What’s new?¶

This is a selection of features added, changes made and bugs fixed with each version. For a full list of changes please see the commits on navis’ Github repository.

Version	Date
1.6.0	07/04/24	BREAKING: dropped support for Python 3.8, per NEP 29 `navis.write_swc()` no longer supports writing Dotprops to SWC files Additions: new property `Treenode.surface_area` new (experimental) functions `navis.read_parquet()` and `navis.write_parquet()` store skeletons and dotprops in parquet files (see here for format specs) new `navis.read_nml()` function to read single NML file (complements existing `navis.read_nmx()` files which are collections of NMLs) new `navis.NeuronConnector` class for creating connectivity graphs from groups neurons with consistent connector IDs. new method for CMTKtransforms: `navis.transforms.CMTKTransform.xform_image()` Improvements: improved performance for: - adding recordings to `CompartmentModel` - `navis.heal_skeleton()` and `navis.resample_skeleton()` improved logic for splitting NBLASTs across multiple cores `navis.xform_brain()`: now allows to specify multiple intermediate template spaces through the `via` parameter and to ignore spaces through the `avoid` parameter i/o functions can now read directly from .tar or .tar.gz files (.zip was already supported) `navis.read_precomputed()` now accepts a `limit` parameter similar to `navis.read_swc()` Fixes: fixed interface to InsectBrainDB `navis.read_precomputed()`: - now correctly parses the info file depending on the source - reading large files (i.e. meshes) directly from a URL should not break anymore fixed writing vertex properties in `navis.write_precomputed()` fixed a bug in `navis.resample_skeleton()` fixed an occasional issue when plotting skeletons with radii fix bug in `navis.subset_neuron()` that caused connectors to be dropped when using mask fixed a bug in `navis.despike_skeleton()` that cause the reverse argument to be ignored fixed two small bugs in `navis.interfaces.neuprint.fetch_mesh_neuron()`
1.5.0	27/07/23	BREAKING: dropped support for Python 3.7 new function: `navis.pop3d()` removes the most recently added object from the vispy 3d viewer new experimental functions for (pairwise) alignment of neurons using the `pycpd` package: `navis.nblast_align()`, `navis.align.align_deform()`, `navis.align.align_rigid()`, `navis.align.align_pca()`, `navis.align.align_pairwise()` `navis.xform_brain()` now recognizes the target template’s units if available new `NeuronList` method: `navis.NeuronList.set_neuron_attributes()` new utility functions: `navis.nbl.compress_scores()`, `navis.nbl.nblast_prime()` improved persistence functions: `navis.persistence_distances()`, `navis.persistence_vector()`, `navis.persistence_diagram()` `navis.longest_neurite()` and `navis.cell_body_fiber()` now also allow removing the longest neurite and CBF, respectively `navis.heal_skeleton()` now accepts a mask parameter that allows restricting where fragments are stitched various other bugfixes
1.4.0	21/12/22	BREAKING: `navis.flow_centrality` was renamed to `navis.synapse_flow_centrality()` and a new non-synaptic `navis.flow_centrality()` function was added. This also impacts the `method` parameter in `navis.split_axon_dendrite()`! vispy is now a soft dependency new function: `navis.read_tiff()` to read image stacks from TIFF files NBLASTs: single progress bar instead of one for each process new `via` parameter for `navis.xform_brain()` new utility function: `navis.nbl.extract_matches()` `navis.write_swc()` can now save Dotprops to SWC files `navis.make_dotprops()` can now downsample point cloud inputs various improvements to `navis.split_axon_dendrite()`, `navis.nblast_allbyall()`, `navis.interfaces.neuprint.fetch_mesh_neuron()`, `navis.interfaces.neuprint.fetch_skeletons()` tons of bug fixes
1.3.1	10/06/22	fixed various bugs
