Step 1 (S1): Generate semantic segmentations¶
Running S1¶
1. Denoise tomograms¶
First, denoise the input tomograms using TomoEED by running the following command:
<tomoeed_directory>/bin/tomoeed full_path_to_input_tomogram.mrc denoised_tomograms/output_tomogram.mrc
input_tomogram.mrc) and place it at denoised_tomograms/output_tomogram.mrc. If running from a different directory than input_tomogram.mrc, you will need to specify the full path to the input tomogram.
Important
Make sure to use the path to denoised tomogram (denoised_tomograms/output_tomogram.mrc) in the s1_param_file_path for tomogram in the inputs section.
2. Generate semantic segmentations¶
Run the following command to generate the semantic segmentations.
Next step is to choose one or more optimal segmentations for each input tomogram and obtaining the corresponding particle cluster IDs. Follow the instructions at visualizing segmentations and obtaining particle cluster ID for more details on this.