Comparison of deep learning models for digital H&E staining from unpaired label-free multispectral microscopy images. (June 2023)

• Record Type: Journal Article
• Authors: Salido, Jesus; Vallez, Noelia; González-López, Lucía; Deniz, Oscar; Bueno, Gloria
• Is Part Of: Computer methods and programs in biomedicine. Volume 235(2023)
• Publication Date: 2023-06
• Subjects: Virtual staining -- Digital staining -- Multispectral imaging -- Digital pathology -- GAN (Generative adversarial network) -- Cycle consistency -- Contrastive learning -- Style transfer -- Image quality assessment; Medicine -- Computer programs -- Periodicals; Biology -- Computer programs -- Periodicals; Computers -- Periodicals; Medicine -- Periodicals; Médecine -- Logiciels -- Périodiques; Biologie -- Logiciels -- Périodiques; Biology -- Computer programs; Medicine -- Computer programs; Periodicals; Electronic journals; 610.28
• DOI: 10.1016/j.cmpb.2023.107528
• Languages: English
• ISSNs: 0169-2607

Abstract

Highlights: Deep learning applied to digital pathology. Virtual staining from unpaired label-free microscopy images. Contrastive learning for virtual staining applied to multispectral images. Generative models with cycle consistency for better digital staining results. Quality image assessment by similarity and chromatic metrics. Graphical abstract: Abstract: Background and objective : This paper presents the quantitative comparison of three generative models of digital staining, also known as virtual staining, in H&E modality (i.e., Hematoxylin and Eosin) that are applied to 5 types of breast tissue. Moreover, a qualitative evaluation of the results achieved with the best model was carried out. This process is based on images of samples without staining captured by a multispectral microscope with previous dimensional reduction to three channels in the RGB range. Methods: The models compared are based on conditional GAN (pix2pix) which uses images aligned with/without staining, and two models that do not require image alignment, Cycle GAN (cycleGAN) and contrastive learning-based model (CUT). These models are compared based on the structural similarity and chromatic discrepancy between samples with chemical staining and their corresponding ones with digital staining. The correspondence between images is achieved after the chemical staining images are subjected to digital unstaining by means of a model obtained to guarantee the cyclic consistency of the generative models. Results: The comparison of the three models corroborates the visual evaluation of the results showing the superiority of cycleGAN both for its larger structural similarity with respect to chemical staining (mean value of SSIM ∼ 0.95) and lower chromatic discrepancy (10%). To this end, quantization and calculation of EMD (Earth Mover's Distance) between clusters is used. In addition, quality evaluation through subjective psychophysical tests with three experts was carried out to evaluate quality of the results with the best model (cycleGAN). Conclusions: The results can be satisfactorily evaluated by metrics that use as reference image a chemically stained sample and the digital staining images of the reference sample with prior digital unstaining. These metrics demonstrate that generative staining models that guarantee cyclic consistency provide the closest results to chemical H&E staining that also is consistent with the result of qualitative evaluation by experts.