Inference

Model File

SKOOTS needs a pretrained model file to run inference on a new image. This should be generated at the conclusion of training, and has the extension *.trch. This file contains both the model weight, but also any configuration options the necessary for inference.

Evaluate a SKOOTS model

We evaluate a trained model file my_model.trch on image new_image.tif by typing in the terminal:

skoots --pretrained-checkpoint "my_model.trch" --image "new_image.tif"

The output and intermediary files will be saved in the same location as new_image.tif. To convert any zarr outputs to tif, run the following command:

skoots --convert *