CLI reference

Every command is available both as cellclass <subcommand> and as the legacy cellclass-<subcommand> executable; both point at the same command object.

cellclass

Train and evaluate cell-image classifiers.

Prepare data

Build and inspect the labelled crop dataset.

dataset

Convert cell images in DIR to a training dataset.

sample

Sample example images from DATASET.

Train and evaluate

Fit a model and measure how well it does.

train

Train a model using an ROI dataset or resume from saved state.

test

Evaluate a trained model against a dataset.

batch

Generate training runs from BATCH.

Deploy

Extract a trained model and submit cluster jobs.

extract

Extract a TorchScript model from training settings FILE.

sbatch

Submit a CellClass training job to SLURM.