WANG Gefei

Hi Cristal, We used slice 6 (from 0 to 8) for pie charts visualization. It is ok to use the entire scRNA-seq dataset since we do not have a scRNA-seq...

Hi Cristal, Cell-type information produced by STitch3D is saved in the output of `model.eval()` function. For the human heart example, after running `result = model.eval(adata_st_list_raw, save=True, output_path=save_path)`, you will get...

Hi Cristal, This may be caused by some problem in the LoadH5Seurat function. You can load the data csv files (counts, locations, meta information, etc.) directly into R, or use...

Hi Cristal, There is not a single-cell RNA-seq reference dataset for slice0 specifically. You can use the entire scRNA-seq dataset as the cell-type reference data for all slices. Best, Gefei

Hi there, Thank you for your interest in our method. We have uploaded related files, including seurat_clust_1620.txt and cluster_anno_table.csv in [this link](https://drive.google.com/drive/folders/1aUBsv6_2i0_-guei1pPWrShz4qM5q46I?usp=sharing). Best, Gefei

Hi there, `path.bin` refers to the path to the folder on your computer containing scripts in https://github.com/cantin-ortiz/molecular-atlas/tree/a409706716520a29471882c535b618a28d6a2b0c/bin. 'path.matrices' refers to the folder containing `atlasspots.RData` and `vivid-colors.RData`, which can be found...

Hi there, Please check you umap and scanpy versions, as in https://github.com/YangLabHKUST/STitch3D/issues/18. Best, Gefei

Hi, you can find preprocessed single-cell data for example 5 in https://singlecell.broadinstitute.org/single_cell/study/SCP1039/a-single-cell-and-spatially-resolved-atlas-of-human-breast-cancers#study-download. The encrypted files can be found [here](https://drive.google.com/drive/folders/1fc709rn6dmAmKO8L7FYcIZbK1a-DylTK?usp=drive_link).

Hi, you can get the files following the instruction: https://github.com/YangLabHKUST/STitch3D/issues/1 https://github.com/YangLabHKUST/STitch3D/issues/5 https://github.com/YangLabHKUST/STitch3D/issues/23#issuecomment-1987879480

Hi, in the function STitch3D.utils.align_spots(), the input AnnData objects are required to contain spatial locations in the attribute .obsm['spatial']. Please make sure the ST AnnData objects are read correctly, or...