Choose one scan folder or many — each folder is one mouse at
one timepoint, exactly as it came off the scanner, with its
DICOM sub-folder inside. Add folders as many times as you
like; they queue up and run together.
Nothing is uploaded. The scans are read and
segmented inside this browser tab, on this machine. No image data is sent
anywhere, which is why this page is safe to open from a shared link.
Drag scan folders here
Select as many as you like in Finder and drag them in together —
this is the only way to add several at once.
or
The file dialog can only take one folder at a time —
that is a browser restriction, not a setting. Click it repeatedly to
queue more, or pick a parent folder to get every scan inside it.
Only .dcm files are read; masks and notes are skipped.
voxels
Already segmented something?
Results are kept in this browser, on this machine. Reopen
them without re-running anything.
Because storage is per-browser,
results do not follow you to another computer and clearing site data
deletes them. Download all writes a zip you control —
masks, QC images, volumes.csv and results.json.
Keyboard shortcuts
Moving around
↑↓
previous / next scan
←→
previous / next slice
scroll
move through slices — or through the reformat you are over
click a pane
move the crosshair; the other panes follow
T
show or hide the coronal and sagittal panes
H
show or hide the crosshair
+−0
zoom in, out, reset
⌘ / ctrl + scroll
zoom around the pointer
space + drag
pan
Reviewing
A
mark the mask as correct
F
flag it for follow-up
Editing — tools
F
freehand — trace round the boundary and let go
P
polygon — click points, adjust them, then Accept
B / E
brush / eraser
A
adaptive brush — paints only what matches under the cursor
G
fill an enclosed gap, or remove a whole blob
X
cut — slice the mask in two along a line
R
ruler — drag to measure in mm
C
navigate — move the crosshair without painting
M
switch between adding and subtracting
[]
smaller / larger brush
alt + drag
temporarily invert brush and eraser
Editing — outlines
press and drag
trace freehand; it fills when you let go
click
add a polygon point; drag one to move it
shift-click a point
delete it
click an edge
insert a point there
⏎
accept and fill the outline
V
paste the last accepted outline onto this slice
⌫
remove the last point
esc
discard the outline
Editing — the rest
⌘Z / ⇧⌘Z
undo / redo
⌘S
save the mask
esc
leave the editor
Draw two slices a few apart, then
Interpolate fills in the ones between by blending the two shapes.
Faster than tracing every slice when a tumour spans several.
The coronal and sagittal panes are
reformats of the axial stack, not the separately acquired
coronal scan — so they always line up with the mask. They are for looking
and navigating; painting happens in the axial pane, because a whole slice of
tumour is only one row tall over there.
Level and window change only how the
scan is displayed. They never affect the mask or the volume.
Where things live
This page has no server. Scans are read
and segmented in this tab and results are stored in this browser, on this
machine — nothing is uploaded and nothing is written to a folder. Use
Download all for a copy you control.
ITK-SNAP
A web page cannot launch another
program — that is the browser sandbox, and no setting changes it. What it
can do is share a folder.
On Chrome or Edge:
press ITK-SNAP folder… and pick a directory once.
Download for ITK-SNAP then writes a scan straight into it, you open
the .itksnap workspace from there, and
Check folder for edits reads your corrections back with one click.
On Firefox or Safari:
the folder API does not exist, so Download for ITK-SNAP gives you a
zip. Unzip it, work on it, then Import corrected masks and select
the edited _tumor.nii.gz files.
Either way the original automated mask is
kept untouched and both volumes are reported separately. Note that macOS
does not associate the .itksnap extension, so use
File > Open Workspace in ITK-SNAP, or set Open With on
the file once in Finder.