dvp-protocol-code

Code for protocol on Deep Visual Proteomics

Setup

1. Clone this repository

git clone https://github.com/MannLabs/dvp-protocol-code.git
# go into the repositorycd dvp-protocol-code

2. Create a suitable python environment

conda create -n dvp python=3.13 -y
# For image analysis
pip install -r requirements/requirements_image.txt
# For proteomics data analysis
pip install -r requirements/requirements_proteomics.txt

3. Download the data

Important

Careful! The utilized image is ~5GB large

cd data/
bash download.sh

References

Mund, A. et al. Deep Visual Proteomics defines single-cell identity and heterogeneity. Nat Biotechnol 40, 1231–1240 (2022).

Nordmann, T. M. et al. Spatial proteomics identifies JAKi as treatment for a lethal skin disease. Nature 1–9 (2024) doi:10.1038/s41586-024-08061-0.

Software

harpy Benjamin Rombaut, Arne Defauw, Frank Vernaillen, Julien Mortier, Evelien Van Hamme, Sofie Van Gassen, Ruth Seurinck, Yvan Saeys. Scalable analysis of whole slide spatial proteomics with Harpy. Bioinformatics (2026), btag122. https://doi.org/10.1093/bioinformatics/btag122

spatialdata Spatialdata: Marconato, L. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods 1–5 (2024) doi:10.1038/s41592-024-02212-x.