What’s new?¶

Version	Date
2.3.0	27/05/23	`pymaid.get_annotation_graph()` deprecated in favour of the new `pymaid.get_entity_graph()`.
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	changed to semantic versioning: major.minor.patch new functions: `find_first_branchpoint()`, `set_nodes_reviewed()`, `prune_by_length()`, `get_skeleton_change()` plotting now accepts matplotlib colormaps tons of small improvements and bugfixes
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	improve `get_nodes_in_volume()` add optional headless mode (set env variable PYMAID_HEADLESS=TRUE)
0.99	12/08/19	use `ujson` library if available for faster unpacking new function: `update_node_confidence()`, `get_connectivity_counts()` various improvements and bug fixes
0.98	21/06/19	new functions: `join_nodes()`, `link_connector()`, `join_skeletons()`, `replace_skeleton()`, `link_connector()`, `delete_nodes()`, `add_connector()` reworked `get_nodes_by_tag()` and renamed to `find_nodes()`
0.97	21/06/19	new functions: `upload_volume()`, `shared_partners()` improved `upload_neuron()`, `from_swc()`, `plot2d()` and more fixes for `remove_annotations()`, `get_neuron()` and more
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	started reworking vispy plot3d: in brief, will try reducing the number of shader programs running new functions: `break_fragments()`, `heal_fragmented_neuron()`, `update_radii()`, `get_neuron_id()`, `neuron2dps()` `Volumes` now allow multiplication and division - will apply to vertex coordinates improved: `from_swc()`, `to_swc()`, `predict_connectivity()`, `stitch_neurons()`, `reroot_neuron()`, `upload_neuron()` fixes in `delete_neuron()`, `rename_neurons()`, `get_history()`, `split_axon_dendrite()`, `remove_duplicates()` updated to networkx 2.2
0.93	05/02/19	various improvements to the Blender interface `pymaid.b3d` improved `predict_connectivity()` new functions to import/transfer neurons to/between Catmaid instances: `pymaid.upload_neuron()` and `pymaid.transfer_neuron()` new function `pymaid.sparseness()` to calculate lifetime sparseness tons of bug fixes
0.92	06/11/18	new pymaid.Volume methods: `to_csv` and `from_csv` new functions: `add_meta_annotations()`, `remove_meta_annotations()`, `get_annotated()` some under-the-hood changes following change in CATMAID’s API general bug fixes and improvements
0.91	31/10/18	new CatmaidInstance attributes to get info on your server: `catmaid_version`, `available_projects` and `image_stacks` new functions: `shorten_name()`, `get_user_stats()`, `intersection_matrix()`, `get_node_location()` various improvements and bugfixes
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: `pymaid.cytoscape.watch_network` constantly pushes updates to 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