search

angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
69 stars 25 forks source link

generate neighborhood mask results in string error #1129

Closed janinemelsen closed 3 months ago

janinemelsen commented 3 months ago

Creating the neighborhood cluster mask using the example dataset as described in the the example_neighborhood_analysis_script led to the following error:

data_utils.generate_and_save_neighborhood_cluster_masks( subset_neighborhood_fovs, overlay_out_dir, all_data_cluster_labeled, segmentation_dir, name_suffix='_neighborhood_mask' )

image
camisowers commented 3 months ago

Hi! It's an issue with the argument order. We'll get a PR in to fix this, but for now you can replace the code in the notebook with the below and it should work!

data_utils.generate_and_save_neighborhood_cluster_masks(
    fovs=subset_neighborhood_fovs,
    save_dir=overlay_out_dir,
    neighborhood_data=all_data_cluster_labeled,
    seg_dir=segmentation_dir,
    name_suffix='_neighborhood_mask')