Canonical plane visualization

The interface for the canonical plane visualization service is illustrated below. The central area is the main window, used to display STAM's canonical planes (①) and the brain region annotations on these planes (②). Users can use the left mouse button and scroll wheel in the main window to move, and zoom in to the resolution of the region of interest. When the user hovers the mouse over an annotation for a brain region or nucleus, the annotation switches to a blue highlighted mode (③), and the full name of the highlighted brain region or nucleus is displayed in the lower-left corner (④).\nThe light gray grid behind the canonical plane and annotations shows the distribution of the STAM coordinate system on the current plane (⑤). As the user moves the mouse, the real-time position of the mouse in the STAM coordinate system is displayed in the lower-left corner of the main window (⑥). Users can also observe the position of the current viewed canonical plane in the entire mouse brain through the navigation window in the upper left corner (⑦), as well as drag the slide inside the navigation window in the upper left corner to jump to other canonical planes of interest.\nUsers can freely switch to other sections using the right-side image gallery (⑧), or switch between different anatomical directions, such as coronal, sagittal, and horizontal planes (⑨). Additionally, users can search for brain regions or nuclei of interest in the input box (⑩) or navigate through the anatomical ontology tree (⑪). If the current viewed profile does not include the searched structure, it will jump to the nearest profile in the same direction that contains the structure.\nAt the bottom of the main window is the button panel for the canonical plane visualization service (⑫). The button functions, from left to right, include: zoom out, zoom in, reset view, full screen, switch to three-dimensional visualization service, switch to arbitrary angle cross-section visualization service, display mode switch, and jump to other profiles in the current anatomical direction. To input the numerical designation of a coronal plane into the text input box in the button group, then click the adjacent “Go” button to jump to the corresponding plane. The viewing perspective, i.e., the current zoom level and position, will be preserved when switching between planes.\nFurthermore, we could traverse from canonical plane visualization service to stereotaxic topography visualization service: On the canonical plane visualization service page, users can highlight a brain region or nucleus of interest, then click the 3D button in the button panel at the bottom of the page, or right-click and choose to jump to the stereotaxic topography visualization service page from the pop-up menu. The brain region or nucleus highlighted in the canonical plane visualization page will also display its three-dimensional model in the stereotaxic topography visualization page.

Stereotaxic topography visualization

Operating Instructions The stereotactic topography service interface is shown in the figure. The central area is the main window. The three arrows labeled by ① indicate the semi-transparent outline of the mouse brain, a three-dimensional coordinate system displayed in numerical grid, and the cranial and intracranial datum marks shown as red dots. The primary purpose of this information is to provide users with intuitive and diverse forms of spatial localization information, all of which are displayed by default upon entering the service interface. On the left of the main window is the data panel ②, which contains three tabs. The "Regions" tab includes the anatomical nomenclature tree of STAM, where users can select any number of structures of interest via checkboxes. The "Vessels" tab contains a complete cerebral vascular atlas registered to the STAM, allowing users to select vascular branches of interest. The "Neurons" tab is used to query and filter neuron morphological data with somas or projection targets located in regions of interest. Data selected or filtered in these three tabs will be displayed in the main window. As shown by the three arrows labeled ③, the orange represents the three-dimensional topography of the brain regions of interest selected in the "Regions" tab ④, the blue represents the three-dimensional morphology of the vascular branches of interest selected in the "Vessels" tab, and the green represents the individual neuron morphological data filtered in the "Neurons" tab. In the anatomical nomenclature tree under the "Regions" tab, a blue square icon could be found at the right side of any brain region or nucleus that consists of substructures. As shown in ⑤, when users click on this icon next to the structure of interest, the original blue square changes to an icon composed of three expanded surfaces. At this point, all substructures of the clicked structure will be visualized in an assembled form in the main window, as indicated by the golden three-dimensional models in ⑥. When the Assembling tab be selected, all substructures will expand from their original positions, and the expansion magnitude can be set in the right panel ⑦. When three-dimensional models of brain regions or nuclei have been loaded in the main window, users can move the mouse over any model of interest, causing its color to change to red, as shown by ⑧. At this time, detailed information about the structure, including its full name, abbreviation, and three-dimensional size, will appear in the lower left corner of the main window, as shown by ⑨.

