Fibre Tip Measure

Images stay on this computer.

Drop images here
or

Measure a fibre tip against the midline

Drop in your section images (any format your browser opens).
Set the scale — type µm per pixel, or click two points a known distance apart.
Place three marks: the fibre tip, then a dorsal and a ventral point on the midline.
Type the AP level you matched the section to, if you have it.

You get ML distance from the midline (signed), depth below the dorsal surface, and height above the ventral surface — measured along your own axis, so a tilted or rotated section still reads correctly.

Image —

Animal / ID

AP (mm from bregma)

Scale

µm per pixel

Known length (µm)

Type µm/px if you know it, or click two points a known distance apart (a scale bar, or a structure you have measured).

Placing

Mark 4 is optional: click the centre of the injection bolus, ventral of the tip. Put the dorsal and ventral marks on the midline — at the brain surface if you want depth from the surface. If the section is upside down, Flip 180° first so dorsal is at the top; the panel warns if the dorsal mark ends up below the ventral one.

ML from midline—

DV below dorsal mark—

above ventral mark—

dorsal–ventral span—

axis tilt—

tip → bolus—

bolus ventral of tip—

bolus ML from midline—

Stereotaxic DV estimate

atlas platepick one

tip above ventral—

tissue vs atlas—

DV from dura—

DV from bregma—

bolus DV from dura—

bolus DV from bregma—

correct for shrinkage (scale by tissue/atlas span)

Needs an atlas plate, plus tip and ventral marks. Put the ventral mark on the lowest midline point of the section — Snap ventral finds it for you. Shrinkage scaling needs the dorsal mark on the brain surface too.

Results (0 measured)

1234 choose mark · f flip 180° · arrows nudge (Shift×10) · [ ] change image. Work is kept in this browser; Save file writes a .json you can reload later or send on.