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labsyspharm / scimap

Spatial Single-Cell Analysis Toolkit
https://scimap.xyz/
MIT License
74 stars 26 forks source link

Using SCIMAP with MERFISH or Visium data #116

Open poloarol opened 1 month ago

poloarol commented 1 month ago

Hello SCIMAP developers,

I wanted to know if it is possible to use either MERFISH or Visium data with this tool, and how would one go about doing so. Because, I keep encountering an error with regarding KeyError: 'imageid'.

Thanks for the cool though and hope to hear from you.

Best, Polo

ajitjohnson commented 1 month ago

Hi Polo,

For most functions in scimap, a column named imageid is required, which corresponds to a unique identifier for each image. This ensures that during spatial analysis, the XY coordinates for each image are treated independently. You can either create a new imageid column (in your single cell table) and assign a unique identifier to each image in your dataset, or, if such a column already exists, ensure you pass its name to the imageid parameter in the relevant functions.