Conor C. Horgan

Conor C. Horgan, Mads S. Bergholt

Deep learning computer vision techniques have achieved many successes in recent years across numerous imaging domains. However, the application of deep learning to spectral data remains a complex task due to the need for augmentation routines, specific architectures for spectral data, and significant memory requirements. Here we present spectrai, an open-source deep learning framework designed to facilitate the training of neural networks on spectral data and enable comparison between different methods. Spectrai provides numerous built-in spectral data pre-processing and augmentation methods, neural networks for spectral data including spectral (image) denoising, spectral (image) classification, spectral image segmentation, and spectral image super-resolution. Spectrai includes both command line and graphical user interfaces (GUI) designed to guide users through model and hyperparameter decisions for a wide range of applications.

Conor C. Horgan, Magnus Jensen, Anika Nagelkerke et al.

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.