Scheme of the DELiVR inference pipeline. All components are packaged in a single Docker container. Raw image stacks serve as input. They are downsampled for atlas alignment and optionally masked (to exclude detection on ventricles). The masked images are then passed on to deep-learning cell detection (inference), which produces binary segmentations. The binarized cell’s center points are subsequently transformed to the Allen Brain Atlas CCF3 space. The cells are visualized in atlas space as (group-wise) heat maps and in image space as color-coded tiff stacks.
