The mouse visual system has increasingly been used as model to study vision. The most important reason for shifting from primate and carnivore models to the mouse is that transgenetic mice can be routinely used in laboratories. Recently, ample evidence has shown that the mouse has a more complex visual system than previously thought, composed of at least ten visual areas. These visual areas are interconnected to form dorsal and ventral visual processing streams, which are similar to those in monkeys and cats. However, the most popular anatomical atlases such as the Allen Reference Atlas and the Mouse Brain in Stereotactic Coordinates only show six and four visual areas, respectively. Clearly, these atlases need to be updated with the most recent knowledge of mouse visual cortex in order to adequately use them to study mouse vision at different levels from cell types and neuronal coding to behavior and finally to computational model. My first interest is to build a three-dimensional common coordinate framework where the data collected from different modalities can be put into the same common space. My second interest is to map the cell numbers in mouse brain because this information is essential for building a computational model and comparing with aging and diseased brain and understand the revolutionary scaling law. My third interest is to understand the intrinsic connections of mouse primary visual cortex. The intrinsic connections derived from layer 2/3 pyramidal neurons in primates and cats may be linked to functional columns such as orientation columns. However, such orientation columns have not been observed in mouse primary visual cortex. The functional role of intrinsic connections in the mouse primary visual cortex remains mystery. Through leading studies such as those described above I aim to make a great contribution to the research programs at the Allen Institute.