Motivated by fundamental questions in cell biology our lab produces biological insights along with specialized analytic tools that reveal hidden patterns in cell imaging data. This GitHub organization serves the purpose to store and maintain the products of our research.

• shape-exp-modeling - Modeling the interplay between cell shape and expression in multiplexed imaging.
• AnomalyDetectionScreening - Framework for hit identification in High Throughput Screening (HTS).
• recurring-transient-communities - Detection of transient communities and hotspots in the developing Drosophila lymph gland, using ARCOS framework on Ca2+ readouts.
• multiplexed-imaging-motifs-visualiser - Motif Visualizer for Multiplexed Imaging. A specialized tool designed to enhance the analysis and visualization of multiplexed imaging data.
• muscle-formation-prediction - Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion.
• SLGC-tissue-similarity-and-grading - Nondestructive Spatial Lipidomics for Glioma Classification Tissue Similarity and Grading.
• DISCOVER - Visual interpretability of image-based classification models by generative latent space disentanglement applied to in vitro fertilization.
• MyocytesFusionSimulationsGeneratorAnalyzer - Myoblast fusion OOP implementations of fusion policies, and simulations analysis compared to experimental data.
• IRM-Spreading-Dynamics - A custom pipeline for quantifying the spatiotemporal dynamics of platelet spreading process under IRM microscopy.
• SpatiotemproalQuantificationMonolayerCellMigrationPipeline - A Matlab pipeline for spatiotemporal quantification of monolayer cell migration. The repository includes Matlab source code. This repository is part of the book series "Neubias Bioimage Analysis". The analysis pipeline includes segmentation, velocity measurements, kymographs and multi-dimensional representations and PCA of wound healing assays.
• PropagationOfCellDeath - Ferroptosis occurs through an osmotic mechanism and propagates independently of cell rupture.

Please do all actions (open issues, file bug reports, file feature requests etc.) in the relevant repositories.