Package index • malecns

Package overview, setup and general functions

malecns malecns-package: malecns: Access to the latest 'Janelia FlyEM' datasets

dr_malecns(): Situation report on your malecns package installation

choose_mcns_dataset(): Switch the default dataset for mcns_* functions

with_mcns() choose_mcns(): Evaluate an expression after temporarily setting malevnc options

mcns_scene(): Construct a neuroglancer scene for CNS dataset

Specify and check body ids

mcns_ids(): Get Male CNS ids in standard formats

mcns_islatest(): Check if a bodyid still exists in the specified malecns DVID node

mcns_xyz2bodyid(): Map XYZ locations to bodyids for the male cns dataset

Neuprint queries including connectivity

mcns_neuprint(): Login to male CNS neuprint server

mcns_neuprint_meta(): Fetch neuprint metadata for malecns neurons

mcns_connection_table(): Connectivity query for CNS neurons

mcns_cosine_plot(): Cosine plot

mcns_predict_group(): Predict the group of neurons using instance or type information

mcns_predict_type(): Predict the cell type of male cns neurons from type and name/instance fields

mcns_soma_side() mcns_somapos(): Find/predict the soma side or position of male cns neurons.

Neuron skeletons and meshes

read_mcns_meshes(): Read a mesh for the current segmentation

read_mcns_neurons(): Read neuronal skeletons via neuprint

Clio/DVID Annotations

mcns_annotate_body(): Set Clio body annotations

mcns_body_annotations(): Return neurojson body annotations via the Clio interface

mcns_dvid_annotations(): Return all DVID body annotations

mcns_set_dvid_annotations(): Set the DVID type, instance or group for some malecns neurons

Geometry and neuropil meshes

mirror_malecns(): Mirror points in malecns space

malecns_shell.surf malecns.surf JRCFIB2022M.surf malecnsvnc_shell.surf malecnsvnc.surf: Surface models of the malecns brain (in nm)