https://github.com/yfukai/m2stitch

MIST-inspired microscope image stitching package
https://github.com/yfukai/m2stitch

python3 stitching

Last synced: 3 months ago
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MIST-inspired microscope image stitching package

• Host: GitHub
• URL: https://github.com/yfukai/m2stitch
• Owner: yfukai
• License: other
• Created: 2021-05-19T15:36:31.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2026-01-29T05:53:24.000Z (5 months ago)
• Last Synced: 2026-03-01T16:36:39.980Z (4 months ago)
• Topics: python3, stitching
• Language: Python
• Homepage:
• Size: 92.9 MB
• Stars: 80
• Watchers: 5
• Forks: 12
• Open Issues: 23
• Metadata Files:
  • Readme: README.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE.rst
  • Code of conduct: CODE_OF_CONDUCT.rst

Awesome Lists containing this project

README

          
M2Stitch

========

|PyPI| |Python Version| |License|

|Read the Docs| |Tests| |Codecov|

|pre-commit| |Black| |Zenodo|

.. |PyPI| image:: https://img.shields.io/pypi/v/m2stitch.svg

   :target: https://pypi.org/project/m2stitch/

   :alt: PyPI

.. |Python Version| image:: https://img.shields.io/pypi/pyversions/m2stitch

   :target: https://pypi.org/project/m2stitch

   :alt: Python Version

.. |License| image:: https://img.shields.io/pypi/l/m2stitch

   :target: https://opensource.org/licenses/MIT

   :alt: License

.. |Read the Docs| image:: https://img.shields.io/readthedocs/m2stitch/latest.svg?label=Read%20the%20Docs

   :target: https://m2stitch.readthedocs.io/

   :alt: Read the documentation at https://m2stitch.readthedocs.io/

.. |Tests| image:: https://github.com/yfukai/m2stitch/workflows/Tests/badge.svg

   :target: https://github.com/yfukai/m2stitch/actions?workflow=Tests

   :alt: Tests

.. |Codecov| image:: https://codecov.io/gh/yfukai/m2stitch/branch/master/graph/badge.svg

   :target: https://codecov.io/gh/yfukai/m2stitch

   :alt: Codecov

.. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white

   :target: https://github.com/pre-commit/pre-commit

   :alt: pre-commit

.. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg

   :target: https://github.com/psf/black

   :alt: Black

.. |Zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5139596.svg

   :target: https://doi.org/10.5281/zenodo.5139596

   :alt: Zenodo

Features

--------

- Provides robust stitching of tiled microscope images on a regular grid, mostly following algorithm by MIST_ but improved in several points.

- Supports missing tiles.

Installation

------------

You can install *M2Stitch* via pip_ from PyPI_:

.. code:: console

   $ pip install m2stitch

Usage

-----

Please see the Usage_ for details.

Contributing

------------

Contributions are very welcome.

To learn more, see the `Contributor Guide`_.

License

-------

Distributed under the terms of the `MIT license`_,

*M2Stitch* is free and open source software.

Issues

------

If you encounter any problems,

please `file an issue`_ along with a detailed description.

Credits

-------

This program is an unofficial implementation of MIST_ stitching algorithm on GitHub_. The original paper is here_.

This project was generated from `@cjolowicz`_'s `Hypermodern Python Cookiecutter`_ template.

.. _MIST: https://pages.nist.gov/MIST

.. _GitHub: https://github.com/usnistgov/MIST

.. _here: https://github.com/USNISTGOV/MIST/wiki/assets/mist-algorithm-documentation.pdf

.. _@cjolowicz: https://github.com/cjolowicz

.. _Cookiecutter: https://github.com/audreyr/cookiecutter

.. _MIT license: https://opensource.org/licenses/MIT

.. _PyPI: https://pypi.org/

.. _Hypermodern Python Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python

.. _file an issue: https://github.com/yfukai/m2stitch/issues

.. _pip: https://pip.pypa.io/

.. github-only

.. _Contributor Guide: CONTRIBUTING.rst

.. _Usage: https://m2stitch.readthedocs.io/en/latest/usage.html

Citation

--------

If you use this program for your research, please cite it and help us build more.

.. code-block:: bib

   @misc{m2stitch,

      author = {Yohsuke T. Fukai},

      title = {m2stitch},

      year  = {2021},

      url   = {https://doi.org/10.5281/zenodo.5139596},

   }

Other Python stitching programs

-------------------------------

One might also be interested in another Python-written stitching tool

ASHLAR_ (bioRxiv_),

with a comparable performance to that of MIST and additional features.

.. _ASHLAR: https://github.com/labsyspharm/ashlar

.. _bioRxiv: https://www.biorxiv.org/content/10.1101/2021.04.20.440625v1