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Installation

napari-isbem communicates with SBEMimage over TCP — they are typically run in separate Python environments (often on separate machines), but can share one if convenient. Either way, they are installed independently.

Version Compatibility

napari-isbem SBEMimage Notes
v0.2.1+ ≥ 2026.xx (upcoming tagged release) Recommended
v0.2.0 2026.02.06 dev (3754ef9) Breaking change from v0.1.0
v0.1.0 2025.11.14 dev (58e36a5) Initial release

!!! warning 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.

napari-isbem

1. Set up a Python environment with napari

If you already have napari ≥ 0.5 installed in a Python 3.12 environment, skip to step 2.

Option A: Using conda

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

If conda is not installed, follow these installation instructions.

Option B: Using uv

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

and test napari opens correctly from the command line with

napari

!!! note napari[all] includes the default Qt backend (PyQt5). If you need a different backend (e.g. PySide2 or PyQt6), see Choosing a different Qt backend in the napari docs.

2. Install the plugin

pip install napari-isbem

To pin a specific version (e.g. if you need to match a particular SBEMimage version):

pip install napari-isbem==0.2.0

Once the installation is complete, open the plugin with

napari -w napari-isbem

SBEMimage

SBEMimage is not a Python dependency of napari-isbem — it is installed separately, possibly on a different machine (the one connected to the microscope).

Already have SBEMimage installed?

Check that your version is compatible with your napari-isbem version using the compatibility table above.

Need to install SBEMimage?

See the SBEMimage installation guide or clone from the SBEMimage repository.

To check out a specific compatible commit (e.g. for napari-isbem v0.2.0):

git clone https://github.com/SBEMimage/SBEMimage.git
cd SBEMimage
git checkout 3754ef9

Development build

When developing the plugin, you can clone repository and install the package in editable mode with

git clone git@github.com:FrancisCrickInstitute/napari-isbem.git
cd napari-isbem
pip install -e .