Arbitrary plane visualization

The interface for the Arbitrary plane visualization is illustrated as followed. The left side features the navigation window, while the right side is the main window. The main window displays the arbitrary angle slice of STAM (①) and the brain region annotations on that slice (②). Users can pan in the main window by holding down the left mouse button, zoom in using Ctrl + scroll wheel, or switch to different neighboring slices along the current angle by using the scroll wheel. On the right side of the main window is the list of brain regions and nuclei (③). When the user moves the mouse over the name of a structure of interest, the annotation for that structure in the main window is highlighted in light gray (④). Users can also move the mouse over the annotation of a structure of interest in the main window, and the name of that structure in the list of brain regions and nuclei on the right will automatically be highlighted. At this time, the name of the structure will also be displayed in the lower-left corner of the main window (⑤). Below the structure name is the scale bar of the slice image in the main window at the current resolution (⑥). In the navigation window on the left side, the central area displays the three-dimensional model of the right half of the mouse brain (⑦). The black plane corresponds to the position and angle of the slice in the main window (⑧). The red, green, and blue circles around the model are used to change the pitching, rotation, and rolling angles of the cross-section (⑨). Users can also input values in the lower-left corner of the navigation window to set the slice angle (⑩). The red, green, and blue arrows in the navigation window are used to determine the position of the slice along the given arbitrary angle in the three-dimensional space (⑪).

Automatic slice registration

Operating Instructions The interface for the brain slice automatic registration service is shown in the figure below. Locate the "Upload Slice" button group ① on the right side, and click the "Upload tiff" button to upload the 2D brain slice image in tif/tiff format for registration from your local device. The uploaded image must be a mouse brain slice sampled at a resolution of 10 micrometers; slices with a resolution of 1 micrometer cannot be processed due to their large size. Once the upload is completed, select the type of the uploaded image in the "Choose the type of uploaded slice" radio button ②. Currently, only PI, DAPI, and Label images are supported. Next, click the "Start" button in the "Calculate the corresponding plane from the atlas" button group ③ and wait for the result from the server. During the calculation process, the "Start" button will be disabled, so please be patient.

Data sharing

Operating Instructions The data sharing service interface is shown in the figure below. The right panel contains a "Select the range" button ①:

Atlas mapping

Operating Instructions As shown in the figure, users can click the "Upload" button ① in the right panel to upload 3D image data or neuronal morphology data that has been previously registered to either the CCF or STAM. The image format must be TIFF, and the neuronal morphology data format must be SWC, with a spatial resolution of 10 micrometers. After the uploading is completed, there would be an empty image on the left side of the "Upload" button. Select the direction of conversion (either from STAM to CCF or vice versa) in the "Select the direction of conversion" radio button ③. Then, click the "Start" button ④ to start the calculation on the STAM server. At this point, the "Start" button enters the waiting status ⑤.

Virtual surgery

Operating Instructions The virtual surgery service is shown in the figure below. At this point, the main window is in Virtual surgery mode ①, and only the Virtual surgery and View setting tabs are available on the right side of the page. The former is used for guiding virtual surgery, while the latter is used to set the display options of the main window. Note that switching to the View setting tab midway through virtual surgery will restart the entire virtual surgery process. Therefore, it's important to finalize all options in the View setting tab before entering the Virtual surgery tab. Firstly, select the brain region for injection. Upon entering Virtual surgery mode, the mouse pointer changes to a virtual injection needle model, as shown by ②, and the “Regions” tab on the left data panel transforms into the “Structure for injecting” tab. Here, users need to choose a brain region for injection. Once selected, the "Select target" button ④ highlighted in the figure becomes clickable.

Next, select the injection target on the chosen brain region. At this point, the user has already selected a brain region for injection on the left data panel ⑤, and its 3D model ⑥ is visualized in the main window. Continuing to click the "Select target" button, a green dot ⑦ follows the mouse cursor on the surface of the brain region's 3D model. The position of this dot is projected onto the coordinate grid of the 3D space and marked with a green crosshair ⑧. The coordinates of this point in all three directions can also be viewed in the bottom-left corner ⑨. Once the user identifies a suitable target location, they can left-click to mark it. At this point, the status on the right panel changes from ⑩ to ⑪, adding a radio button. If the user is unsatisfied with the marked location, they can click the "Clear target" button on the panel to re-mark the injection target.

Next, select the surgery planning type. STAM offers two options: manual planning and automatic planning, corresponding to the "Manually" and "Auto" options in the radio button that appears as ⑪. If the user clicks "Manually" to enter manual planning type, the marked injection target turns into a blue dot ⑫. A red dashed line ⑬ originates from the injection target and extends towards the current mouse position. The intersection of this dashed line with the outline of STAM ⑭ (i.e., the injection site) is marked in green. Once the user identifies a suitable injection path, they can left-click to mark it. The marked path will appear as a solid blue line ⑮ in the main window, with the injection site marked as a blue cone ⑯. The names of brain regions and nuclei that the path passes through will be arranged along the solid line according to their spatial positions. In the right panel, information about the angle between the injection path and three standard anatomical directions, the injection target, and the injection site is displayed ⑰. If the user wishes to restart the entire virtual surgery process, they can click the "Reset" button ⑱ on the right panel.