Unable to generate transcripts.csv.gz and morphology_mip.ome.tif files.
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I have try to run this set of codes several times, but i am unable to get transcripts.csv.gz and morphology_mip.ome.tif files.
from bidcell import BIDCellModel
BIDCellModel.get_example_data()
model = BIDCellModel("params_small_example.yaml")
model.run_pipeline()
Can someone help explain to me what i am doing wrongly.
Hi, these files may be downloaded from public sources or be your own data. For example, the full dataset (Xenium Output Bundle In Situ Replicate 1) may be downloaded from https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast. The breast cancer reference data are provided with this package under data/sc_references, or ./example_data/sc_references if you have run example_small.py. Please ensure the correct paths are provided for the parameters under files in xenium_example_config.yaml, in particular, the paths for the transcripts (transcripts.csv.gz) and DAPI (morphology_mip.ome.tif) files.
Hi there,
Thank you for the response and clarification.
Kind regards,
Phil