This repository contains the processing pipelines, analysis scripts, and figure-generation code associated with the paper:
A Systematic Cross-Modal Approach Identifies Astrocytic VCAM1 as a Regulator of Hippocampal Synapse Development
Cydric Geyskens, Dan Dascenco, Elke Leysen, Efstathia Kotoula, Kjen Bogaert, Joris Vandenbempt, Francisco Pestana, (Benjamin Pavie, Steffen Fieuws,) Lars Lefever, Pedro Magalhaes and Joris de Wit.
The code spans multiple experimental modalities (spatial transcriptomics, super-resolution imaging, and proteomics) and is organized by figure. Each sub-repository includes scripts for raw data processing pipelines, downstream data analysis, and figure reproduction.
phd/
├─- spatial-transcriptomics/ # Spatial transcriptomics analysis scripts
├── candidate-profiling/ # systematic profiling of candidate CSPs
├── image-analysis/
│ ├── synapse-counting/ # Automated image processing and synapse quantification
│ └── in-vitro-synapse-counting/ # Semi-automated Fiji pipeline for in-vitro data
└── ip-proteomics/ # DIA-NN proteomics analysis and downstream statistics
| Figure | Experiment/Modality | Raw Data Repo | Code Repo |
|---|---|---|---|
| 1, S1 | Image-based Spatial Transcriptomics | BioImage Archive: S-BIAD2879 | phd/spatial-transcriptomics/scverse |
| 2, S2 | Candidate profiling | / | phd/candidate-profiling |
| 3, S3 | co-IP Proteomics | ProteomeXchange: PXD070371 & PXD070422 | phd/ip-proteomics |
| 4, S4, S5, S6 | Synapse In-Vivo Imaging Data | BioImage Archive: S-BIAD2530 | phd/image-analysis/synapse-counting |
| 4, S7 | Synapse In-Vitro Imaging Data | BioImage Archive: S-BIAD2430 | phd/image-analysis/in-vitro-synapse-counting |
Each sub-repo contains its own dependencies, either Conda, Apptainer or Docker.
C.G. developed and implemented all data processing pipelines and statistical analyses.
F.P. advised on the Resolve Bioscience spatial transcriptomics workflow analysis.
B.P. reviewed the synapse image processing workflow.
S.F. advised on statistical modeling.
P.M. and D.D. provided guidance on proteomics analysis.For questions or requests, please contact: Cydric Geyskens (cydric.geyskens@kuleuven.be) or Joris de Wit (joris.dewit@kuleuven.be)
If you use this code, please cite:
Geyskens, C., et al. (2026). A Systematic Cross-Modal Approach Identifies Astrocytic VCAM1 as a Regulator of Hippocampal Synapse Development. GitHub Repository