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 : [e-mail]本数据集为使用simTissue工具（https://github.com/tdefa/SimTissue）模拟的小鼠肺组织单分子荧光原位杂交（smFISH, single-molecule fluorescence in situ hybridization）实验仿真数据。该仿真数据源自以下文献中的单细胞RNA测序（scRNA-seq, single-cell RNA sequencing）与smFISH实验结果：Curras-Alonso, S., Soulier, J., Defard, T. 等. 小鼠肺部辐射损伤应答交互式单细胞图谱. 自然·通讯, 2023, 14: 2445. https://doi.org/10.1038/s41467-023-38134-z 各文件夹内容说明如下： 1. `df_spots`文件夹：存储每张图像的荧光斑点坐标，其像素采样尺度zxy为[300, 0.108, 0.108]；其中`cell`列对应细胞核掩码与细胞质掩码中所属细胞的细胞ID（cell_id）。 2. `cytoplasm`文件夹：存储细胞质分割掩码。为更贴近真实smFISH组织实验场景，部分细胞未模拟细胞核。 3. `nuclei`文件夹：存储细胞核分割掩码，并非所有细胞均带有细胞核。 4. `dict_centroid`文件夹：存储每个细胞核的质心坐标。 5. `df_cell_type`文件夹：存储每个细胞的真实细胞类型标签。 联系方式：[e-mail]