catmaid 0.10.0

catmaid 0.9.9

  • 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.
  • Fix bug in 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 0.9.8

catmaid 0.9.7

catmaid 0.9.6

  • Give read.neurons.catmaid() an optional fetch.annotations argument that adds a second metadata data.frame as an attribute to the resultant neuronlist() object (#18).
  • Fix handling of CATMAID version string (#103)

catmaid 0.9.5

  • Stop 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).
  • Pass on pid in 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)

catmaid 0.9.4

catmaid 0.9.3

  • workaround for bug in catmaid_version() (#103). Still waiting on changes in CATMAID for more permanent fix.
  • fix import error with jsonlite version >=1.6

catmaid 0.9.2

catmaid 0.9.1

  • Add catmaid_get_labels, catmaid_set_labels, catmaid_remove_labels to manipulate labels (aka tags) on treenodes and connectors (#95)
  • Add catmaid_get_all_labels
  • Add nsoma function to return number of somata (#96)
  • Add catmaid_get_treenodes_detail to get location and other information for many nodes at once (#94)
  • Teach catmaid_get_connectors_between to find names for pre/post skids (optional, #93)
  • Teach catmaid_get_neuronnames to handle duplicate requests efficiently (#91)
  • Teach catmaid_login to accept arguments in a list (#91)

catmaid 0.9.0

This 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 >= from github.

  • switch to Ops.catmaidneuron to match nat 1.9.0 in prep (and add version requirement)
  • Simple search for skids with exact annotation match (#89) Now you can do: catmaid_skids(“ORN”) or read.neurons.catmaid(“ORN”)
  • Fix bug in catmaid_skids error message when looking for one skid (#90)

catmaid 0.8.1

  • Add function to get volumes from catmaid (#82)
  • Add functions to read/write catmaid json selection files
  • make catmaid_neuronnames returns NA for NA skids

catmaid 0.8

This is a major version update because of the new support (and recommendation) to use environment variables for login (.Rprofile is still supported).

  • support fetching login information from environment variables (#80)
  • catmaid_get_compact_skeleton now returns list of vectors (#79) (used to be a list of lists, but this was less convenient and not helpful)
  • fix query_by_neuron_or_annotation adding empty annotations attribute

catmaid 0.7.2

  • Add catmaid_get_label_stats (use it to find neurons with soma)
  • Add copy_tags_connectors (bring over tags/connector info)
  • improve summary.catmaidneuron (#78)
  • plot3d bugfix when there are NA points (and soma=T) (#77)

catmaid 0.7.1

  • only plot soma when explicitly tagged (rather than plotting a sphere at the root of the neuron if not tagged) (#62)
  • only plot3d connectors if they exist (#73)
  • Ensure nodes do not normally plot for catmaidneurons (#74)
  • doc fix for catmaid_get_treenode_table (#75)

catmaid 0.7

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.

  • support for CATMAID token-based authentication (#35)
  • Add catmaid_get_connectors_between to return connections between (multiple) pre and postsynaptic partners - thanks to Zhihao Zheng (#53, #56)
  • Add function to parse CATMAID urls e.g. to extract xyz position (#55)
  • Add rename_neuron function (#54)
  • Add catmaid_version function (#58)
  • Add catmaid_user_history function (#57)
  • Add catmaid_get_annotations_for_skeletons function (#38)
  • Add catmaid_remove_annotations_for_skeletons function (#43)
  • 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)
  • stop catmaid_skids returning duplicates when there are multiple matching annotations (#44)
  • ensure that connectors are also scaled when xforming neurons (#47)
  • catmaid_query_by_annotation returns neuron column as character vector (#46)
  • catmaid_get_connector_table returns partner_skid columns as an integer (#48)
  • fix bug in url for catmaid_get_review_status function (#45)
  • Give sensible name to 1st column of connector data.frame (#42)
  • ensure neurons without connectors scale properly (#41)
  • fix bug in catmaid_connection_setenv() when some elements are null (#50)
  • catmaid_get_annotations_for_skeletons - fix bug in skid order (#39)
  • ensure catmaid_get_contributor_stats passes on connection (#37)
  • ensure all functions pass on connection to catmaid_fetch (#60)
  • connectors.neuronlist should handle neurons without connectors (#29)
  • catmaid_skids should pass on pid (#64)
  • fix catmaid_get_connector_table to reflect 2016.09.01-65 API change (#65)
  • fix bug in catmaid_user_history with small queries (#70)

catmaid 0.6

  • support for upcoming httr 1.0 release
  • fix: ensure catmaid connection objects are passed to all downstream functions e.g. so that you can you use different servers in the same session.
  • fix queries that match multiple annotations when using a defined connection object
  • fix: ensure that catmaid_fetch works even if server does not have a terminal / and remote path is also missing a slash
  • fix: servers don’t have to be https

catmaid 0.5

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)

catmaid 0.4

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).

  • catmaid_query_by_neuronname was renamed to catmaid_query_by_name (since it can query by both neuron or annotation name as well as returning both annotations and neurons)
  • read.catmaid.neurons has richer attached metadata (see
  • read.catmaid.neurons can make simple queries (see
  • add catmaid_query_by_annotation to fetch objects tagged with a matching annotation (rather than searching by object name).
  • add connectors to get connector (synapse) information from a neuron
  • add catmaid_catmaid_get_connector_table to see a list of incoming/outgoing connections for a given neuron.
  • add plot3d.catmaidneuron to enable convenient plotting of synapses
  • fix catmaid_get_neuronnames should return names in the same order as passed skids (see
  • the catmaid skeleton_id is consistently referred to as skid in argument names and return values
  • depend on nat (and therefore rgl). Import rather than depend on jsonlite.
  • minor doc fixes

catmaid 0.3

  • cache login credentials for automatic reuse
  • option to set/get environment variables for passwords etc
  • Add catmaid_query_connected, catmaid_get_annotationlist, catmaid_query_by_neuronname
  • low level catmaid_fetch function covers GET and POST requests