{"name":"napari-isbem","display_name":"iSBEM","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-isbem.make_isbem_widget","title":"Open iSBEM","python_name":"napari_isbem._widgets:iSBEMWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-isbem.make_isbem_widget","display_name":"iSBEM","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-isbem","version":"0.2.2","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A plugin to allow targeted acquisition in SBEMimage.","description":"# iSEBM: Automated ROI Targeting in Volume Electron Microscopy\n\n[![License MIT](https://img.shields.io/pypi/l/napari-isbem.svg?color=green)](https://github.com/FrancisCrickInstitute/napari-isbem/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-isbem.svg?color=green)](https://pypi.org/project/napari-isbem)\n[![tests](https://github.com/FrancisCrickInstitute/napari-isbem/workflows/tests/badge.svg)](https://github.com/FrancisCrickInstitute/napari-isbem/actions)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-isbem)](https://napari-hub.org/plugins/napari-isbem)\n<!-- [![Python Version](https://img.shields.io/pypi/pyversions/napari-isbem.svg?color=green)](https://python.org) -->\n<!-- [![codecov](https://codecov.io/gh/FrancisCrickInstitute/napari-isbem/branch/main/graph/badge.svg)](https://codecov.io/gh/FrancisCrickInstitute/napari-isbem) -->\n\nRonchi, Paolo, Graham Ross, Alana Burrell, et al. 2026. **‘iSBEM: An Open-Source Workflow for Automated ROI Targeting in Volume Electron Microscopy’.** Preprint, bioRxiv, June 6. https://doi.org/10.64898/2026.06.05.730298.\n\nA [napari] plugin to enable targeted imaging in [SBEMimage]. Regions of interest identified in X-Ray Microscopy (XRM) (or other correlative modality) images can be registered to the SBF-SEM data, and the plugin communicates with SBEMimage over TCP to automatically update acquisition regions in real-time. Read the accompanying [preprint] and the [documentation] for more information.\n\n![](.assets/hero.png)\n\n----------------------------------\n\n## Version Compatibility\n\n`napari-isbem` communicates with SBEMimage over TCP — they do not necessarily need to be run in the same Python environment. You need compatible versions of each:\n\n| napari-isbem | SBEMimage | Notes |\n|---|---|---|\n| v0.2.1+ | ≥ [2026.06](https://github.com/SBEMimage/SBEMimage/releases/tag/2026.06) | Recommended |\n| v0.2.0 | 2026.02.06 dev ([`3754ef9`](https://github.com/SBEMimage/SBEMimage/tree/3754ef96bc19426995bcfae012410a90a2b5f0ae)) | Breaking change from v0.1.0 |\n| v0.1.0 | 2025.11.14 dev ([`58e36a5`](https://github.com/SBEMimage/SBEMimage/tree/58e36a5f55d4cbc0b4f18b6db780f4808a6520d4)) | Initial release |\n\n>  [!IMPORTANT]\n> v0.2.0 introduced a breaking change in the SBEMimage metadata format. napari-isbem v0.2.x is **not** compatible with earlier SBEMimage versions, and v0.1.0 is **not** compatible with later ones.\n\n> [!TIP]\n> To install a specific version, use `napari-isbem==<version>`, for example `pip install napari-isbem==0.1.0`, or download directly from the [releases] page.\n\n## Installation\n\n### Installing napari\n\nCreate a Python 3.12 environment with napari installed (skip this step if you are already a napari user and have napari installed in your environment).\n\nUsing Python with [uv]:\n\n```\nuv venv napari-isbem --python 3.12\nsource napari-isbem/bin/activate\nuv pip install 'napari[all]==0.5' qtpy\n```\n\nUsing conda:\n\n```\nconda create -n napari-isbem python=3.12 napari=0.5 pyqt -c conda-forge\nconda activate napari-isbem\n```\n\n### Installing the plugin\n\n```\n# with uv\nuv pip install napari-isbem\n# to install a specific version, e.g. v0.2.0\nuv pip install napari-isbem==0.2.0\n# with pip/conda\npip install napari-isbem\n```\n\nLaunch with\n\n```\nnapari -w napari-isbem\n```\n\n### SBEMimage\n\nSBEMimage is installed separately (it is not a Python package dependency of napari-isbem). See the [SBEMimage installation guide](https://sbemimage.readthedocs.io/en/latest/installation.html) or clone from the [SBEMimage repository](https://github.com/SBEMimage/SBEMimage).\n\nMore detailed instructions for all scenarios can be found in the [installation documentation](https://FrancisCrickInstitute.github.io/napari-isbem/installation/).\n\n## Usage\n\nTo get started, follow the step by step illustrated [user guide](USER_GUIDE.md). For more detailed information on the features and settings, see the [full documentation](https://FrancisCrickInstitute.github.io/napari-isbem).\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-isbem\" 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://napari.org/\n[SBEMimage]: sbemimage.readthedocs.io\n[preprint]: https://www.biorxiv.org/content/10.64898/2026.06.05.730298v1\n[documentation]: https://FrancisCrickInstitute.github.io/napari-isbem\n[tox]: https://tox.readthedocs.io/en/latest/\n[uv]: https://docs.astral.sh/uv/pip/environments/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n[MIT]: http://opensource.org/licenses/MIT\n[file an issue]: https://github.com/FrancisCrickInstitute/napari-isbem/issues\n[releases]: https://github.com/FrancisCrickInstitute/napari-isbem/releases\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Graham Ross, Joost de Folter, Fiona Young","author_email":null,"maintainer":null,"maintainer_email":"Fiona Young <fiona.young@crick.ac.uk>, Joost de Folter <joost.defolter@crick.ac.uk>","license":null,"classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","SimpleITK","napari-ome-zarr","napari-tiff","ome-zarr","opencv-python","scikit-image","scikit-learn","scipy","qtpy","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","pytest-mock; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":">=3.9","requires_external":null,"project_url":["Documentation, https://franciscrickinstitute.github.io/napari-isbem/","Repository, https://github.com/FrancisCrickInstitute/napari-isbem"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}