP (aka iRFP713) | 690 | 713 | 6.2 | piRFP |
| miRFP720 | 702 | 720 | 6 | pmiRFP720-N1 |
| iRFP720 | 702 | 720 | 5.8 | piRFP720-N1 |
Photoactivatable
| Protein | Excitation (nm) | Emission (nm) | Activation (nm) | Brightness | Plasmids |
|---|---|---|---|---|---|
| PAiRFP1 | 690 | 717 | 660 or 750 | 3.2 | pPAiRFP1-N1 |
| PAiRFP2 | 692 | 719 | 660 or 750 | 3 | pPAiRFP2-N1 |
Additional Resources
Content last reviewed: 4 December 2025
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