catmaid
server (#158, @SridharJagannathan)vfbcatmaid()
convenience functionprint.catmaid_connection
method to give a nice summary of connection
properties in the console.catmaid_get_meta_annotations()
, catmaid_query_meta_annotations()
,
catmaid_set_meta_annotations()
, catmaid_remove_meta_annotations()
thanks to @alexanderbates for the PR (#130).catmaid_lock_neurons()
, catmaid_unlock_neurons()
thanks to @alexanderbates for the PR (#130).soma()
fetches the XYZ location of the soma.
somaindex()
fetches the raw index of the skeleton node associated
with the soma (in range 1..N, number of vertices).
somaid()
fetches the identifier of the skeleton node associated with the soma
thanks to @alexanderbates for the PR (#128).Label
column inside neurons to identify the soma (#143).catmaid_get_volumelist()
and catmaid_get_volume()
when the project
(pid) is not 1 (#144).catmaid_query_connected()
now returns stats for all connections but
also allows a confidence threshold to be set. The default threshold of 1
is a new more permissive behaviour (#113).
Thanks to Sebastian Cachero / @schlegelp for the bug report.catmaid_connection_getenv()
and friends in getting environment
variables on some OSes. It turns out that we should switch to recommending
variables of the form catmaid_*
(#110).
Thanks to @SridharJagannathan for detective work and a PR with a fix.catmaid_get_connectors_between()
when getting neuron names.
There was an off by one error for the postsynaptic partner name (#109).
Thanks to @mmc46 for the bug report.catmaid_userids()
function converts user login names to ids.catmaid_connection()
gets a new config
argument to allow curl options to
be set (#108). catmaid_get_connector_table()
always refer to the query skeleton and not
the partner neuron (#107)read.neurons.catmaid()
an optional fetch.annotations argument that
adds a second metadata data.frame as an attribute to the resultant
neuronlist()
object (#18).catmaid_get_connector_table()
returning duplicate rows when there are
multiple connections between the same partner neurons at a given connector.
Thanks to Shanice Bailey and Istvan Taisz for the bug report (#106).catmaid_skids()
, thereby fixing an issue with
read.neurons.catmaid()
with annotation queries when project id is not 1.
Thanks to Marta Costa for the bug report (#105)write_catmaid_selection()
accepts annotations/name specscatmaid_version()
(#103). Still waiting on changes in CATMAID
for more permanent fix.catmaid_get_volumelist()
about new API return format (#102)catmaid_get_treenode_table()
with API (#101)catmaid_query_by_name()
treat query as regex (#100)catmaid_get_node_count()
to get the number of nodes per skeletoncatmaid_get_treenodes_detail()
to search by labels - can use this e.g.
to find all nodes (regardless of neuron) with a certain tag e.g. soma
.nsoma()
for duplicate skids; also speed-upcatmaid_login()
explain why passing server directly doesn't workcatmaid_get_connector_table()
catmaid_get_compact_skeleton()
/read.neuron.catmaid()
catmaid_get_node_count()
to handle NAs/dupesThis version is synced with the upcoming release of nat v1.9.0 which streamlines some functionality but has some breaking changes in behaviour. It must be used with nat >=1.8.12.900 from github.
This is a major version update because of the new support (and recommendation) to use environment variables for login (.Rprofile is still supported).
This is a substantial release with many new functions/enhancements, changes to match the API defined by the 2016.10.18 CATMAID release, support for token-based authentication and numerous bug fixes.
Add catmaid_add_volume to add 3D meshes to catmaid (#69)
catmaid_get_connector_table can now accept multi skid specifications (#49)
catmaid_get_connectors_between returns more informative errors (#51)
fix "No encoding supplied: defaulting to UTF-8." warning (#59)
This release check for http status errors in catmaid (in case there is trouble connecting to site, bad URL etc) ... and errors in returned JSON when request is invalid export funcs to get/set login details as environment variables ... and clear those env vars (all useful for testing)
This release significantly enhances functionality for querying for neurons by annotation or name, while also simplifying a number of plotting/analysis tasks involving connectors (synapses).
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