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_pkgdown.yml
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reference:
- title: Package information
desc: ~
contents:
- '`catnat-package`'
- title: CATMAID API
desc: Functions to interact with CATMAID API. These typically build on the existing catmaid R package.
contents:
- '`catmaid_annotate_partners`'
- '`catmaid_connector_nodes`'
- '`catmaid_controlled_upload`'
- '`catmaid_delete_neuron`'
- '`catmaid_find_likely_merge`'
- '`catmaid_get_neuronid`'
- '`catmaid_get_server`'
- '`catmaid_get_tag`'
- '`catmaid_interactive_join`'
- '`catmaid_join_skeletons`'
- '`catmaid_link_connectors`'
- '`catmaid_lock_neurons`'
- '`catmaid_node_time`'
- '`catmaid_set_meta_annotations`'
- '`catmaid_skeletons_in_bbx`'
- '`catmaid_update_radius`'
- '`catmaid_upload_neurons`'
- title: Autosegmentation
desc: Convenience functions for working with autosegmentation results
contents:
- '`fafb_frags_ids`'
- '`fafb_seg`'
- '`fafb_seg_conn`'
- '`fafb_segs_stitch_volumes`'
- '`fafbseg_join_connectors_in_ngl_volumes`'
- '`fafbseg_transfer_tags`'
- '`read.neurons.fafbseg`'
- title: Uncategorised functions
desc: ~
contents:
- '`WriteVTKalphashape`'
- '`arbour.clusters`'
- '`as.mesh3d.kde`'
- '`ashape2mesh3d`'
- '`assign.connector.info`'
- '`assign_cable.polarity`'
- '`assign_lh_neuron`'
- '`assign_strahler`'
- '`assignside`'
- '`average.tracts`'
- '`cluster_synapses_within_skeleton`'
- '`clusterbysynapses`'
- '`combine.alphashape`'
- '`skeleton_connectivity_matrix`'
- '`connectivity_similarity`'
- '`connector_URL`'
- '`node.contribution.to.skeletons`'
- '`correctsoma`'
- '`create_skeleton_from_nrrd`'
- '`create_tracing_samplesheet`'
- '`distance.from.first.branchpoint`'
- '`downstream.deletion.test`'
- '`axonic_points`'
- '`flow.centrality`'
- '`get.hxsurf`'
- '`get.skeleton.from.flycircuit`'
- '`get.synapses`'
- '`get_connected_skeletons`'
- '`inside_neuropils`'
- '`label_neuron.class`'
- '`local_conn`'
- '`make.anatomical.model`'
- '`make.mirror.transform`'
- '`manually_assign_axon_dendrite`'
- '`map_fafbsegs_to_neuron`'
- '`mark.microtubules`'
- '`napplyTransform`'
- '`nblast_bothways`'
- '`neurites`'
- '`neurons.inside`'
- '`open_l1`'
- '`overlap.connectivity.matrix`'
- '`pointsinsidemesh`'
- '`primary.neurite`'
- '`prune.catmaidneuron`'
- '`prune_by_tag`'
- '`prune_distal`'
- '`prune_in_volume`'
- '`prune_online`'
- '`prune_strahler.catmaidneuron`'
- '`prune_vertices.catmaidneuron`'
- '`resample.catmaidneuron`'
- '`rescue.dps`'
- '`scan4matching`'
- '`seebroken3d`'
- '`seesplit3d`'
- '`select_neurons`'
- '`select_points`'
- '`set_segmentation_location`'
- '`shift.neurons`'
- '`sholl_data`'
- '`soma`'
- '`subtree`'
- '`synapsecolours.neuron`'
- '`tracer.plot`'
- '`transform3dalphashape`'
- '`update_neurons`'
- '`write.spin.split.swc`'