1.3.0	10/05/22	as of this version `pip install navis` won’t install a vispy backend (see install instructions for details) new interface to fetch data from Virtual Fly Brain: `navis.interfaces.vfb` tools to build custom NBLAST score matrices (big thanks to Chris Barnes!), see the new tutorial Bayesian implementation of the network traversal model: `BayesianTraversalModel` (big thanks to Andrew Champion!) NBLASTs: new `approx_nn` parameter (sacrifices precision for speed) example neurons now come with some meta data new morphometrics functions: `navis.segment_analysis()` & `navis.form_factor()` new function to write meshes: `navis.write_mesh()` lots of fixes and improvements in particular for i/o-related functions
1.2.1	25/02/22	hot fix for `navis.split_axon_dendrite()`
1.2.0	24/02/22	new function: `navis.betweeness_centrality()` new function: `navis.combine_neurons()` to simply concatenate neurons new set of persistence functions: `navis.persistence_vectors()`, `navis.persistence_points()` and `navis.persistence_distances()` improvements to various functions: e.g. `navis.bending_flow()`, `navis.synapse_flow_centrality()`, `navis.split_axon_dendrite()`, `navis.longest_neurite()` `navis.read_swc()` now accepts a `limit` parameter that enables reading on the the first N neurons (useful to sample large collections) `navis.write_nrrd()` and `navis.read_nrrd()` can now be used to write/read Dotprops to/from NRRD files `navis.nblast()` (and variants) now accept a `precision` parameter that allows setting the datatype for the matrix (useful to keep memory usage low for large NBLASTs) `navis.simplify_mesh()` (and therefore `navis.downsample_neuron()` with skeletons) now uses the `pyfqmr` if present (much faster!) improved the interface to Neuromorpho added a new interface with the Allen Cell Types Atlas (see `navis.interfaces.allen_celltypes`) myriads of small and big bugfixes
1.1.0	18/11/21	new function `navis.sholl_analysis()` plotly is now correctly chosen as default backend in Google colab fixes a critical bug with plotting skeletons with plotly 5.4.0
1.0.0	11/11/21	Breaking changes: `MeshNeuron`: `__getattr__` does not search `trimesh` representation anymore NBLASTs: queries/targets now MUST be `Dotprops` (no more automatic conversion, use `make_dotprops()`) renamed functions to make it clear they work only on `TreeNeurons` (i.e. skeletons): `smooth_neuron` -> `smooth_skeleton()` `reroot_neuron` -> `reroot_skeleton()` `rewire_neuron` -> `rewire_skeleton()` `despike_neuron` -> `despike_skeleton()` `average_neurons` -> `average_skeletons()` `heal_fragmented_neuron` -> `heal_skeleton()` `stitch_neurons` -> `stitch_skeletons()` `cut_neuron` -> `cut_skeleton()` removals and other renamings: `navis.clustering` module was removed and with it `navis.cluster_xyz` and `ClustResult` class renamed `cluster_by_synapse_placement` -> `synapse_similarity()` renamed `cluster_by_connectivity` -> `connectivity_similarity()` renamed `sparseness` -> `connectivity_sparseness()` renamed `navis.write_google_binary` -> `write_precomputed()` `geodesic_matrix()` renamed parameter `tn_ids` -> `from_` New things & Bugfixes: `NeuronList`: `apply()` now allows omitting failures (see `omit_failures` parameter) `VoxelNeuron`: new (experimental) class representing neurons as voxels `read_nrrd()` now returns `VoxelNeuron` instead of `Dotprops` by default currently works with only a selection of functions `TreeNeuron`: can now be initialized directly with `skeletor.Skeleton` new method: `snap()` `MeshNeuron`: `in_volume()`, `subset_neuron()` and `break_fragments()` now work on `MeshNeurons` new properties: `.skeleton`, `.graph` and `.igraph` new methods: `skeletonize()` and `snap()` can now be initialized with `skeletor.Skeleton` and `(vertices, faces)` tuple plotting: `color_by` parameter now works with `MeshNeurons` `Dotprops`: new property: `.sampling_resolution` (used e.g. for scaling vectors for plotting) new method `snap()` experimental support for non-isometric `.units` for neurons NBLASTs: new parameter `limit_dist` allows speeding up NBLASTs with minor precision loss new experimental parameter `batch_size` to NBLAST neurons in batches overall faster initialization with large lists of neurons SWC I/O (`read_swc()` & `write_swc()`): by default we will now deposit neuron meta data (name, id, units) in the SWC header (see `write_meta` parameter) meta data in SWC header can also be read back (see `read_meta` parameter) filenames can now be parsed into specific neuron properties (see `fmt` parameter) node IDs now start with 0 instead of 1 when writing SWC files I/O to/from Google neuroglancer’s precomputed format: total rework of this module renamed `navis.write_google_binary` -> `write_precomputed()` new function: `read_precomputed()` plotting: new function `navis.plot_flat()` plots neurons as dendrograms `plot3d()` with plotly backend now returns a plotly `Figure` instead of a figure dictionary new k3d backend for plotting in Jupyter environments: try `navis.plot3d(x, backend='k3d')` new parameter for `plot2d()` and `plot3d()`: use `clusters=[0, 0, 0, 1, 1, ...]