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bioRxiv · 10.1101/2021.05.01.442219

DeepLIIF: Deep Learning-Inferred Multiplex ImmunoFluorescence for IHC Quantification

Ghahremani, P.·Li, Y.·Kaufman, A.·Vanguri, R.·Greenwald, N.·Angelo, M.·Hollmann, T. J.·Nadeem, S.
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Abstract

Reporting biomarkers assessed by routine immunohistochemical (IHC) staining of tissue is broadly used in diagnostic pathology laboratories for patient care. To date, clinical reporting is predominantly qualitative or semi-quantitative. By creating a multitask deep learning framework referred to as DeepLIIF, we present a single-step solution to stain deconvolution/separation, cell segmentation, and quantitative single-cell IHC scoring. Leveraging a unique de novo dataset of co-registered IHC and multiplex immunofluorescence (mpIF) staining of the same slides, we segment and translate low-cost and prevalent IHC slides to more expensive-yet-informative mpIF images, while simultaneously providing the essential ground truth for the superimposed brightfield IHC channels. Moreover, a new nuclear-envelop stain, LAP2beta, with high (>95%) cell coverage is introduced to improve cell delineation/segmentation and protein expression quantification on IHC slides. By simultaneously translating input IHC images to clean/separated mpIF channels and performing cell segmentation/classification, we show that our model trained on clean IHC Ki67 data can generalize to more noisy and artifact-ridden images as well as other nuclear and non-nuclear markers such as CD3, CD8, BCL2, BCL6, MYC, MUM1, CD10, and TP53. We thoroughly evaluate our method on publicly available benchmark datasets as well as against pathologists semi-quantitative scoring. The code, the pre-trained models, along with easy-to-run containerized docker files as well as Google CoLab project are available at https://github.com/nadeemlab/deepliif.

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Ghahremani, P., Li, Y., Kaufman, A., Vanguri, R., Greenwald, N., Angelo, M., Hollmann, T. J., Nadeem, S.. 2021-05-02. DeepLIIF: Deep Learning-Inferred Multiplex ImmunoFluorescence for IHC Quantification. https://doi.org/10.1101/2021.05.01.442219

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