probeplanner 0.1.2

Plan probe locations

Probe planner

A tool to help plan where to implant electrodes, plobes and fibers.

It visualizes the probe given the location of it's tip (in AP/ML/DV coordinates expressed micrometers) and it's angles (relative to the ML and AP plane, as you'd tilt a stereotax). As the probe is moved around this application displays which brain regions the probe is going through.

Installation

    pip install probeplanner

Usage

The easiest way to use probepanner is through the command line interface. In your terminal use:

pplanner

to launch the application. You can get a help docstring:

(brainrender) ❯ pplanner --help
Usage: pplanner [OPTIONS]

Options:
  -aim-at, --at TEXT              Name of brain region to aim at
  -hemisphere, --h TEXT           target hemisphere
  -AP-angle, --AP INTEGER         angle on AP plane  [default: 0]
  -ML-angle, --ML INTEGER         angle on ML plane  [default: 0]
  -highlight, --hl TEXT           names of brain regions to highlight
                                  (separated by space)  [default: ]

  -debug, --debug                 Debug?  [default: False]
  --help                          Show this message and exit.

The main arguments are:

• aim-at which lets you aim at a brain region by passing its name (e.g. 'CUN' will set the tip of the probe in the cuneiform)
• AP and ML let you specify the angle of the probe on the two main planes
• highlight lets you pass a list of regions names (e.g. 'CUN MOs SCm') to be highlighted during use.