SpatioTemporal Labeler is a cross-platform desktop editor for manual and semi-automatic 3D/4D medical image segmentation. It supports dynamic and time-resolved MRI, including 4D flow MRI, in NIfTI and NRRD files, with linked spatial-temporal views, real-time 3D label rendering, temporal propagation, and metadata-preserving I/O.
- Linked X-Y/X-Z/Y-Z spatial and X-T/Y-T/Z-T temporal views with a shared X/Y/Z/T cursor
- Peak-signal frame selection, time navigation, and display-only temporal-axis stretch
- Current-frame or all-frame label editing with physical brush/eraser footprints and one-gesture undo
- Copy and paste complete frames or only the active label within a label sequence with configurable shortcuts and one-step undo
- Interpolate selected labels between two keyframes with physical signed distance fields while preserving other labels as barriers
- Interpolate across the time-axis end by default, treating periodic sequences as a cyclic path between the chosen keyframes; the option can be disabled for non-periodic segments
- Automatically estimate and display systole start, systolic peak, and diastole-start phase guides while keeping label keyframes user-defined
- Named frame markers below the time slider: cardiac phases are automatic,
Kadds manual markers, clicking jumps to a frame, right-clicking changes colour or deletes a marker, and checked markers can be used as interpolation keyframes - Add any number of user-edited label keyframes and interpolate every gap across the full periodic sequence in one undoable operation
- Adjacent-frame temporal propagation using physical displacement, intensity matching, and label/threshold barriers
- Synchronized 2D overlays and independently colored 3D label surfaces while navigating time
- Separate threshold-mask constraints with all-frame editing and threshold-bypass modes
- Multiple image/label sequences with RAS-mapped previews and 3D-label-to-4D frame mapping
- Metadata-preserving 3D/4D NRRD and NIfTI read/write
Download the package for your platform from the latest release. Portable packages include Python, Qt, VTK, and all runtime dependencies.
| Platform | Release asset | Run |
|---|---|---|
| Windows 10/11 x64 | SpatioTemporalLabeler-<version>-windows-x64.zip |
Extract and open SpatioTemporalLabeler/SpatioTemporalLabeler.exe |
| Linux x86_64 | SpatioTemporalLabeler-<version>-linux-x86_64.tar.gz |
Extract and run SpatioTemporalLabeler/SpatioTemporalLabeler |
Each package also contains per-user install and uninstall scripts. No administrator access is required.
Every release includes a pure Python wheel and source distribution. Install the current release directly from GitHub:
python -m pip install "https://github.com/AssociatedPrimeIdeal/SpatioTemporalLabeler/releases/download/v0.4.10/spatiotemporal_labeler-0.4.10-py3-none-any.whl"Alternatively, download the wheel from the release and install it locally:
python -m pip install spatiotemporal_labeler-0.4.10-py3-none-any.whlLaunch the installed application with spatiotemporal-labeler. Python 3.9 or newer is required. Runtime dependencies are installed automatically by pip.
The repository includes an 18-frame PCMRA image and matching label sequence in examples/sample-data.
spatiotemporal-labeler examples/sample-dataWhen a directory is provided, every direct .nrrd, .nii, and .nii.gz file is loaded. Files whose names contain seg, mask, or label are opened as label sequences; the remaining files are opened as image sequences.
When present, pcmra.seq.nrrd is selected as the initial display image and seg.seq.nrrd as the initial label sequence. A 4D image initially opens on the earliest frame with the largest whole-frame sum of absolute finite voxel intensities; NaN and infinite values are ignored.
You can also launch without arguments and load or drop NRRD/NIfTI files:
spatiotemporal-labeler| Input | Action |
|---|---|
B, E, S, L, G |
Brush, eraser, scissors lasso, contour fill, or temporal propagation |
Hold I / H |
Pick labels / hide 2D label overlays |
Press/release CapsLock, Q, or W |
Toggle all-frame threshold-constrained, current-frame threshold-bypass, or all-frame threshold-bypass editing; hold during a stroke for a temporary mode |
[ / ] |
Decrease/increase brush or eraser diameter |
Left / Right |
Previous/next time frame (wraps from the last frame to the first and back) |
Up / Down |
Next/previous orthogonal spatial slice |
V |
Cycle X-T/Y-T/Z-T display-only time-axis stretch (1x/2x/4x) |
K |
Add a named marker to the current time frame |
R |
Reset the hovered preview or the main 2D views |
Ctrl+C / Ctrl+V |
Copy the current frame's labels / paste them into the current frame |
Ctrl+Shift+Left / Ctrl+Shift+Right |
Copy the previous/next frame into the current frame |
View > Interpolate |
Open the keyframe label interpolation panel |
Enter / Esc |
Apply a pending contour / cancel a contour or lasso |
Ctrl+S / Ctrl+Shift+S |
Save / save as |
Ctrl+W |
Close all loaded files |
Ctrl+Z / Ctrl+Y / Ctrl+Shift+Z |
Undo / redo |
| Input | Action |
|---|---|
| Left drag | Use the selected editing tool in a spatial view |
| Right drag | Temporarily erase without changing the selected tool |
Hold Shift and move / Shift + left drag |
Locate the shared cursor / pan a 2D view |
| Middle drag in 2D / middle or right drag in 3D | Adjust window width and window level / pan and zoom |
Ctrl + wheel / Shift + wheel |
Zoom a 2D view / change brush diameter |
| Wheel in a spatial view | Change its orthogonal slice |
| Alt + left drag in 3D | Rotate the 3D camera |
| Double-click | Activate an image preview, change a label color, maximize a view, or confirm a contour depending on the target |
| Drag a locator-line arrow | Move the linked X, Y, or Z cursor coordinate |
Enable All time frames to apply ordinary spatial gestures in every frame. Temporal propagation has its own default all-frame range and does not use this option. It begins from a spatial-view source patch, then independently matches each voxel only into adjacent frames; it does not grow within a frame and stops in a direction after an unmatched frame.
Choose All frames (current-frame threshold) to filter a spatial brush, eraser, contour, or scissors gesture using the applied threshold in the frame where it starts, then apply the same region to every frame regardless of their thresholds. The threshold mask stays checked, and the complete edit is one undo step. You can assign an optional shortcut in Settings; tapping toggles the mode, while holding it through a stroke applies it temporarily.
Image and label sequences are normalized internally to canonical RAS [X,Y,Z,T]; 3D sources use a singleton T axis. Saving reverses the source transform and preserves the original dimensionality and relevant NRRD/NIfTI metadata. When a spatially matching 3D label sequence is opened over a 4D image, it can be copied to every frame (the default) or placed in one selected frame; the mapped result becomes a new unsaved 4D label sequence. Other editing requires a matching voxel grid.
SpatioTemporal Labeler is distributed under the GNU General Public License v3.0.