Package index • malevnc

General package functions

malevnc malevnc-package: malevnc: Support for Working with Janelia FlyEM Male VNC Dataset

dr_manc(): Status report for the malevnc package

Server connections and Neuroglancer URLs

choose_malevnc_dataset() choose_flyem_dataset(): Choose active male VNC / FlyEM dataset

manc_neuprint(): Login to MANC neuprint server

manc_dvid_node() manc_dvid_nodeinfo(): Information about DVID nodes / return latest node

manc_scene(): Return a Neuroglancer scene URL for MANC dataset

dvid_tools() install_dvid_tools(): Interface to the python dvid_tools module from Philipp Schlegel

flyem_shorten_url() flyem_expand_url(): Shorten a Neuroglancer URL using the Janelia FlyEM link shortener

Body information and ids

manc_ids(): Flexible specification of manc body ids

manc_xyz2bodyid(): Find the bodyid for an XYZ location

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

manc_size(): Return the size (in voxels) of specified bodies

manc_mutations(): Get all the modifications associated with one or more DVID nodes

manc_somapos() manc_rootpos(): Return the soma or root position of MANC bodyids

Read annotations

manc_body_annotations() clio_fields(): Return clio-store body annotations for set of ids or a flexible query

manc_dvid_annotations(): Return all DVID body annotations

manc_point_annotations(): Return point annotations from Clio store

manc_meta(): Return full metadata from Clio/DVID for MANC bodyids (cached by default)

manc_neuprint_meta(): Fetch neuprint metadata for MANC neurons

manc_user_annotations(): Read point annotations from DVID using neuprint authentication

clio_auth() clio_token() clio_set_token(): Clio authorisation infrastructure using Google via the gargle package + JWT

Make annotations

manc_annotate_body(): Set Clio body annotations

manc_annotate_soma(): Annotate an XYZ location in Clio as a soma or root

manc_set_lrgroup(): Set Left-Right matching groups for neurons in DVID and optionally Clio

manc_check_group_complete(): Check if group is complete

manc_set_dvid_instance() manc_set_dvid_annotations(): Set DVID annotations for one or more ids.

Connectivity

manc_connection_table(): Convenience wrapper for neuprint connection queries for VNC dataset

manc_leg_summary() manc_side_summary(): Simple summaries of which regions different neurons innervate

Meshes, Skeletons and Geometry

read_draco_meshes() read_manc_meshes(): Read draco encoded 3D meshes from tarballs (as used by Janelia FlyEM)

manc_read_neurons(): Read MANC skeletons via neuprint

mirror_manc() symmetric_manc(): Mirror points or other 3D objects along the MANC midline

manc_lr_position(): Calculate the left-right position wrt to the symmetrised MANC midline

manc_view3d(): Set a standard viewpoint for MANC data

download_manc_registrations(): Download MANC (EM) to JRC (light level) registrations

Cartoon summaries

colour_leg_muscles() leg_muscle_palette(): Create SVG figure with leg muscles coloured based on supplied colour palette

Data objects

mancneckseeds: Seed plane for the Neck Connective

mancsomapos: Soma locations for all intrinsic neurons of the ventral nerve cord

MANC.surf JRCFIBVNC2020MNP.surf: Surface model of neuropils in the MANC dataset

MANC.tissue.surf MANC.tissue.surf.sym MANC.nerves: Simplified (and symmetrized) tissue surface of MALEVNC

MANC.tracts: Meshes of 22 MALEVNC tracts.

MANCsym: MANC symmetric template