Rapid DNA origami nanostructure detection and classification using the YOLOv5 deep convolutional neural network

Abstract

The intra-image identification of DNA structures is essential to rapid prototyping and quality control of self-assembled DNA origami scaffold systems. We postulate that the YOLO modern object detection platform commonly used for facial recognition can be applied to rapidly scour atomic force microscope (AFM) images for identifying correctly formed DNA nanostructures with high fidelity. To make this approach widely available, we use open-source software and provide a straightforward procedure for designing a tailored, intelligent identification platform which can easily be repurposed to fit arbitrary structural geometries beyond AFM images of DNA structures. Here, we describe methods to acquire and generate the necessary components to create this robust system. Beginning with DNA structure design, we detail AFM imaging, data point annotation, data augmentation, model training, and inference. To demonstrate the adaptability of this system, we assembled two distinct DNA origami architectures (triangles and breadboards) for detection in raw AFM images. Using the images acquired of each structure, we trained two separate single class object identification models unique to each architecture. By applying these models in sequence, we correctly identified 3470 structures from a total population of 3617 using images that sometimes included a third DNA origami structure as well as other impurities. Analysis was completed in under 20 s with results yielding an F1 score of 0.96 using our approach.

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“…Deep learning research has been reported in many fields, including medicine [8,[11][12][13][14][15][16][17]. In cytology, several formidable barriers need to be overcome to achieve widespread adoption, such as preimaging collection and preparation factors.…”

An Improved Detection Algorithm for Ischemic Stroke NCCT Based on YOLOv5

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Dominant Analytical Techniques in DNA Nanotechnology for Various Applications

“…Manual analysis through counting not only is tedious but can also inject bias into the analysis. Machine learning tools are being developed to facilitate high-throughput quantitative evaluation of DNA nanostructures through AFM analysis (Figure A) …”

“…(A) Machine-learning enabled high-throughput analysis of a heterogeneous mix of DNA origami structures comprised of triangle, rectangle, and “imposter” DNA cylinders. The YOLO-v5 trained neural network successfully identified the triangles (blue boxes) and rectangles (red boxes) and dismisses the cylinders . (B) Imaging of unstained DNA origami nanoplates on commercial carbon films.…”