UELer: a Jupyter-based framework for interactive exploration of multiplexed imaging datasets

Summary Multiplexed imaging and spatial proteomics generate complex datasets that require both computational analysis and visual inspection. However, these tasks mostly occur in separate environments because interactive viewers generally require a local display or an additional data server beyond the remote Jupyter sessions itself where large datasets are computationally analyzed. We here present UELer, an interactive viewer that links multi-channel image views with quantitative analysis results directly within Jupyter notebooks, requiring no dedicated infrastructure beyond the notebook session. Cells selected through computational analysis and summary plots can be inspected directly in their tissue context, and selections made in the image can be made available to any downstream analysis. Together, these capabilities support interactive data exploration, iterative cell annotation, and reproducible retrieval of selected regions. Availability and Implementation UELer is a Python package built on ipywidgets and runs in Jupyter environments supporting ipywidgets 8.1 or later, tested in JupyterLab and Visual Studio Code on Linux, macOS, and Windows. It is freely available under GPL-3.0 license and can be installed via pip. Source code and documentation are available at https://github.com/HartmannLab/UELer and https://hartmannlab.github.io/UELer/. An online, no-install version runs remotely via BinderHub (https://mybinder.org/v2/gh/HartmannLab/UELer/main), accessible through the script/run_ueler_binder.ipynb notebook.