In a collaborative effort lead by Prof. Pierre Magistretti, the KAUST-EPFL Alliance for Integrative Modeling of Brain Energy Metabolism analyzes the distribution of various organelles in the brain. Towards that goal, project manager Dr. Corrado Calì acquired a serial block-face electron microscopy stack of a piece of cortex that was […]

Automated segmentation of mitochondria and ER in cortical cells


In a pilot study, the lab of Dr. Prisca Liberali at FMI, Switzerland, acquired a complete serial block-face electron microscopy stack of an intestinal organoid. We developed a deep-learning pipeline for the automated segmentation of all organoid cells and their nuclei. The accurate segmentation of the thin filopodia of these […]

Automated segmentation of intestinal organoid cells and nuclei


In a study recently published in Neuron and featured in Nature Methods, the lab of Dr. Botond Roska performed targeted single-cell-initiated transsynaptic tracing to label retinal ganglion cells that provide input to individual principal cells in the mouse lateral geniculate nucleus (LGN). Subsequently, more than 500 labeled ganglion cells were […]

Deciphering the modes of visual integration in the Lateral Geniculate ...



Ariadne-service and PyKnossos was used to reconstruct essentially all neurons in the olfactory bulb of a larval zebrafish. A detailed description of the dataset and software was recently published in Nature Scientific Data. The study (published in Nature Neuroscience) identified novel, rare cell types and revealed a specific topological organization of the […]

Dense EM-based reconstruction of the interglomerular projectome in the zebrafish ...


The goal of this challenge is to evaluate algorithms for automatic reconstruction of neurons and neuronal connectivity from serial section electron microscopy data. Ariadne-service was involved in generating the neurite segmentation for the challenge. Visit cremi.org for more information on the challenge.

MICCAI challenge on circuit reconstruction from electron microscopy images