btsp-cli

btsp-cli is a Python command-line tool for exporting orthogonal slice PNGs from paired NRRD image and label volumes.

Environment Setup

Create and activate the Conda environment:

conda create -n sp python=3.11
conda activate sp

Install the project in editable mode with development dependencies:

python -m pip install -e ".[dev]"

Single-File Usage

Export 6 PNG slices for one paired sample:

sp print \
  --nrrd \
  --data data/MR201202161060.image.nrrd \
  --label label/MR201202161060.label.nrrd \
  --point "[120,180,9]" \
  --output output \
  --header se

This writes:

• {header}_{point}_x_image.png
• {header}_{point}_x_label.png
• {header}_{point}_y_image.png
• {header}_{point}_y_label.png
• {header}_{point}_z_image.png
• {header}_{point}_z_label.png

Directory Usage

Apply one shared point to every matched sample pair in two directories:

sp print \
  --nrrd \
  --data data \
  --label label \
  --point "[120,180,9]" \
  --output output \
  --workers 4

Samples with out-of-bounds shared points are skipped without aborting the full batch.

Directory Usage With CSV Points

Use a CSV file to supply per-sample points and restrict processing to listed samples only.

CSV schema:

name_header,point
MR201202161060,"[120,180,9]"
MR201206080468,"[98,164,8]"

Command:

sp print \
  --nrrd \
  --data data \
  --label label \
  --point-csv points.csv \
  --output output \
  --header se \
  --workers 4

In directory mode, output headers are automatically expanded to {header}_{sample_name} to avoid overwriting files across samples.