Package HelpProvides an overview of key functions and classes |
|
---|---|
Programmatic access to the CATMAID API |
|
Catmaid LoginFunctions handling connections to a catmaid server |
|
Connect/authenticate to a CATMAID server, returning a connection object |
|
|
Import/Export catmaid connection details to system variables (e.g. for tests) |
CATMAID skeleton functionsFetching raw skeleton information |
|
Return the raw data for a CATMAID neuronal skeleton |
|
Return tree node table for a given neuron |
|
Get review status of neurons from CATMAID |
|
Names and AnnotationsQuerying, fetching and setting neuron names and annotations |
|
Get list of neurons/annotations querying by neuron/annotation name |
|
Get names of neurons from CATMAID |
|
Rename (presently) a single neuron or other entity (e.g. annotation) |
|
Find skeleton ids (skids) for various inputs including textual queries |
|
|
Get or set annotations for neurons from CATMAID |
Get list of annotations (including user information) from CATMAID |
|
Get statistics for all labels in a project from a CATMAID server |
|
Synaptic ConnectionsQuerying and fetching neuronal connectivity information |
|
Find neurons connected to a starting neuron |
|
Return connector table for a given neuron |
|
Return information about connectors joining sets of pre/postsynaptic skids |
|
Return skeleton ids for pre/postsynaptic partners of a set of connector_ids |
|
Interfacing with NatFetching and using catmaid skeletons for use with the NeuroAnatomy Toolbox (nat) package. |
|
Read neuron(s) from CATMAID server into NeuroAnatomy Toolbox (nat) format |
|
Plot skeleton and connectors for neuron retrieved from CATMAID |
|
Get data.frame of connector (synapse) information from a neuron or neuronlist |
|
Handling volume meshesAdding / converting volume meshes to CATMAID from regular R mesh representations |
|
Convert a mesh to CATMAID format |
|
Add a 3D mesh surface to catmaid volume manager |
|
Fetch a mesh volume from CATMAID |
|
Fetch a data frame containing details of all volumes on CATMAID server |
|
CATMAID statistics and usersNeuron and user lists and statistics |
|
Get contributor statistics for neurons from CATMAID |
|
Fetch list of catmaid users for current/specified connection/project |
|
Fetch user contribution history |
|
CATMAID URLs and JSON filesWorking with the URLs or JSON files used to save and exchange CATMAID state |
|
Parse a CATMAID URL to extract parameters including xyz location |
|
Read a CATMAID selection file |
|
Make a CATMAID selection file based on neuronlist or skids |
|
Low level functionsFunctions primarily intended for developer use |
|
Send http GET or POST request to a CATMAID server |
|
Copy the tag / connector info from a catmaid neuron to a new neuron |
|
Return the entity ids for one or more model ids |
|
Return the CATMAID version running on the server |