This repository implements image analysis and quantification for immune response to different SARS-CoV-2 variants. The publication describing this work will be available soon.

This work is a follow-up to this publication.

The assay contains cells that express the spike proteins of different SARS-CoV-2 variants, the nucleocapsid protein and control cells not expressing any viral proteins.

The immunofluorescence data is analyzed with the following approach:

• Segmenting nuclei with StarDist.
• Predicting cell foreground and boundaries with a UNet.
• Segmenting cells with a seeded watershed based on predictions from the first two steps.
• Classifying cells into variants / ncapsid / control using a ResNet.
• Determining the antibody to the different variants based on classification results and per-cell immunofluorescence intensity.

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