Describe the bug
Not sure if this is a bug: 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:
Describe the bug Not sure if this is a bug: 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!