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
Leave at 0 to see everything. The smallest real tumour
in this study was 22 voxels, so anything above ~30 starts discarding
tumours the model did find.
Model
Checking…
The model is downloaded once and
kept in this browser. It never leaves your machine, and neither do the
scans it runs on.
Test-time mirroring
runs the network once per reflection — four passes for a 2D model, eight
for a 3D one — and averages them. On the fold that has been scored it made
no measurable difference to accuracy, so it is off by default. Turn it on
to reproduce a run that was scored with it.
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
The keys follow ITK-SNAP's, so habits
carry over. The worklist is the one addition ITK-SNAP does not have: arrow
keys switch scan and slice there, and reviewing is Y/N.
Tools — ITK-SNAP's numbers
1
crosshair — click moves the cursor; right-drag zooms, middle-drag pans
2
zoom/pan — left-drag pans, right-drag zooms
3 / P
freehand outline — opens the editor if needed
4 / B
paintbrush — opens the editor if needed
5
the snake's job is done by the model here
6 / R
ruler — drag to measure in mm, works while reviewing too
Segmentation display
S
hide / reveal the mask
A / D
more transparent / more opaque
X
show or hide annotations (rulers)
⇧X or H
show or hide the crosshair
⌘J
set the contrast from the image automatically
Moving around
↑↓
previous / next scan (worklist only)
←→
previous / next slice — in the
editor the arrows move the cursor by a voxel, 5 with ⇧
PgUpPgDn
previous / next slice, everywhere
scroll
move through slices — or through the reformat you are over
click a pane
move the crosshair; the other panes follow
C
centre the views on the cursor
T
show or hide the coronal and sagittal panes
⇧⌘G
show or hide the T1 next to the T2 — the two
scroll together, and clicking either moves the cursor in both
+−0⌘F
zoom in, out, reset, fit
⌘ / ctrl + scroll
zoom around the pointer
space + drag
pan
Reviewing
Y
mark the mask as correct
N
flag it for follow-up
Editing — tools
E
eraser — two shapes, chosen in the toolbar:
brush takes voxels away as you drag, area
draws round a region and takes everything inside it away when you press
⏎, the way ITK-SNAP's outline does in erase mode. The choice is
remembered.
G
fill an enclosed gap, or remove a whole blob
K
cut — slice the mask in two along a line
M
switch between adding and subtracting
[] or +−
smaller / larger brush
right-drag
erase with the brush (paint, with the eraser)
alt + drag
same, held on the keyboard
brush shapes
round, square, or adaptive — adaptive paints only
what matches the intensity under the cursor
Editing — the freehand outline
trace round the boundary
let go back where you started — the
outline closes itself, exactly as in ITK-SNAP
click
add a single point; clicks and curves mix freely
click the first point or ⏎
also closes it
then: drag a point
move it
shift-click a point
delete it
click an edge
insert a point there
⏎
accept and fill
V
paste the last accepted outline onto this slice
⌫
remove the last point (while drawing)
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.
The T1 pane
(⇧⌘G) is the separately acquired T1 axial series, when the
session has one — many do not. It is a different acquisition on a different
grid (15 slices at 1.20 mm against the T2's 18 at 1.10 mm), so it is shown
beside the T2 rather than over it, and the two are tied together through
physical millimetres: the T1 always shows the slice through the point the
cursor is on. It is for looking only — it is never segmented and never
affects a volume.
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.