Toolbar: Medical Image

For convenience in working with medical image data, the Medical Image tab of the Toolbar brings together several related icons, many of which also appear in other tabs. See also: ChimeraX DICOM Reference, DICOM in VR tutorial, DICOM segmentation tutorial, ChimeraX for Medical Image Analysis

File
	open DICOM	same as Menu: File... Open DICOM Folder
Home	toggle main window between 3D graphics and recent files (Rapid Access)	same as clicking bottom right icons
Home	save snapshot of main window	save ~/Desktop/imageN.png supersample 3 (N = 1,2, ...)
Display
Map	single Z-plane at the center of the current region; assign right mouse button to move planes	volume planes z style image imageMode "full region" + mousemode right "move planes"
Map	tilted-slab image display, with initial slab in the middle of the data, 10 planes thick and perpendicular to the data Z axis; assign right mouse button to rotate slab	volume with style image and imageMode "tilted slab" (exact command depends on the data) + mousemode right "rotate slab"
Map	XYZ orthoplanes at the center of the full data; assign right mouse button to move planes ; see also ui view	volume to set orthoplanes with style image region all (exact command depends on the data) + mousemode right "move planes"
Map	full region; assign right mouse button to crop volume	volume region all imageMode "full region" + mousemode right "crop volume"
Map	toggle outline box	volume with the showOutlineBox option
	airways preset for image display	volume appearance airways
	chest preset for image display	volume appearance chest
	brain preset for image display	volume appearance brain
	initial thresholds preset for image display, e.g., for single planes	volume appearance initial
Graphics	view all, standard orientation	view orient
Map	step 1, full resolution of data	volume step 1
Map	step 2, subsampled at every other point	volume step 2
	2D-XYZ projection for image display	volume projectionMode 2d-xyz
	3D projection for image display	volume projectionMode 3d
	raycasting for image display	volume projectionMode rays

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Mouse Modes in the Medical Image Toolbar

The last (rightmost) icons assign the function or “mouse mode” of:

• hand-controller buttons in ChimeraX virtual reality (details...)
• the right mouse button (= trackpad + Alt on Windows, trackpad + on Mac) in the ChimeraX graphics window

icon	mouse mode	function
Right Mouse	crop volume	show volume data outline box and adjust region size by dragging any face; see also volume
Right Mouse	move planes	show single plane of clicked volume data if full region shown initially; move plane or slab along its axis to show a different section
Right Mouse	rotate slab	activate tilted slab slicing of volume data (image style only), rotate the slab to adjust the slicing angle; the center of rotation from clicking over the slab is the center of the slab, and from clicking elsewhere is the center of the volume box; assigned button + Shift translates the slab along its axis; in VR, this mode both rotates and translates the slab
Right Mouse	tape measure	click to anchor distance measurement, drag to desired endpoint; click in empty space to “erase” (details...)
Right Mouse	windowing	adjust volume data image display thresholds collectively: vertical motion adjusts window level (moves all thresholds in parallel to higher or lower values), horizontal motion adjusts window width (moves thresholds symmetrically farther apart or closer together), and the dominant type of motion wins out; for adjusting multiple windows within a single histogram, see details
	(multiple)	toggle mouse button functions: assign them as specified in the Mouse (3D) settings of the Segmentations tool, or restore the previous functions; see also segmentations mouseModes
	(multiple)	toggle VR hand-controller functions: assign them as specified in the VR Controller settings of the Segmentations tool, or restore the previous functions; see also segmentations handModes