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jenna-tomkinson committed Nov 28, 2022
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Expand Up @@ -31,7 +31,7 @@ conda env create -f 4.processing_features.yml

### Step 2a: Set Up Paths

Within the [extract_single_cell_features.ipynb](4_processing_features/extract_single_cell_features.ipynb) notebook, change the paths to reflect the local paths or names for your machine for the various parameters (e.g. CellProfiler directory, output directory, path to sqlite file, etc.)
Within the [extract_single_cell_features.ipynb](4_processing_features/extract_single_cell_features.ipynb) notebook, you can chnage the paths to reflect the local paths or names for your machine (**IF** you changed anything from the original pipeline)for the various parameters (e.g. CellProfiler directory, output directory, path to sqlite file, etc.)

### Step 2b: Run Extract Single Cell Features

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