Import slices
Add your section images and tell BrainStack how they were cut. The list is kept in anatomical order, with slice 1 at the top.
Slices in order
- No images yet
Working detail
Every image is shrunk by the same factor, so a pixel means the same distance in every slice.
How were the slices cut?
Preview
Select a slice to preview it.
Set the scale
Each 3D pixel is (pixel size) × (pixel size) × (slice spacing). Get the pixel size from your microscope if you can; the other two methods are estimates or need a scale bar.
Distance between slices
Centre-to-centre distance between consecutive images. Cut 50 µm sections and imaged every 4th? Enter 200.
Pixel size
Result
Image
Dye & channels
Choose the channel with the red dextran. Any other channel (e.g. DAPI) is used as the brain. If the dye is the only channel, the brain outline comes from the tissue's own faint glow.
Red dextran
Channels
Tissue outline
The yellow line should hug the tissue. Slide right if tissue is missed, left if background is included.
Preview
Align slices
Line every slice up with its neighbours. Then scrub through the overlay and fix any that look off.
Overlay check
Magenta = neighbouring slice · green = this slice · white = they line up
Automatic alignment
Not aligned yet.
Which way does each slice face?
All slices should face the same way. Click a slice to mirror it (red frame = mirrored), then press Auto-align again. The automatic check is a suggestion; it can miss slices whose outline looks similar both ways round.
Fix this slice by hand
Tip: click a box and use ↑/↓ to nudge. For a mirrored slice, tick Mirror, then Re-align this slice.
Straighten the whole stack
Drag to rotate · scroll to zoom · right-drag to pan. Red = dye, grey = brain outline, yellow dot = centre of the dye.