What’s new?

Version

Date

2.1.0

04/04/22

With this release we mainly follow some renamed functions in navis but we also make pymaid play more nicely with public CATMAID instances and of course fix a couple bugs. One important thing to mention is that the default max_threads for pymaid.CatmaidInstance is now 10 (down from 100). This also applies to pymaid.connect_catmaid(). If your internet can handle more connections, feel free to up it back to 100.

2.0.0

21/11/20

This release marks a huge break in the way pymaid works: it is now fully dependent on and compatible with navis. - CatmaidNeuron and CatmaidNeuronList are now subclasses of navis.TreeNeuron and navis.NeuronList, respectively - all functions not specific to CATMAID have been removed in favour of the equivalent navis function - for consistency, all use of treenode have been replace with node: for example, the treenode_id column in node tables is now node_id - API docs and tutorials have been updated to use navis functions instead

1.1.0

4/4/20

  • changed argument names, types and order for CATMAIDInstance to facilitate connecting to public Catmaid servers

  • was: (server, authname, authpassword, authtoken, ...), now is (server_url, token, http_user=None, http_pw=None, ...)

1.0.1

23/1/20

0.101 to 0.103

25/09/19

  • teach upload_neuron() and transfer_neuron() to make use of new source fields in CATMAID

  • pymaid will now warn if run in Jupyter lab without plotly renderer extension

  • renamed function to_dotproduct() to to_dotprops()

  • auto-detect if no display available

  • various improvements and bugfixes

0.100

03/09/19

0.99

12/08/19

0.98

21/06/19

0.97

21/06/19

0.96

22/05/19

  • fixed bug in plot3d() using plotly

0.95

17/05/19

  • new function: get_connectors_in_bbox()

  • new multi-ray option for in_volume() for complicated meshes

  • other improvements: from_swc()

  • many bugfixes

0.94

09/04/19

0.93

05/02/19

0.92

06/11/18

0.91

31/10/18

0.90

20/09/18

  • vispy 3d viewer overhaul: prettier, better picking, new shortcuts

  • indexing of CatmaidNeuronList via .skid[] now returns results in order of query

  • new function: find_nodes()

  • new function: connection_density()

  • improved split_axon_dendrite()

  • improved to_swc() and from_swc()

  • improved neuronlist math and comparisons

  • plot2d() and plot3d() now accept lists of colors

  • has_soma() is now much faster

  • faster neuron import in blender_3d

  • improved docstrings

  • various bugfixes

0.89

14/08/18

  • new function: watch_network() constantly pushes updates Cytoscape

  • new function: get_nth_partners() returns neurons connected via n hops

  • by default, plot3d() now chooses the backend automatically: vispy for terminal sessions, plotly for Jupyter notebook/lab

  • get_skids_by_annotation() now accepts negative search criteria

  • from_swc() now imports multiple SWCs at a time

  • major improvements to caching system

  • by default, progress bars will now vanish after completion

  • followed changes in CATMAID API regarding node tables

  • various bugfixes

0.88

29/07/18

  • data caching for faster queries, see caching demo

  • new function: smooth_neuron()

  • resample_neuron() now resamples radius too

  • guess_radius() interpolation now takes distance along spines into account

  • despike_neuron() is now able to catch spikes that consist of multiple nodes

  • calc_cable() is now deprecated

  • general improvements to docstrings

0.87

20/07/18

  • get_team_contributions() now takes link creation into account

  • get_time_invested() should be way faster now

  • geodesic_matrix() now returns a SparseDataFrame to save memory

  • added pymaid.CatmaidNeuron.to_dataframe() method

  • general improvements and docstrings

0.86

16/07/18

  • arithmetric operations with CatmaidNeuron/Lists will now warn if skeleton IDs match but neuron objects are not identical. See here for explanation.

  • fixed a bug when using regex to query for neurons that led to duplicate skeleton IDs being returned

0.85

13/07/18

  • fixed a series of critical bugs in plot3d(), pymaid.Volume.combine(), cut_neuron(), pymaid.CatmaidNeuronList.remove_duplicates(), get_skid_from_node() and neuron2json()

  • cut_neuron() now accepts multiple cut nodes

  • improved depth coloring in plot2d()

  • added depth coloring to plot2d() with method ‘3d’ - see here for examples