Assessing the Proinflammatory Potential of Sterile Fecal Microbiome Filtrate from Ulcerative Colitis Patients Using an Intestine-on-Chip Platform and Automated Image Analysis

Tobias Schaal, Parastoo Akbarimoghaddam, Valentin D. Wegner, Arndt Steube, Elena Gardey, Adrian Feile, Mohamed Abdelwahab Hassan, Zoltán Cseresnyés, Andreas Stallmach, Alexander Mosig, Marc Thilo Figge, Johannes Stallhofer

Gut Microbes

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  1. Schaal_AkbarimoghaddamEtAl2025_FMF
  2. Codes
Analysis workflow.jip 2 MB Chip mask by weka-Epithelial.ijm 5 KB Chip mask by weka-Vascular.ijm 5 KB Tiles realignment-Vascular.ijm 2 KB

This folder contains the data and image analysis codes required to reproduce our findings. More information on how to run the analysis, can be found in Readme.txt!


Contents

Data: Raw microscopy images and biomolecular data

Codes: Image analysis scripts and piplines used for generating the results

Image processing: Data generated from image analysis workflows

Image-based measurements: Quantifications derived from the images

Readme.txt: More information on data structure and codes