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 |
The last (rightmost) icons assign the function or “mouse mode” of:
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 |
We gratefully acknowledge support from the NIAID for ChimeraX development related to medical image analysis.