The scientific mission of the Project MindScope is to understand neocortex, the part of the mammalian brain that gives rise to perception, memory, intelligence, and consciousness. We seek to quantitatively evaluate the hypothesis that neocortex is a relatively homogeneous tissue, with smaller functional modules that perform a common computational function replicated across regions. We here focus on the mouse as a mammalian model organism with genetics, physiology, and behavior that can be readily studied and manipulated in the laboratory. We seek to describe the operation of cortical circuitry at the computational level by comprehensively cataloging and characterizing its cellular building blocks along with their dynamics and their cell type-specific connectivities. The project is also building large-scale experimental platforms (i.e., brain observatories) to record the activity of large populations of cortical neurons in behaving mice subject to visual stimuli. A primary goal is to understand the series of operations from visual input in the retina to behavior by observing and modeling the physical transformations of signals in the corticothalamic system. We here focus on the contribution that computer modeling and theory make to this long-term effort.T he neocortical sheet is a layered structure with a thickness that varies by a factor of two to three, whereas its surface area varies by 50,000 between the small smoky shrew and the massive blue whale. A unique hallmark of mammals, neocortex is a highly versatile, scalable, ∼2D computational tissue that excels at real time sensory processing across modalities and making and storing associations as well as planning and producing complex motor patterns. Neocortex consists of smaller modular units (columnar circuits that reach across the depth of cortex) broadly repeated iteratively across the cortical sheet. These modules vary considerably in their connectivity and properties between regions, with some controversy whether there is, indeed, a single canonical function performed by any and all neocortical columns.A deep understanding of cortex necessitates measuring relevant biophysical variables, such as recording action and membrane potentials, and relating them to genetically identified cell types. Mapping, observing, and intervening in widespread but highly specific cellular activity are more readily accomplished in the mouse, Mus musculus, than in the human brain. The brain of the laboratory mouse is more than three orders of magnitude smaller than the human brain in weight (0.4 vs. 1,350 g) and contains 71 million vs. 86 billion nerve cells for the entire brain and 14 million vs. 16 billion nerve cells for neocortex (1).The Allen Institute for Brain Science is engaged in a 10-y, highthroughput, milestone-driven effort to characterize all cortical cell types for the mouse cortex to build a small number of distinct experimental and computational platforms, called brain observatories, for studying behaving mice and to construct abstract and biophysically realisti...