# Simple and Robust Deep Learning Approach for Fast Fluorescence Lifetime Imaging

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## Abstract

**:**

## 1. Introduction

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_{2}) [3,4,5,6,7]. In combination with Förster resonance energy transfer (FRET), FLIM–FRET has been widely used as a “quantum ruler” to quantify protein–protein conformations and interactions [8,9]. Fluorescence lifetimes are local properties of fluorophores depending only on the physicochemical state of the local microenvironment (e.g., pH, ionic strength). They are free of artifacts due to fluctuations in laser power, optical path, and fluorophore concentrations. There are time and frequency domain approaches for measuring fluorescence lifetimes [10,11]. Among them, time-correlated single-photon counting (TCSPC) [12] has been widely used due to its superior photon efficiency, high signal-to-noise ratio, and superior temporal resolution [13]. TCSPC records photon arrival times after shining laser pulses and yields decay histograms, from which fluorescence lifetimes can be extracted. Theoretically, a fluorescence decay histogram can be expressed as [14]:

## 2. Methods and Theory

#### 2.1. Architecture Design

#### 2.2. Training Dataset Preparation

**·**) is the FLIM instrument response function, approximated by a Gaussian function with FWHM = 167 ps. The asterisk ($\ast $) refers to a convolution operator. The total photon counts $Y=\int y\left(t\right)dt$ of synthetic signals range from 100 to 1 × 10

^{4}. The SNR of a signal is defined as:

#### 2.3. Training and Evaluation

^{−4}in the standard back-propagation [36]. The training dataset contains 40,000 different signals and their corresponding lifetimes. Both mono- and biexponential decays were included in training datasets. For monoexponential signals, the lifetime range is [0.1, 5] ns, and for biexponential signals, ${\tau}_{1}and{\tau}_{2}$ are set in [0.1, 1], [1, 5] ns. The trained lifetimes cover a wide range of lifetimes of commonly used fluorophores for biomedical applications. Figure 2b shows the signals under different SNRs, the green curve stands for decay, and the red curve means IRF.

^{−4}, indicating that the network is well trained as the estimated lifetimes are close to their ground truths. Because of the simple network structure, the number of hyperparameters is only 26,081. The training time is half an hour on a typical desktop using a central processing unit (CPU).

## 3. Simulation Results

## 4. Experimental Results and Discussion

#### 4.1. Rhodamine 6G and Rhodamine B Solutions

#### 4.2. Convallaria majalis Cells

## 5. Conclusions

## Author Contributions

## Funding

## Institutional Review Board Statement

## Informed Consent Statement

## Data Availability Statement

## Acknowledgments

## Conflicts of Interest

## References

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**Figure 1.**(

**a**) Logic of the deep learning algorithm based on a predictive model considering training and testing phases. (

**b**) Comparison of fluorescence lifetime prediction methods related to inference time and accuracy for one FLIM image.

**Figure 2.**(

**a**) MLP-Mixer architecture. The MLP-Mixer consists of per-patch linear embeddings, mixer layers, and a regression layer. The mixer block contains one token-mixing MLP (MLP1) and one channel-mixing MLP (MLP2), each consisting of two fully connected layers and a GELU nonlinearity. Other components include skip connections, dropout, and layer norm on channels. (

**b**) Decays under different SNRs, the green curve stands for decay, and the red curve means IRF. (

**c**) Mean square error (MSE) plots of the training and validation loss for τ_ave.

**Figure 3.**Boxplots of estimations under different signal-to-noise ratios (SNRs) with the four methods, in which the median and quartiles with whiskers reach up to 1.5 times the interquartile range. The violin plot outlines illustrate kernel probability density; for example, the width of the shaded area represents the proportion of the data. (

**a**) Short lifetime (set at 1 ns) and (

**b**) long lifetime (set at 4 ns) estimations from synthetic data; (

**c**,

**d**) corresponding bias and standard deviation plots for (

**a**) short and (

**b**) long lifetimes.

**Figure 4.**${\tau}_{A}$ estimation error planes of the MLP-Mixer, 1D-CNN, NLSM, and VPM at different fraction ratios α under different signal-to-noise ratios. For signals following a biexponential decay model where ${\tau}_{1}\in \left(0.5,1.5\right)ns,{\tau}_{2}\u03f5\left(2.5,3\right)ns$. The error planes (

