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labsyspharm / scimap

Spatial Single-Cell Analysis Toolkit
https://scimap.xyz/
MIT License
71 stars 24 forks source link

batch samples analysis #85

Open yas92 opened 9 months ago

yas92 commented 9 months ago

Hi

May I ask about whether scimap can be running on batch samples data together on nextflow?

ajitjohnson commented 8 months ago

hi @yas92 are you using scimap via mcmicro in nextflow?

yas92 commented 8 months ago

@ajitjohnson I am running Scimap on a Jupyter notebook, but my input data was derived from MCMICRO via nextflow.

ajitjohnson commented 8 months ago

when you import your data into scimap using the mcmicro_to_scimap function, simply pass a list of csv files corresponding to different images in the feature_table_path parameter.

e,g.

feature_table_path = [ "\path to image 1.csv",   "\path to image 2.csv",   "\path to image 3.csv"]

This would allow you to import your entire dataset and analyze them together. Each image's unique identifier stored under adata.obs['imageid']