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.