Workflow

Input Directory Structure (see Input Files for details)	Pipeline Diagram	Output Directory Structure (see Output Files for details)
INPUT_DIR ├── config.yml ├── csv/ ├── markers.csv/ ├── mask/ ├── seg/ └── tif/		OUTPUT_DIR ├── area/ ├── checkpoints/ ├── clustering/ ├── contrast/ ├── cycles/ ├── intensity/ ├── metaQC/ ├── PCA/ ├── pruning/ └── ROIs/

Table of contents

• Input
• Output