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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Error with Pixie #1085

Closed Nitya20001 closed 9 months ago

Nitya20001 commented 9 months ago

This is my first time running the pixie notebook. I added my tiff files for each channel, the deep cell segmentation output, etc in the data folder that was created when I downloaded the ark analysis package.

However, when I run the function below to create the pixel SOM weights:

pixel_pysom = pixel_som_clustering.train_pixel_som( fovs, channels, base_dir, subset_dir=pixel_subset_dir, norm_vals_name=norm_vals_name, som_weights_name=pixel_som_weights_name, num_passes=1, seed=42 )

I get this error:

The file/path, channel_norm_post_rownorm.feather, could not be found..

Please help!

alex-l-kong commented 9 months ago

Closing, as it's a duplicate of #1089. @Nitya20001 in the future please reply to the original issue you opened to follow up.