SpatioTemporal Labeler is a cross-platform desktop editor for 3D and 3D+t medical image segmentation, including 4D flow MRI workflows. It combines linked spatial and temporal views with real-time 3D label rendering and metadata-preserving NRRD/NIfTI I/O.
- Linked X-Y, X-Z, Y-Z, and selectable X-T/Y-T/Z-T views
- Hover status with voxel indices, RAS coordinates, image intensity, and label value
- Coalesced all-label 3D updates during time navigation
- Multiple image sequences, label sequences, and integer labels
- Unified image/label import classification, drag-and-drop, and resizable selectable-plane previews for other loaded images
- Physical round or square brush and eraser footprints
- Immediate 2D/3D scissors lasso for label erase or replacement, including all-time-frame edits
- Closed-contour raster drawing with interior fill
- Right-drag temporary erase, Shift-hover linked positioning, Shift-drag panning, and middle-drag window level/width with per-image persistence and live values in other-image previews
- Optional all-time-frame spatial editing as one undoable operation
- Applied threshold mask entry with percentage sliders, automatic methods, live candidate preview, replacement, checkbox/delete control, and bypass
- Per-label opacity from the label-row context menu plus a global label opacity control
- Live window level/width sliders in a separate display panel
- 2D/3D seed region growing that stops at other labels
- Per-label morphology with physical
mmradii andmm³component volumes - Physical signed-distance interpolation between user-selected label keyframes
- Automatic all-frame replication or selected-frame placement when mapping 3D labels to a 4D image
- Independent closed, smoothed, decimated surface rendering for each label
- Persistent 3D style, lighting, smoothing, and detail controls in Settings
- Metadata-preserving read/write for 3D/4D NRRD and NIfTI files
- English and Simplified Chinese interface
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/v0.2.7/spatiotemporal_labeler-0.2.7-py3-none-any.whl"Alternatively, download the wheel from the release and install it locally:
python -m pip install spatiotemporal_labeler-0.2.7-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.
You can also launch without arguments and load or drop NRRD/NIfTI files:
spatiotemporal-labeler| Input | Action |
|---|---|
| Left drag | Use the selected brush, eraser, scissors lasso, or contour tool |
| Alt + left drag in 3D | Rotate the 3D camera |
| Right drag | Temporarily erase without changing the selected tool |
| Hold Shift and move | Move the linked spatial cursor without editing |
| Shift + left drag | Pan a 2D view |
| Middle drag | Adjust window width horizontally and window level vertically in the dragged view |
| Double-click an other-image preview | Make that image sequence active |
| Ctrl + wheel | Zoom a 2D view |
| Shift + wheel | Change brush or eraser diameter |
| Wheel in a spatial view | Change its orthogonal slice |
| Drag a locator-line arrow | Move that X, Y, or Z cursor coordinate and update linked slices |
| Double-click | Confirm a pending contour, otherwise fill/restore the entire 2x2 view panel |
B, E, S, L, G |
Brush, eraser, scissors lasso, contour, or seed grow |
Hold I and move |
Pick labels continuously without changing the selected tool |
Hold H |
Temporarily hide all 2D label overlays |
R |
Reset 2D zoom and pan, or auto-window and reset the hovered other-image preview |
| Left / Right | Step through time frames |
Hold CapsLock |
Temporarily apply spatial edits to all frames |
Hold Q |
Bypass a checked applied threshold mask while drawing or erasing |
Ctrl+Z, Ctrl+Y |
Undo or redo |
Esc |
Cancel a pending contour or active lasso preview |
Enable All time frames to repeat one spatial gesture at the same X/Y/Z coordinates in every frame. Temporal-view edits always affect the exact time pixels drawn.
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.