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Planning a Track
Experimental. The planner is new and has not been checked against a track anybody has actually driven. Read a plan against anatomy you already know before you rely on it.
Left panel, Plan a track. Give it a structure, a hemisphere and three approach angles; it gives you the entry point, the angles to dial into the manipulator, and how far to drive from the brain surface.
- Pick a target — type a name or abbreviation into the planner's own search box, and click a result. (A structure already selected carries over.)
- Pick a hemisphere — Left / Right.
- Set the angles — all three default to 0, which is a straight vertical dorsal approach.
| Angle | Sign | Effect |
|---|---|---|
| Tilt | tip forward + | Tilts about the mediolateral axis. Positive drives the tip anterior, so the entry is behind the target |
| Roll | tip right + | Rolls about the anteroposterior axis. Positive drives the tip to the right, so the entry is left of the target |
| Yaw | heading | Turns the heading that the tilt and roll point in. With both at 0 the track is vertical and there is nothing to turn, so the field is disabled |
Straight down resets all three.
A plan for the right MSO at 18° of roll. Under the angles are an Offset — where to aim relative to the printed label — and an optional probe depth and footprint radius.
| Row | Meaning |
|---|---|
| Target | AP · ML · DV of the target — the median of its printed labels, folded onto the side you chose |
| Approach | The angle from vertical, and which way the tip points, in words |
| Entry | AP · ML · DV where the track meets the brain surface |
| Drive | The distance from the surface to the target — the number you drive |
| Sides | The vertical drop and the horizontal offset that the track is the hypotenuse of |
| Straight down | What the drive would be on a vertical approach, for comparison |
The plan for that approach: an 8.07 mm drive from an entry 2.49 mm across from the target, against 7.51 mm straight down — and, under it, every structure the track passes through with the depth at which it enters and leaves.
The header line names the target, the side, the plate it falls on, and how many labels the figure came from. Under the table, Along the track lists every structure the track crosses with the depth range it spans, so you can read what the electrode goes through on its way down.
The track draws live on the plate, on both projections, and in the 3D view.
On the plate it is solid where it genuinely lies in that section (within half a section of the plate's AP) and dashed where it is only the projection of a track passing in front of or behind that plane. An entry or target that is not on the current plate is ghosted for the same reason.
The same track on plate 46: solid where it lies in this section, dotted where it is the projection of a track passing in front of or behind the plane.
Right-triangle sides adds the vertical drop and horizontal offset as two legs — what you set on the arm before you lower it.
- The label sits outside the traced outline of its plate — the atlas prints some abbreviations beside the section and points at them with a leader. The track is measured to it anyway; read the entry with that in mind.
- The entry is on the flank of the section, not its dorsal surface — this track goes in through the side of the head.
- No surface lies along this direction from the target — there is nothing to enter through on that heading.
This is the part most worth understanding. If you have set a working frame, the plan is expressed in your frame, not the atlas's — because the angles you type are the ones you will set on the manipulator.
At 17° of nose-down pitch, a track that is vertical on the manipulator enters about 2.1 mm further back than the plate alone would suggest.
- Copy notes — the plan as plain text, including the frame it was planned in and any measurement you had on the plate.
- Download — the same as a text file.
- Copy link — a URL that restores the whole plan: target, side and all three angles.
The brain surface the planner measures against is the outline of the atlas's own drawn section, traced off the plates. It reaches DV 0 and never crosses it, and 98% of printed labels fall inside it.
It is a fixed, sectioned brain — not the surface under intact dura — and it knows nothing about vessels, the sinus or the ventricles. Sections are 350 µm apart, so an entry AP is only resolved to the nearest plate.
The design behind the planner, and the questions that had to be settled first: TARGETING_PLAN.md.