YOLOv5-FPN: A Robust Framework for Multi-Sized Cell Counting in Fluorescence Images
Abstract
:1. Introduction
- We utilized YOLOv5, a state-of-the-art object detection algorithm, for cell counting in fluorescence microscopy images.
- We employed the FPN as a feature extractor to handle cells of different sizes in the images.
- We annotated the cell images with bounding boxes using a labeling tool for training the YOLOv5 model.
- We augmented the original dataset of 283 images to 600 images with rotation, scaling, and flipping to improve the model’s performance.
- We evaluated the performance of the YOLOv5 model with an FPN on the cell counting task and compared it to other YOLOv5 model versions.
2. Literature Review
3. Baseline Architecture
3.1. Overview of YOLOv5 Architecture
3.2. Overview of FPN Architecture and Implementation
3.3. Combining YOLOv5 and FPN
3.3.1. Backbone
3.3.2. Neck
3.3.3. Head
4. Methodology
4.1. Dataset Preparation
4.2. Dataset Augmentation
- Horizontal flipping: The images were horizontally flipped to generate new images.
- Rotation: The images were rotated at different angles to create variations in the cell positions and orientations.
- Brightness and contrast adjustment: The brightness and contrast of the images were adjusted within a range of −40 to +40 to simulate different lighting conditions and highlight the dim and dull cells.
4.3. Customizing YOLOv5
Algorithm 1 Customized YOLOv5 Model with FPN. |
|
5. Results
6. Discussion
7. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
2D | Two Dimensional |
3D | Three Dimensional |
CNN | Convolution Neural Network |
CSP | Cross-Stage Partial |
DCNN | Deep Convolution Neural Network |
FCN | Fully Convolution Network |
FPN | Feature Pyramid Network |
GAN | Generative Adversarial Network |
IoU | Intersection Over Union |
PAN | Path Aggregation Network |
mAP | Mean Average Precision |
Mtb | Mycobacterium tuberculosis |
SSD | Single-Shot Detector |
UNET | U-Shaped Convolutional Network |
YOLO | You Only Look Once |
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Methods | Advantages | Limitations | Applied to Cell Detection and Counting |
---|---|---|---|
Image Processing based | Simple and computationally efficient | Limited accuracy and robustness | [54,66,67] |
No need for large datasets or complex algorithms | Struggle with complex cell morphologies and low SNR | ||
Easy to implement and interpret | |||
Machine Learning based | Can handle complex cell morphologies and low SNR | Requires labeled training data | [52,61,68] |
More accurate and robust than image processing based | Sensitive to variability in data and imaging protocol | ||
Can be adapted to different imaging modalities | Requires feature engineering, which can be time-consuming | ||
Deep Learning based | State-of-the-art accuracy for cell detection and counting | Highly dependent on the quality and quantity of training data | [69,70,71] |
Highly robust to variability in data and imaging protocol | Can be computationally expensive | ||
Does not require feature engineering, saving time and effort | May be less interpretable than traditional methods |
416 × 416 | 640 × 640 | 840 × 840 | |||||||
---|---|---|---|---|---|---|---|---|---|
Precision | Recall | mAP | Precision | Recall | mAP | Precision | Recall | mAP | |
YOLOv5s | 0.741 | 0.701 | 0.732 | 0.787 | 0.744 | 0.764 | 0.756 | 0.723 | 0.741 |
YOLOv5n | 0.738 | 0.661 | 0.681 | 0.779 | 0.695 | 0.73 | 0.759 | 0.734 | 0.749 |
YOLOv5fpn | 0.796 | 0.741 | 0.799 | 0.758 | 0.740 | 0.748 | 0.748 | 0.708 | 0.732 |
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Aldughayfiq, B.; Ashfaq, F.; Jhanjhi, N.Z.; Humayun, M. YOLOv5-FPN: A Robust Framework for Multi-Sized Cell Counting in Fluorescence Images. Diagnostics 2023, 13, 2280. https://doi.org/10.3390/diagnostics13132280
Aldughayfiq B, Ashfaq F, Jhanjhi NZ, Humayun M. YOLOv5-FPN: A Robust Framework for Multi-Sized Cell Counting in Fluorescence Images. Diagnostics. 2023; 13(13):2280. https://doi.org/10.3390/diagnostics13132280
Chicago/Turabian StyleAldughayfiq, Bader, Farzeen Ashfaq, N. Z. Jhanjhi, and Mamoona Humayun. 2023. "YOLOv5-FPN: A Robust Framework for Multi-Sized Cell Counting in Fluorescence Images" Diagnostics 13, no. 13: 2280. https://doi.org/10.3390/diagnostics13132280
APA StyleAldughayfiq, B., Ashfaq, F., Jhanjhi, N. Z., & Humayun, M. (2023). YOLOv5-FPN: A Robust Framework for Multi-Sized Cell Counting in Fluorescence Images. Diagnostics, 13(13), 2280. https://doi.org/10.3390/diagnostics13132280