# Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization

## TL;DR

The Cell Mapping Toolkit is a pipeline that integrates various data types to create detailed maps of subcellular organization.

## Contribution

It introduces a unified framework for integrating and visualizing diverse protein datasets in a reproducible manner.

## Key findings

- The toolkit supports end-to-end processing of datasets from different modalities.
- It enables the creation of hierarchical maps with rich metadata and provenance documentation.
- The pipeline is freely available with comprehensive documentation and examples.

## Abstract

Cells are organized as a hierarchy of macromolecular assemblies, ranging from small protein complexes to entire organelles. Various technologies have been developed to elucidate subcellular architecture at different scales, such as mass spectrometry approaches for mapping protein biophysical interactions and immunofluorescence imaging for mapping protein localization. We present the Cell Mapping Toolkit, which is designed to systematically integrate data from different modalities into unified hierarchical maps of subcellular organization. The toolkit facilitates an end-to-end pipeline including processing datasets, integrating modalities, and visualizing the final cell map with rich metadata including provenance documentation at each step. The Cell Mapping Toolkit provides researchers with tools for analyzing, integrating, and visualizing diverse protein datasets in a robust and reproducible framework.

The code is freely available and is hosted on GitHub at https://github.com/idekerlab/cellmaps_pipeline. Comprehensive documentation and practical examples are provided at https://cellmaps-pipeline.readthedocs.io/.