Automated analysis pipeline for High Content Screens. Processes 384-well plates with 9 fields per well (10,368 images per plate) to quantify aggregate-positive cells. Performs illumination correction, deep learning segmentation (StarDist for nuclei, Cellpose for cells), and co-localization analysis to characterize aggregate inclusions in cells.
A specialized visualization tool for high-content screening microscopy data, supporting GE InCell Analyzer conventions and focus metrics. Designed for interactive exploration of plate-based imaging experiments with built-in quality control and data navigation features.
A Python/C package for image processing of large, 3D (volumetric) image data. Designed for storing NumPy arrays in raw file format, handling NRRD metadata used in bio-imaging, and performing computations on image data with optional OpenMP parallelism. Used in multiple publications for whole-brain light-sheet microscopy analysis.
Analysis tools for prion disease research using 3D whole-brain imaging data.
Image processing pipeline for microglia and plaque segmentation in whole murine brains, developed for a study on prime editing of the β1 adrenoceptor to restore physiological REM sleep in an Alzheimer's disease mouse model. Combines machine learning-based instance segmentation (ilastik) with deformable registration to the Allen Brain Atlas for region-specific quantification of pathological markers.
Pipeline for quantifying brainwide, region-specific effects of the antidiabetic drug netoglitazone in Alzheimer's mouse models. Processes whole-brain 3D image stacks for automated microglia segmentation, surface-artifact removal, voxelization/smoothing, and registration to the Allen Brain Atlas.
Pipeline for quantifying and mapping the brainwide spatial distribution of proteins delivered by engineered Toxoplasma gondii secretion systems. Detects ZsGreen+ cell volume from whole-brain 3D light-sheet microscopy (mesoSPIM) images, with artifact filtering and registration to the Allen Brain Atlas.
Computational Science & Engineering
Dr. sc. ETH Zurich
