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HaojiaWu / CellScopes.jl

A Julia package for single cell and spatial data analysis
MIT License
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Inquiry about Data Conversion in CellScopes #9

Open YuxiZhang-0113 opened 1 month ago

YuxiZhang-0113 commented 1 month ago

Dear CellScopes team, Hello! I have always admired your team's outstanding publications in kidney research. Recently, I tested CellScopes, and I must say it is truly impressive. I was amazed by its ability to import the original Tiff files of Visium data and its seamless handling of various spatial transcriptomics data. I have two questions:

  1. Can a CartanaObject be converted into a Seurat or Scanpy object?
  2. Can the objects obtained using the cs.add_visium_img function be exported as Seurat or Scanpy objects?
HaojiaWu commented 1 month ago

Hi @YuxiZhang-0113 ,

Great to hear that CellScopes is helpful to you! Currently, converting CellScopes objects to Seurat or Scanpy objects is not available. I also like to use Seurat and Scanpy for data processing, especially for functionalities not yet available in CellScopes, such as data integration, SCTransform, label transfer, etc.

What I usually do is manually import the results from Scanpy and Seurat into CellScopes. For example, if you have completed clustering in Seurat or Scanpy, you can save the cell clustering or cell annotation as a CSV file. Then, read the CSV file into Julia and add a cell annotation column to the cartanaobj.spmetaData.cell from the Seurat or Scanpy clustering. After this, you can use the normal functions in CellScopes to perform further analysis.

YuxiZhang-0113 commented 1 month ago

hi @HaojiaWu ， Thank you for your response and detailed explanation! Additionally, I found the example you shared on https://github.com/BuilderPie/Human_DKD_Visium to be very helpful in addressing this issue.