A versatile deep learning architecture for classification and label-free prediction of hyperspectral images
Open accessAbstract
Hyperspectral imaging is a technique that provides rich chemical or compositional information not regularly available to traditional imaging modalities such as intensity imaging or color imaging based on the reflection, transmission, or emission of light. Analysis of hyperspectral imaging often relies on machine learning methods to extract information. Here, we present a new flexible architecture, the U-within-U-Net, that can perform classification, segmentation, and prediction of orthogonal imaging modalities on a variety of hyperspectral imaging techniques. Specifically, we demonstrate feature segmentation and classification on the Indian Pines hyperspectral dataset and simultaneous location prediction of multiple drugs in mass spectrometry imaging of rat liver tissue. We further demonstrate label-free fluorescence image prediction from hyperspectral stimulated Raman scattering microscopy images. The applicability of the U-within-U-Net architecture on diverse datasets with widely varying input and output dimensions and data sources suggest that it has great potential in advancing the use of hyperspectral imaging across many different application areas ranging from remote sensing, to medical imaging, to microscopy.
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The unsupervised autoencoder models do not utilize any ground truth information during training, in contrast with previous supervised machine learning approaches for Raman cell imaging.
“Finally, we remark that our unsupervised autoencoder models do not utilize any ground truth information during training, in contrast with previous supervised machine learning approaches for Raman cell imaging and characterization where specific target concentrations are used as labels to train the model (e.g., using separately acquired fluorescence images) (90–93).”
From Hyperspectral unmixing for Raman spectroscopy via physics-constrained autoencoders (2024) · cites this paper as [90]
The Methods section (“Training Parameters, Data Preparation, and Hardware”; page not available) says SRS images were used as inputs and fluorescence images as the truth for training, supporting the contrast with training that uses ground-truth information. It does not say that specific target concentrations were used as labels for its Raman cell-imaging models; that detail is not supported by this source. (LLM, conf=0.87)
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- Authors
- Manifold, B., Men, S., Hu, R., & Fu, D.
- Affiliations
- University of Washington (US)
- Corresponding author
- Manifold, Bryce
- Fu, Dan
- Venue
- Nature Machine Intelligence
- Published
- 2021-03-11
- Volume
- 3
- Issue
- 4
- Pages
- 306-315
- ISSN
- 2522-5839 (ISSN-L)
- PMC
- PMC8528004
- OpenAlex
- W3134761005
- Cited by
- 152
- References
- 70
- Citations by year
- 2026: 16 · 2025: 42 · 2024: 36 · 2023: 30 · 2022: 20 · 2021: 8
- FWCI
- 10.55
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Machine Intelligence (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Beckman Young Investigator Award
- Topics
- Physical Sciences › Engineering › Media Technology › Remote-Sensing Image Classification
- Physical Sciences › Chemistry › Analytical Chemistry › Spectroscopy and Chemometric Analyses
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Advanced Neural Network Applications
- Keywords
- hyperspectral imaging, U-Net architecture, image classification, image segmentation, mass spectrometry imaging, stimulated Raman scattering microscopy, Indian Pines dataset, rat liver tissue, remote sensing
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