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_pkgdown.yml
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_pkgdown.yml
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reference:
- title: Package Help
desc: Provides an overview of key functions and classes
contents: catmaid-package
- title: Catmaid Login
desc: Functions handling connections to a catmaid server
contents:
- catmaid_login
- vfbcatmaid
- catmaid_connection_setenv
- title: CATMAID skeleton functions
desc: Fetching raw skeleton information
contents:
- catmaid_get_compact_skeleton
- catmaid_get_treenode_table
- catmaid_get_node_count
- catmaid_get_review_status
- catmaid_get_treenodes_detail
- catmaid_change_history
- catmaid_islatest
- catmaid_latestid
- title: Names and Annotations
desc: Querying, fetching and setting neuron names and annotations
contents:
- catmaid_query_by_name
- catmaid_get_neuronnames
- catmaid_rename_neuron
- catmaid_skids
- catmaid_meta_annotations
- catmaid_get_annotations_for_skeletons
- catmaid_get_annotationlist
- catmaid_lock_neurons
- title: Node labels (aka tags)
desc: Fetching, setting and removing tags from tree nodes or connectors
contents:
- catmaid_get_labels
- catmaid_set_labels
- catmaid_remove_labels
- catmaid_get_label_stats
- nsoma
- title: Synaptic Connections
desc: Querying and fetching neuronal connectivity information
contents:
- catmaid_query_connected
- catmaid_get_connector_table
- catmaid_get_connectors_between
- catmaid_get_connectors
- catmaid_adjacency_matrix
- title: Interfacing with Nat
desc: Fetching and using catmaid skeletons for use with the NeuroAnatomy Toolbox
(nat) package.
contents:
- read.neuron.catmaid
- catmaid_update_neuronlist
- plot3d.catmaidneuron
- connectors
- soma
- title: Handling volume meshes
desc: Adding / converting volume meshes to CATMAID from regular R mesh representations
contents:
- as.catmaidmesh
- catmaid_add_volume
- catmaid_get_volume
- catmaid_get_volumelist
- title: CATMAID statistics and users
desc: Neuron and user lists and statistics
contents:
- catmaid_get_contributor_stats
- catmaid_get_user_list
- catmaid_user_history
- catmaid_get_time_invested
- title: CATMAID URLs and JSON files
desc: Working with the URLs or JSON files used to save and exchange CATMAID state
contents:
- catmaid_parse_url
- read_catmaid_selection
- write_catmaid_selection
- title: Data
desc: Sample data included with the package
contents: AV4b1
- title: Low level functions
desc: Functions primarily intended for developer use
contents:
- catmaid_fetch
- copy_tags_connectors
- catmaid_entities_from_models
- catmaid_version
navbar:
structure:
left:
- home
- intro
- reference
- articles
- tutorials
- news
- help
right:
- natverse
- github
components:
home:
icon: fa-home fa-lg
href: index.html
reference:
text: Reference
href: reference/index.html
articles:
text: Articles
menu:
- text: Introductory Example - Drosophila Larval Olfaction
href: articles/example-drosophila-larva-olfactory-system.html
news:
text: Changelog
href: news/index.html
github:
icon: fa-github fa-lg
href: https://github.com/jefferis/rcatmaid
natverse:
text: natverse
href: https://natverse.github.io
help:
text: Help
href: SUPPORT.html