write_neurons_for_amira: write neurons out in a directory hierarchy suitable for Amira

In jefferis/nat.amira: Interface Between NeuroAnatomy Toolbox and Amira Visualisation Software

Description

Note that this function only works for neuron (rather than dotprops) objects and is limited to a single level directory hierarchy to organise the neurons.

Usage

write_neurons_for_amira(nl, rdir, score = 4, ...)

Arguments

nl	a neuron list containing traced neurons
rdir	The root directory of the project
score	Default integer score for each neuron, or a function to be applied to the path of each output neuron file which returns integer scores. See details.
...	Additional arguments for write.neurons and eventually write.neuron

Details

The score of a neuron was traditionally used to limit which neurons were displayed in Amira by recording a user-defined assessment of how well registered each brain was on a 1 to 5 scale. It may also be used to define a display hierarchy such that no more than n neurons should be displayed.

Value

Path to the master script object to open in Amira

See Also

write.neurons, write.neuron

Examples

td=tempdir()
master_script=write_neurons_for_amira(Cell07PNs, td, subdir=Glomerulus)
## Not run: 
open_amira(master_script)

## End(Not run)

jefferis/nat.amira documentation built on Aug. 11, 2019, 9:56 a.m.