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

Contact  : thomas.defard@mines-paristech.fr