PathwayFinder

Zenodo (CERN European Organization for Nuclear Research)

Abstract

This page contains additional resources that complement the paper "PathwayFinder Enables Linked Exploration of Cell Types and Gene Modules in Spatially Resolved Transcriptomics Data". PathwayFinder is built as plug-ins of the ManiVault Studio application building system. Installer for Windows: This installer (pathwayfinder_1.0_offline.exe) includes plugins to reproduce the analysis discussed in our paper. After installation, the projects used in this paper are listed on the application's start page. Users can select a project, after which the corresponding file will be automatically downloaded and loaded. Hardware requirements: A minimum of 16GB of memory is required to load this data, and 32GB+ is highly recommended for optimal performance. Tutorial: is available at https://www.manivault.studio/tutorials/pathwayfinder/ Example Project: To reproduce the results in the paper, we recommend using the `.mv` project files, which contains both the data and GUI configurations. Opening these `.mv` files will restore the saved UI layout, no manual setup needed.1. MERFISH mouse brain section38 from Yao et al.: This project is demonstrated in Figure 1, Figure 2, Figure 7 and Supplemental Figure 1. 2. MERFISH mouse brain ABCA-4 from Zhang et al.: This project is demonstrated in Figure 3.3. Xenium Prime mouse brain hemisphere from 10x Genomics: This project is demonstrated in Figure 4 and Supplemental Figure 1. 4. MERFISH mouse brain hypothalamus from Yao et al.: This project is demonstrated in Figure 5, Figure 6, Supplemental Figure 2 and Supplemental Figure 3. Supplemental Video: A supplemental video demonstrating the interactive capabilities of the PathwayFinder exploration pipeline. This visual guide helps to illustrate the features discussed in the paper. Source code: PathwayFinder source code is available at our GitHub repositories, specifically DualViewPlugin and DualAnalysisPlugin.

Authors 7

1. Chang Li Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center

2. Julian Thijssen Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center

3. Thomas Kroes Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center

4. Lisa L. Koorneef Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center

5. Thomas Höllt

   University of Bergen · Delft University of Technology

   Affiliation as printed

   Delft University of Technology

   University of Bergen

6. Louise van der Weerd Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center

7. Boudewijn P. F. Lelieveldt Aachen

   Leiden University Medical Center · Delft University of Technology

   Affiliation as printed

   Leiden University Medical Center

   Delft University of Technology