STAM's two-dimensional visualization service provides a digital map-style online browsing function with 700 coronal planes, 256 sagittal planes, and 367 horizontal planes. Users can observe individual standard profiles at different resolutions, navigate profiles at different locations along the same direction, and switch between the three standard profile directions. Each standard profile is a 20μm-thick projection image overlaid with a coordinate grid and annotated with boundaries of neuroanatomical structures.[More]

STAM's three-dimensional visualization service reconstructs the three-dimensional topography of 916 brain regions and nuclei.Users are capable of exploring the overall appearance as well as details of any anatomical structure of interest in three-dimensional space, from different perspectives and magnification levels. Additionally, through the assembly view feature, users can unfold the sub-structures contained within each brain region and nucleus, providing a detailed examination of the internal components.[More]

We also offer the service of visualizing slices at arbitrary angles. Users can choose the angle of interest and examine the isotropic 1-micron resolution cytoarchitectural brain slice at that angle. This service provides newly generated slices with annotations for brain regions and nuclei.[More]

We provide an automatic brain slice registration service. Users can upload single brain slice images stained with PI or DAPI. This service, through approximately 1 minute server-side computation, will generate a corresponding atlas slice from STAM that is closest in position to the uploaded brain slice. The computed angle and position will then be displayed in the main window.[More]

We provide open access and download services for the 3D cytoarchitecture image dataset of the whole mouse brain used for constructing STAM. Users can select any region of interest within the 3D space of STAM and download the original images of the selected region at different sampling rates.[More]

We support users in uploading 3D image data and neuronal morphology data previously registered to the Common Coordinate Framework (CCF). then mapping it onto STAM, and directly visualizing it in 3D space. We also support reverse mapping, which allows data of the same type that has been registered to STAM to be mapped onto the CCF.[More]

We have developed a virtual surgery navigating service. Users can simulate the stereotaxic surgical procedure of injecting viruses into the mouse brain through interactive operations. Based on user inputs, the STAM provides the information on the distance and injection angle between the injection site and origin defined by cranial or intracranial datum marks. Additionally, we offer the intelligent injection path planning: users can specify brain regions they wish to avoid, and the service will automatically calculate an appropriate path. If no suitable path can be found, the service will also give a notification.[More]

This service provides the reslicing of atlas annotation images, generating canonical atlas planes, as well as arbitrary-angle plane. This is a central hub connecting other functionalities of STAM. User can create a satisfactory plane in this service, and then jump to other services. [More]

This service integrates neuron morphology data from multiple sources, by registering them onto STAM and then visualizing them in the 3D space of STAM. We achieve the spatial localization of these neurons, by showing the brain structures where their soma, terminals and branching points are located in. We also provide the quantitative analyses of these neurons, including the distribution of terminals, the projection patterns, and the distribution of projection lengths in different brain structures. By counting the soma and terminals of these registered neurons, we develop a connectivity map of the whole brain, which reveals the neuron numbers of any given input and output brain structures, accompanied with a mutual query service. [More]