cellprofiling / hdca-fetallung-spatialproteomics

Custom software written for analysis of spatial proteomics data from fetal lung acquired in the HDCA project.

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HDCA-FetalLung-SpatialProteomics

Custom software written for analysis of spatial proteomics data from fetal lung acquired in the Human Developmental Cell Atlas project. The example_pipelines folder contains example python code applied to analyze the single-cell data derived from pipex analysis of spatial proteomics images. The ImageJ_Macro folder contains the imagej macro that was used in the preprint for a pipex-independent analysis of marker expression in artery-close immune cells.

Reusing the code? How to cite this software / data?

The software provided in this repository is licensed under the MIT license provided in the repository. Please note the individual copyright notices in the ImageJ_Macro and example_pipelines folders, individually applying to the ImageJ_Macro or example_pipelines.

The software was developed for data analysis as presented in this preprint by Sariyar et al..

When using the code in this repository, please cite this preprint.

Long citation:

High-parametric protein maps reveal the spatial organization in early-developing human lung
Sanem Sariyar, Alexandros Sountoulidis, Jan Niklas Hansen, Sergio Marco Salas, Mariya Mardamshina,
Anna Martinez Casals, Frederic Ballllosera Navarro, Zaneta Andrusivova, Xiaofei Li, Paulo Czarnewski,
Joakim Lundeberg, Sten Linnarsson, Mats Nilsson, Erik Sundström, Christos Samakovlis, Emma Lundberg, Burcu Ayoglu.
bioRxiv 2024.01.25.577163; doi: https://doi.org/10.1101/2024.01.25.577163