stitchmeta

Extract metadata from microscopy image tiles and write FEABAS-compatible coordinate files for stitching pipelines.

Installing stitchmeta

The preferred way of installing stitchmeta is using pip.

Installing the release version using pip

stitchmeta can be installed using pip to obtain the current release:

python -m pip install stitchmeta

Installation from source

Clone this repository and install from the local source tree:

git clone https://github.com/thomasisensee/stitchmeta.git
cd stitchmeta
python -m pip install .

Development installation

For development, it is recommended to use an editable install:

python -m pip install --editable .[tests]

Having done so, the test suite can be run using pytest:

python -m pytest

Quick start

Expected input layout:

dataset_root/
  001/
    tile_a.tif
    tile_b.tif
  002/
    ...

Run extraction:

stitchmeta extract \
  -i dataset_root \
  -o feabas_coords

The command writes one FEABAS text file per section (001.txt, 002.txt, ...).

Python API

from stitchmeta import extract

summary = extract(
    input_root="dataset_root",
    output_dir="feabas_coords",
    reader_name="fibics_tiff",
    invert_y=True,
    error_policy="partial",
)

Extending to other datasets

Register a new reader class implementing the TileReader interface and use it through reader_name in the API or CLI.

Acknowledgments

This repository was set up using the SSC Cookiecutter for Python Packages.