batch samples analysis

[yas92]

Hi

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

[ajitjohnson]

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

[yas92]

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

[ajitjohnson]

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']