API Reference

Reading/Writing Data

add_bookmarks(data[, verify, server, node])	Add or edit user bookmarks.
edit_annotation(bodyid, annotation[, ...])	Edit annotations for given body.
ids_exist(ids[, chunk_size, progress, ...])	Check if given IDs exist.
get_adjacency(sources[, targets, ...])	Get adjacency between sources and targets.
get_annotation(bodyid[, server, node, verbose])	Fetch annotations for given body.
get_assignment_status(pos[, window, bodyid, ...])	Return assignment status at given position.
get_available_rois([server, node, step_size])	Get a list of all available ROIs in given node.
get_body_position(bodyid[, server, node])	Get a single position for given body ID.
get_connections(source, target[, ...])	Return list of connections between source(s) and target(s).
get_connectivity(bodyid[, pos_filter, ...])	Return connectivity table for given body.
get_labels_in_area(offset, size[, server, node])	Get labels (todo, to split, etc.) in given bounding box.
get_last_mod(bodyid[, server, node])	Fetch details on the last modification to given body.
get_master_node(id[, server])	Get UUID of the current master node.
get_meshes(x[, fix, output, on_error, ...])	Fetch precomputed meshes for given body ID(s).
get_n_synapses(bodyid[, server, node])	Return number of pre- and postsynapses associated with given body.
get_roi(roi[, step_size, form, save_to, ...])	Get ROI as mesh or voxels.
get_segmentation_info([server, node])	Return segmentation info as dictionary (cached).
get_sizes(ids[, chunk_size, progress, ...])	Get sizes (in supervoxels) for given body IDs.
get_skeletons(x[, save_to, output, ...])	Fetch skeleton for given body ID.
get_skeleton_mutation(bodyid[, server, node])	Fetch mutation ID of given body.
get_sparsevol(bodyid[, scale, ret_type, ...])	Fetch sparsevol (voxel) representation for given neuron.
get_sparsevol_size(bodyid[, server, node])	Fetch sparsevol (voxel) info for given neuron.
get_synapses(bodyid[, pos_filter, ...])	Return table of pre- and postsynapses associated with given body.
get_user_bookmarks([server, node, user, ...])	Get user bookmarks.
mesh_neuron(bodyid[, scale, step_size, ...])	Create mesh for given neuron(s).
setup([server, node, user])	Set default server, node and/or user.
skeletonize_neuron(bodyid[, scale, server, ...])	Skeletonize given body.
snap_to_body(bodyid, positions[, server, node])	Snap a set of positions to the closest voxels on a given body.
locs_to_ids(pos[, chunk_size, progress, ...])	Get body IDs at given positions.
list_projects([server])	List available projects on the server.
ids_exist(ids[, chunk_size, progress, ...])	Check if given IDs exist.

Tools

detect_tips(x[, use_clf, psd_dist, ...])

Detect potential open ends on a given neuron.

Utility

check_skeleton(bodyid[, sample, node, server])	Test if skeleton is up-to-date.
gen_assignments(x[, save_to, meta])	Generate JSON file that can be imported into neutu as assignments.
heal_skeleton(x[, root, inplace])	Merge fragmented skeleton back together.
parse_swc_str(x)	Parse SWC string into a pandas DataFrame.
reroot_skeleton(x, new_root[, inplace])	Reroot skeleton to new root.
save_swc(x, filename[, header])	Save SWC DataFrame to file.