iSEBM: Automated ROI Targeting in Volume Electron Microscopy

Ronchi, 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.

A 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.

Version Compatibility

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:

[!IMPORTANT] 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.

[!TIP] 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.

Installation

Installing napari

Create 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).

Using Python with uv:

uv venv napari-isbem --python 3.12
source napari-isbem/bin/activate
uv pip install 'napari[all]==0.5' qtpy

Using conda:

conda create -n napari-isbem python=3.12 napari=0.5 pyqt -c conda-forge
conda activate napari-isbem

Installing the plugin

# with uv
uv pip install napari-isbem
# to install a specific version, e.g. v0.2.0
uv pip install napari-isbem==0.2.0
# with pip/conda
pip install napari-isbem

Launch with

napari -w napari-isbem

SBEMimage

SBEMimage is installed separately (it is not a Python package dependency of napari-isbem). See the SBEMimage installation guide or clone from the SBEMimage repository.

More detailed instructions for all scenarios can be found in the installation documentation.

Usage

To get started, follow the step by step illustrated user guide. For more detailed information on the features and settings, see the full documentation.

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-isbem" is free and open source software.

Issues

If you encounter any problems, please file an issue along with a detailed description.