MCU data

Data from the smFISH + 4i experiment in the paper "Cellular state landscape and herpes simplex virus type 1 infection progression are connected" by Pietilä et al., 2023:
- Pixel coordinates within single cells and their multiplexed cell unit (MCU)-identity (Figure 4f): mcu_pixel_coordinates_mcuIDs.csv.gz
- Summary of normalised 4i marker intensities in MCUs (Figure 4a): mcu_marker_intensities.csv
- Summary of MCU occupancy (Figure 4b): mcu_occupancy.csv
- SPS values of MCUs (Figure 4f): mcu_sps.csv
- Summaries of UMAP coordinates of MCUs (Figure 4c,d): mcu_umap_allCells.csv and mcu_umap_infectedCells_12h.csv
- Single-cell features to cluster infected cells into subpopulations (Figure 4e): mcu_leiden_infectedCells_12h.csv
- Single-cell morphology features of cell subpopulations (Figure 4g): mcu_leiden_morphology_features.csv

HeLa cells were infected with HSV-1, fixed at different time points (indicated by "timePoint"), and iterative indirect immunofluorescence imaging (4i) was performed as described in the paper. Cells were classified into uninfected cells without infected neighbors, uninfected cells with infected neighbors, and infected cells (indicated by “classification_infection”) as described in the paper. Single-pixel intensities are provided as corrected and normalised intensity values. Single-cell morphology features are provided as normalised values. MCU construction from single-pixel intensities, correction, normalisation, and Leiden clustering were performed as described in the paper.