Package Help

Provides an overview of key functions and classes

elmr-package

Bridge light and EM flybrain datasets

Fetching and searching neurons

Fetch and transform neurons or NBLAST them

fetchn_fafb() fetchdp_fafb()

Fetch neurons from FAFB CATMAID server, transforming them as appropriate

nblast_fafb()

NBLAST EM tracing against FlyCircuit (or other databases of) neurons

Working with neuron structures

simplify_neuron()

Simplify a neuron to the longest tree with n branch points

prune_twigs()

Remove all twigs less than a certain path length from a neuron

unspike()

Remove artefactual spikes in neuron tracing due to registration errors

distal_to()

Return indices of points in a neuron distal to a given node

stitch_neuron()

Stitch two neurons together at their closest endpoints

stitch_neurons()

Stitch multiple fragments into single neuron using nearest endpoints

plot3d(<ngraph>)

Plot 3d representation of neuron (ngraph) with directed edges

Interacting with CATMAID server

open_fafb()

Generate URLs to open FAFB CATMAID in browser at a given XYZ location

Summarising tracer contributions

summarise_contribution() suggest_authorship() write_authors() write_ack()

Summarise tracer contributions / suggest authorship for set of neurons

Support functions

Functions intended primarily for developer use

tpsreg() xformpoints(<tpsreg>)

Thin plate spline registrations via nat::xform and friends

fafb_world_mapper()

Convert coordinates between different FAFB assemblies

Data

Data objects

FAFB

templatebrain for assembled FAFB full adult female brain EM volume

FAFB.surf

FAFB brain and neuropil surface objects

elm.landmarks

ELM Landmarks created by Bock & Saalfeld groups at Janelia

dense_core_neurons

Sample EM tracings (homologous pair of neurons wrapping around lateral horn)