bcf-scape 0.1.0

SCAPE light-sheet microscopy data processing (deskewing, max-projection, batch I/O).

bcf-scape

bcf-scape is a modular Python library for processing SCAPE light-sheet microscopy data: deskewing OME-TIFF stacks, computing Z / Y max-projections, and batch-processing multi-position / multi-timepoint acquisitions.

GPU-accelerated via pyclesperanto.

Developed and maintained by the Scientific Computing Facility at MPI-CBG.

Installation

pip install bcf-scape

The package imports as scape:

import scape

Quick start

Command line

python -m scape.pipeline \
    --settings settings.toml \
    --tiff     /data/raw/scan.ome.tif \
    --output   /data/processed/Deskewed/

or via the console script:

scape --help

Python API

from scape.config.settings import load_settings_from_file
from scape.pipeline import run

settings = load_settings_from_file("settings.toml")
run(settings, "/data/raw/scan.ome.tif", "/data/processed/Deskewed/")

TOML configuration

ProcessingSettings round-trips to a human-readable TOML file:

from scape.config.settings import ProcessingSettings

settings = ProcessingSettings()
settings.lightsheet_angle_in_degrees = 39
settings.save_toml("my_run.toml")

# Later …
settings = ProcessingSettings.load_toml("my_run.toml")

Modules

Module	Responsibility
scape.pipeline	End-to-end deskewing pipeline (CLI entry point)
scape.config.settings	ProcessingSettings + TOML I/O
scape.metadata.parser	OME-TIFF metadata extraction
scape.preprocessing.image_handler	Channel/timepoint selection, dual-camera flips
scape.processing.deskew_engine	Deskewing primitives
scape.batch.processor	Multi-position / multi-timepoint orchestration
scape.output.saver	TIFF writing helpers
scape.visualization.viewer	Interactive Jupyter previews

Citation

If this package contributes to a publication, please acknowledge the Scientific Computing Facility at MPI-CBG. Contact [e-mail] for the formal citation entry.

Links

• Source: https://git.mpi-cbg.de/scicomp/scidev_team/bcf_scape

License

BSD-3-Clause. See LICENSE.

Copyright © 2026 Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG).