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Pixel clustering with Pixie - error #1084

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Nitya20001 opened this issue Nov 22, 2023 · 0 comments
Closed

Pixel clustering with Pixie - error #1084

Nitya20001 opened this issue Nov 22, 2023 · 0 comments
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bug Something isn't working

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@Nitya20001
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Nitya20001 commented Nov 22, 2023

MicrosoftTeams-image (8)

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!

@Nitya20001 Nitya20001 added the bug Something isn't working label Nov 22, 2023
@angelolab angelolab locked and limited conversation to collaborators Nov 28, 2023
@alex-l-kong alex-l-kong converted this issue into discussion #1089 Nov 28, 2023

This issue was moved to a discussion.

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