**a**,

**d**,

**g**) SNR 26 dB, (

**b**,

**e**,

**h**) SNR 34 dB, (

**c**,

**f**,

**i**) SNR 38 dB, and α = 0.2, 0.5, 0.8.

**Figure 5.**Two-photon FLIM experiments of Convallaria majalis cells. (

**a**–

**d**) Intensity images under different SNRs (3 s, 15 s, 30 s, and 90 s acquisition time). Lifetime images recovered from (

**e**–

**h**) the MLP-Mixer, (

**i**–

**l**) 1D-CNN, (

**m**–

**p**) NLSM, and (

**q**–

**t**) VPM. (

**u**–

**x**) Lifetime histograms for each case.

Algorithm | Total Parameters | FLOPs | Total Training Time (s) | Inference Time |
---|---|---|---|---|

MLP-Mixer | 61,306 | 5.9 B | 1871.0 | 12.54 s |

1D-CNN | 17,409 | 5.4 B | 2270.65 | 34.06 s |

Rhodamine B | SNR 26~32 | SNR 32~38 | SNR 38~44 | τ_REF (ns) | |

MLP-Mixer | ${\tau}_{mean}$ (ns) | 1.70 | 1.73 | 1.71 | 1.72 [37] |

Std | 0.40 | 0.46 | 0.50 | ||

Bias | 1.16% | 0.58% | 0.58% | ||

${\tau}_{mean}$ (ns) | 1.68 | 1.65 | 1.69 | ||

1D-CNN | Std | 0.59 | 0.54 | 0.52 | |

Bias | 2.33% | 4.07% | 1.74% | ||

${\tau}_{mean}$ (ns) | 1.55 | 1.61 | 1.63 | ||

NLSM | Std | 0.39 | 0.24 | 0.27 | |

Bias | 9.88% | 6.40% | 5.32% | ||

${\tau}_{mean}$ (ns) | 1.62 | 1.64 | 1.67 | ||

VPM | Std | 0.52 | 0.47 | 0.45 | |

Bias | 5.81% | 4.56% | 2.96% | ||

Rhodamine 6G | SNR 26~32 | SNR 32~38 | SNR 38~44 | τ_REF (ns) | |

MLP-Mixer | ${\tau}_{mean}$ (ns) | 4.00 | 4.04 | 4.07 | 4.06 [38] |

Std | 0.59 | 0.46 | 0.62 | ||

Bias | 1.48% | 0.5% | 0.25% | ||

${\tau}_{mean}$ (ns) | 4.22 | 3.93 | 3.94 | ||

1D-CNN | Std | 0.78 | 0.7 | 0.72 | |

Bias | 3.94% | 3.20% | 2.95% | ||

${\tau}_{mean}$ (ns) | 3.58 | 3.68 | 3.75 | ||

NLSM | Std | 0.53 | 0.27 | 0.34 | |

Bias | 11.82% | 9.36% | 7.64% | ||

${\tau}_{mean}$ (ns) | 3.79 | 3.89 | 3.92 | ||

VPM | Std | 0.87 | 0.61 | 0.48 | |

Bias | 6.65% | 4.19% | 3.45% |

**Table 3.**SSIM values under different photon counts in Figure 5.

Data | MLP-Mixer | 1D-CNN | NLSM | VPM |
---|---|---|---|---|

HPC | 0.98 | 0.95 | 0.94 | 0.95 |

MPC | 0.96 | 0.94 | 0.91 | 0.94 |

LPC | 0.95 | 0.93 | 0.81 | 0.93 |

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**MDPI and ACS Style**

Wang, Q.; Li, Y.; Xiao, D.; Zang, Z.; Jiao, Z.; Chen, Y.; Li, D.D.U.
Simple and Robust Deep Learning Approach for Fast Fluorescence Lifetime Imaging. *Sensors* **2022**, *22*, 7293.
https://doi.org/10.3390/s22197293

**AMA Style**

Wang Q, Li Y, Xiao D, Zang Z, Jiao Z, Chen Y, Li DDU.
Simple and Robust Deep Learning Approach for Fast Fluorescence Lifetime Imaging. *Sensors*. 2022; 22(19):7293.
https://doi.org/10.3390/s22197293

**Chicago/Turabian Style**

Wang, Quan, Yahui Li, Dong Xiao, Zhenya Zang, Zi’ao Jiao, Yu Chen, and David Day Uei Li.
2022. "Simple and Robust Deep Learning Approach for Fast Fluorescence Lifetime Imaging" *Sensors* 22, no. 19: 7293.
https://doi.org/10.3390/s22197293