Simulation of smFISH experiments on mouse lung tissue with simTissue

Simulations of smFISH experiments on mouse lung tissue simulated with the package simTissue (https://github.com/tdefa/SimTissue)
These simulations are generated from scRNA-seq data and smFISH experemient from: Curras-Alonso, S., Soulier, J., Defard, T. et al. An interactive murine single-cell atlas of the lung responses to radiation injury. Nat Commun 14, 2445 (2023). https://doi.org/10.1038/s41467-023-38134-z
the folder 'df_spots' contains the spot coordinates of each image:- The pixel scale zxy is [300, 0.108, 0.108]
the column cell is the cell_id of the corresponding cell in the nucleus mask and cytoplasm mask.
the folder 'cytoplasm' contains the cytoplasm masks.- some cells are simulated without a nucleus to better mimic smFISH tissue experiment
the folder 'nuclei' contains the nucleus segmentation. Not all cells have a nucleus
the folder 'dict_centroid' contains the coordinate of the centroid of each nucleus.
the folder df_cell_type contains the ground truth cell type name of each cell
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