For fluorescence imaging: SNR = S / √(S + B + R²), where S = signal electrons, B = background electrons, R = read noise (electrons RMS). At high signal (S >> R²), SNR ≈ √S (shot-noise limited). At low signal (S < 5 typically required for reliable identification.
Quality Metric
Signal-to-Noise Ratio
Can you see your signal above the noise?
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Definition
The ratio of detected signal to the uncertainty (noise) in that measurement. Higher SNR means clearer images and more reliable quantification. SNR determines whether dim features like single mRNA spots can be detected.
Technical Details
Simplified
Imagine trying to hear someone whisper in a noisy room. SNR tells you how loud the whisper is compared to the background noise. Higher SNR means you can clearly hear (see) what you're looking for; lower SNR means it gets lost in the noise.
Why It Matters
For smFISH, each mRNA spot produces perhaps 100-500 photons. With ~90% QE and background/read noise, the SNR determines whether spots are reliably detected or lost in noise. SNR directly affects spot counting accuracy.
Practical Example
smFISH spot with 300 detected electrons, 50 background electrons, 1.5e⁻ read noise: SNR = 300/√(300 + 50 + 2.25) ≈ 16. This is excellent—spots will be clearly visible above noise.