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Methods for measuring co-localization of ion images
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Measuring co-localization of ion images

This repository is devoted to a project on measuring co-localization of mass spectrometry images. The project is carried out by the Alexandrov team at EMBL Heidelberg. We created a webapp for ranking pairs of ion images, engaged external experts to rank images from their public data from METASPACE, consolidated the results into a gold standard set of ranked pairs of ion images, and, finally, developed and evaluated various measures of co-localization.


  • Katja Ovchinnikova: pixel-based co-localization method development, gold standard preparation
  • Alexander Rakhlin: deep learning based co-localization method development
  • Lachlan Stuart: development and implementation of the RankColoc web app
  • Sergey Nikolenko: PI for the deep learning work
  • Theodore Alexandrov: supervision, gold standard preparation

Creating gold standard ion images

Using public METASPACE datasets

We used public datasets from METASPACE, a community-populated knowledge base of metabolite images. Please see the section Acknowledgements acknowledging contributors of the used data.

RankColoc was rapidly prototyped using the METASPACE codebase as a foundation, allowing its back-end, image display and ranking to be reused. The RankColoc-specific changes can be found in this commit range.


Gold standard

The gold standard is available here. The ion images are available under gs_imgs1 and gs_imgs2 file names. To join both files into one arhive run cat gs_imgs* > gs_imgs.tar.gz

The initial expert rankings can be found in rankings.csv, the filtered gold standard with average rankings is in coloc_gs.csv.

Colocalization measures

Measures requiring no learning

Measures requiring no learning are available in the jupyter notebook ion_intensity_coloc_measures.ipynb here.

Measures based on deep learning

Measures based on deep learning are available here.

Future steps

We are planning to integrate the best methods into


Unless specified otherwise in file headers or LICENSE files present in subdirectories, all files in this repository are licensed under the Apache 2.0 license.

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