Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2009.13318

High-throughput molecular imaging via deep learning enabled Raman spectroscopy

Conor C. Horgan·Magnus Jensen·Anika Nagelkerke·Jean-Phillipe St-Pierre·Tom Vercauteren·Molly M. Stevens·Mads S. Bergholt
View original source ↗Read source document ↗Export metadata ↓

Abstract

Raman spectroscopy enables non-destructive, label-free imaging with unprecedented molecular contrast but is limited by slow data acquisition, largely preventing high-throughput imaging applications. Here, we present a comprehensive framework for higher-throughput molecular imaging via deep learning enabled Raman spectroscopy, termed DeepeR, trained on a large dataset of hyperspectral Raman images, with over 1.5 million spectra (400 hours of acquisition) in total. We firstly perform denoising and reconstruction of low signal-to-noise ratio Raman molecular signatures via deep learning, with a 9x improvement in mean squared error over state-of-the-art Raman filtering methods. Next, we develop a neural network for robust 2-4x super-resolution of hyperspectral Raman images that preserves molecular cellular information. Combining these approaches, we achieve Raman imaging speed-ups of up to 160x, enabling high resolution, high signal-to-noise ratio cellular imaging in under one minute. Finally, transfer learning is applied to extend DeepeR from cell to tissue-scale imaging. DeepeR provides a foundation that will enable a host of higher-throughput Raman spectroscopy and molecular imaging applications across biomedicine.

Explore related subjects

eess.IVcs.CVphysics.med-ph

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Conor C. Horgan, Magnus Jensen, Anika Nagelkerke, Jean-Phillipe St-Pierre, Tom Vercauteren, Molly M. Stevens, Mads S. Bergholt. 2020-09-28. High-throughput molecular imaging via deep learning enabled Raman spectroscopy. https://doi.org/10.1021/acs.analchem.1c02178

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

KELP: K-space-conditioned Estimation of Learned Sampling Patterns for Scan-Adaptive Multi-Coil MRI

Deep learning techniques have gained considerable attention for accelerating MRI acquisition while maintaining image quality. In this work, we present a convolutional neural network (CNN)-based framework for predicting scan-adaptive undersampling patterns directly from low-frequency multi-coil $k$-space data. Unlike approaches that optimize sampling patterns during training or rely on nearest-neighbor search at inference, our method is trained using precomputed scan-adaptive optimized masks as supervised labels and predicts a scan-specific sampling pattern in a single forward pass. The training procedure alternates between optimizing the sampling network and a reconstruction network, allowing the learned masks to adapt to reconstruction performance. Experiments on the fastMRI multi-coil knee dataset demonstrate competitive reconstruction quality compared with existing population- and scan-adaptive sampling approaches at $4\times$ and $8\times$ acceleration factors. In addition, the proposed method enables efficient scan-specific mask prediction with inference cost independent of the training dictionary size.

eess.IV↗
arXiv2026

LaminoDiff: Generative Computed Laminography via Near-Isotropic Spectral Supervision and Anisotropic Geometry

Computed Laminography (CL) is widely used for nondestructive inspection of extended planar objects, but its restricted angular coverage produces an anisotropic point spread function, missing-cone spectral incompleteness, and severe aliasing with interlayer leakage. This paper presents LaminoDiff, a physics-constrained diffusion framework for CL reconstruction. During training, a CT-derived near-isotropic supervision target is reconstructed from full-angle Computed Tomography (CT) projections physically degraded to match CL detector noise and focal-spot blur while retaining full angular coverage; it is withheld from inference. At inference, the reverse process uses only the CL observation. An Anisotropic Representation (AR) constructs depth-aware channels from three adjacent slices: a neighbor average, a center-neighbor residual, and the retained current slice, followed by directional in-plane feature extraction. Experiments on simulated and real multilayer printed circuit board data, including ball grid array and high-frequency stub samples, show that LaminoDiff improves artifact suppression, edge preservation, and depth stratification over analytic Feldkamp--Davis--Kress and representative learning-based baselines.

eess.IV↗
arXiv2026

IViT: A Novel Interpretable Visual Transformer for Skin Disease Detection

The clinical diagnosis of skin diseases is susceptible to interference from inter-class similarity of skin lesions, and over-reliance on clinicians'experience easily leads to subjective bias. Although existing deep learning aided diagnosis methods achieve competitive accuracy, they suffer from the black-box opacity of Vision Transformer (ViT) and poor adaptability to medical few-shot scenarios. Moreover, mainstream explainable algorithms generally face the bottleneck of significant accuracy degradation when improving interpretability. This paper proposes an interpretable ViT (IViT) constrained by Quadratic Programming (QP). The introduced pre-trained transfer learning adapts to few-shot feature extraction. A discrete QP feature selection framework is constructed to screen generic and discriminative features consistent with clinical diagnostic logic. A multi-objective loss function is designed to reduce feature redundancy and optimize activation distribution while preserving classification performance. Experimental results on six standard skin disease datasets show that IViT achieves an accuracy of 93.80%, only 0.21% lower than the baseline, with feature redundancy reduced by 29.5%. Its core activation regions are consistent with clinically concerned lesion areas. The proposed model balances accuracy and interpretability, providing a reliable solution for the clinical deployment of few-shot intelligent skin disease diagnosis.

eess.IV↗