spatialproteomics
Spatialproteomics is an interoperable toolbox for analyzing highly multiplexed fluorescence image data. This analysis involves a sequence of steps, including segmentation, image processing, marker quantification, cell type classification, and neighborhood analysis.
Principles
Multiplexed imaging data comprises at least 3 dimensions (i.e. channels, x, and y) and often contains additional data such as segmentation masks or cell type annotations associated with it. In spatialproteomics, we use xarray to create a data structure that keeps all of these data dimension in sync. This data structure can then be used to apply all sorts of operations to the data. Users can segment cells, perform different image processing steps, quantify protein expression, predict cell types, and plot their data in various ways. By providing researchers with those tools, spatialproteomics can be used to quickly explore highly multiplexed spatial proteomics data directly within jupyter notebooks.
Getting Started
Please refer to the documentation for details on the API and tutorials.
Installation
To install spatialproteomics, first create a python environment and install the package using
pip install spatialproteomics
The installation of the package should take less than a minute.
System Requirements
Hardware Requirements
spatialproteomics requires only a standard computer with enough RAM to support the in-memory operations. Certain steps of the pipeline, such as segmentation, benefit from using a GPU.
Software Requirements
The base version of spatialproteomics depends on the following packages:
xarray
zarr
numpy
scikit-image
scikit-learn
opencv-python
matplotlib
Citation
Meyer-Bender, M., Voehringer, H., Schniederjohann, C., Koziel, S., Chung, E., Popova, E., ... & Huber, W. (2026). Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data. Nature Methods, 1-10.
2 maintainers
Release files for spatialproteomics 0.8.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| spatialproteomics-0.8.6.tar.gz | 93.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| spatialproteomics-0.8.6-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 191.6 kB
Release files / spatialproteomics-0.8.6.tar.gz
| Download URL | spatialproteomics-0.8.6.tar.gz |
|---|---|
| Size | 93.0 kB |
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| Download URL | spatialproteomics-0.8.6-py3-none-any.whl |
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