The MBA histology pipeline is used for all tissue processing in the MBA project. The pipeline consists of several discrete stations, as shown in the figure below. (A) C57BL/6 mice are screened to match specific age and weight requirements. Each selected animal then receives injection of a neuronal tracer (classical or viral) into a predetermined brain region. After the incubation period (tracer specific, but typically 3-21 days), the animal is perfused, and the brain is extracted and frozen in a customized mold that allows for two brains to be frozen side by side (B). The block containing two brains is then serially cryosectioned (C) using the tape-transfer method (specifically engineered for the MBA pipeline), and all sections are mounted directly onto slides. Alternating sections are separated to form two distinct series per brain. One series is processed for conventional cell body staining (D). The alternate slide series is either processed for tracer detection through histochemistry (E) or is directly coverslipped for fluorescent imaging (in the case of viral tracers). Whole-slide digital imaging is performed using a Hamamatsu / Olympus Nanozoomer HT system that is capable of scanning in brightfield (8 bits per color channel) and in fluorescence (12 bits per color channel) modes. The resulting raw data (G) are processed through a custom MATLAB program (H), in which the individual sections are cropped and converted into a specialized file format that is conducive to downstream processing. The result of the experimental pipeline is a large data stack of several hundred sections per brain. Raw image data (0.5µm pixel dimensions) are stored online without lossy compression (I and J). All process metadata, along with investigator observations, are stored in an integrated custom-designed Laboratory Information Management System (LIMS), which helps keep track of all samples and pipeline activities (K).