# napari-imsmicrolink
[](https://github.com/nhpatterson/napari-imsmicrolink/raw/master/LICENSE)
[](https://pypi.org/project/napari-imsmicrolink)
[](https://python.org)
[](https://github.com/nhpatterson/napari-imsmicrolink/actions)
[napari] plugin to perform MALDI IMS - microscopy registration using laser ablation marks as described in [Anal. Chem. 2018, 90, 21, 12395–12403](https://pubs.acs.org/doi/abs/10.1021/acs.analchem.8b02884). This plugin is a work-in-progress but is mostly functional.
__N.B.__ This tool is __NOT__ a general purpose registration framework to find transforms between IMS (MALDI or otherwise)
and microscopy. It is built to align MALDI IMS pixels to their corresponding laser ablation marks as captured by microscopy AFTER the IMS experiment.
This approach has the advantage of providing direct evidence of registration performance as IMS pixels are aligned
to their _explicit spatial origin_ in microscopy space, improving overall accuracy and confidence of microscopy-driven IMS
data analysis.
## Installation
You can install `napari-imsmicrolink` via [pip]:
pip install napari-imsmicrolink
### Typical experiment workflow
1. Acquire pre-IMS microscopy (autofluorescence, brightfield) - _optional_
2. Perform normal IMS sample preparation.
3. Acquire post-IMS microscopy (autofluorescence, brightfield) with matrix still on sample
that reveals laser ablation marks.
4. Gather IMS data that contains XY integer coordinates for the IMS experiment
(.imzML, Bruker spotlist (.txt, .csv), Bruker peaks.sqlite (_FTICR_),
Bruker .tsf (TIMS qTOF only))
5. Run `napari-imsmicrolink` with data 3 and 4
6. Once registered, use `wsireg` to align other microscopy modalities to IMS-registered post-IMS
microscopy
----------------------------------
This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.
<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started
and review the napari docs for plugin developers:
https://napari.org/docs/plugins/index.html
-->
## Contributing
Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.
## License
Distributed under the terms of the [MIT] license,
"napari-imsmicrolink" is free and open source software
## Issues
If you encounter any problems, please [file an issue] along with a detailed description.
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[file an issue]: https://github.com/nhpatterson/napari-imsmicrolink/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
Raw data
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"description": "# napari-imsmicrolink\n\n\n[](https://github.com/nhpatterson/napari-imsmicrolink/raw/master/LICENSE)\n[](https://pypi.org/project/napari-imsmicrolink)\n[](https://python.org)\n[](https://github.com/nhpatterson/napari-imsmicrolink/actions)\n\n[napari] plugin to perform MALDI IMS - microscopy registration using laser ablation marks as described in [Anal. Chem. 2018, 90, 21, 12395\u201312403](https://pubs.acs.org/doi/abs/10.1021/acs.analchem.8b02884). This plugin is a work-in-progress but is mostly functional.\n\n__N.B.__ This tool is __NOT__ a general purpose registration framework to find transforms between IMS (MALDI or otherwise)\nand microscopy. It is built to align MALDI IMS pixels to their corresponding laser ablation marks as captured by microscopy AFTER the IMS experiment. \nThis approach has the advantage of providing direct evidence of registration performance as IMS pixels are aligned \nto their _explicit spatial origin_ in microscopy space, improving overall accuracy and confidence of microscopy-driven IMS \ndata analysis.\n\n## Installation\n\nYou can install `napari-imsmicrolink` via [pip]:\n\n pip install napari-imsmicrolink\n\n### Typical experiment workflow\n1. Acquire pre-IMS microscopy (autofluorescence, brightfield) - _optional_\n2. Perform normal IMS sample preparation.\n3. Acquire post-IMS microscopy (autofluorescence, brightfield) with matrix still on sample\nthat reveals laser ablation marks.\n\n4. Gather IMS data that contains XY integer coordinates for the IMS experiment\n (.imzML, Bruker spotlist (.txt, .csv), Bruker peaks.sqlite (_FTICR_),\n Bruker .tsf (TIMS qTOF only))\n\n5. Run `napari-imsmicrolink` with data 3 and 4\n\n6. Once registered, use `wsireg` to align other microscopy modalities to IMS-registered post-IMS\nmicroscopy\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/docs/plugins/index.html\n-->\n\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [MIT] license,\n\"napari-imsmicrolink\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n[file an issue]: https://github.com/nhpatterson/napari-imsmicrolink/issues\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n",
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