` to assigns clusters and have them automatically coloured accordingly `plot2d()` now allows `radius=True` parameter transforms: support for elastix (`navis.transforms.ElastixTransform`) whether transforms are invertible is now determined by existence of `__neg__` method most functions that work with `TreeNeurons` now also work with `MeshNeurons` new high-level wrappers to convert neurons: `navis.voxelize()`, `navis.mesh()` and `navis.skeletonize()` `make_dotprops()` now accepts `parallel=True` parameter for parallel processing `smooth_skeleton()` can now be used to smooth arbitrary numeric columns in the node table new function `navis.drop_fluff()` removes small disconnected bits and pieces from neurons new function `navis.patch_cloudvolume()` monkey-patches cloudvolume (see the new tutorial) new function `navis.write_nrrd()` writes `VoxelNeurons` to NRRD files new functions to read/write `MeshNeurons`: `read_mesh()` and `navis.write_mesh()` new function `navis.read_nmx()` reads pyKNOSSOS files new function `smooth_mesh()` smoothes meshes and `MeshNeurons` improved/updated the InsectBrain DB interface (see the tutorial) under-the-hood fixes and improvements to: `plot2d()`, `split_axon_dendrite()`, `tortuosity()`, `resample_skeleton()`, `mirror_brain()` first pass at a `NEURON` interface (see the new tutorial) first pass at interface with the Allen’s MICrONS datasets (see the new tutorial) `NAVIS_SKIP_LOG_SETUP` environment variable prevents default log setup for library use improved `cable_overlap()`
0.6.0	12/05/21	new functions: `navis.prune_at_depth()`, `navis.read_rda()`, `navis.cell_body_fiber()` many spatial parameters (e.g. in `navis.resample_skeleton()`) can now be passed as unit string, e.g. `"5 microns"` many functions now accept a `parallel=True` parameter to use multiple cores (depends on `pathos`) `navis.read_swc()` and `navis.write_swc()` can now read/write directly from/to zip files reworked `navis.read_json()`, and `navis.write_json()` `nblast` functions now let you use your own scoring function (thanks to Ben Pedigo!) added `threshold` parameter to `navis.read_nrrd()` fixed NBLAST progress bars in notebook environments `navis.nblast_smart()`: drop `quantile` and add `score` criterion new functions to map units into neuron space: `map_units()` and `navis.to_neuron_space()` functions that manipulate neurons will now always return something (even if `inplace=True`) `navis.cut_skeleton()` now always returns a single `NeuronList` `navis.mirror_brain()` now works with `k=0/None` Dotprops all `reroot_to_soma` parameters have been renamed to `reroot_soma` `navis.TreeNeuron` now has a `soma_pos` property that can also be used to set the soma by position fixed a couple bugs with CMTK transforms made transforms more robust against points outside deformation fields better deal if node ID of soma is `0` (e.g. during plotting) `navis.neuron2tangents()` now drops zero-length vectors fixed `navis.guess_radius()`
0.5.3	10/04/21	new functions: `navis.nblast_smart()`, `navis.synblast()`, `navis.symmetrize_brain()` `navis.plot3d()` (plotly): `hover_name=True` will show neuron names on hover `navis.plot2d()`: `rasterize=True` will rasterize neurons (but not axes or labels) to help keep file sizes low `navis.simplify_mesh()` now supports 3 backends: Blender3D, `open3d` or `pymeshlab` `navis.make_dotprops()` can now produce `Dotprops` purely from skeleton edges (set `k=None`) reworked `navis.write_swc()` (faster, easier to work with) a new type of landmark-based transform: moving least square transforms (thanks to Chris Barnes) vispy `navis.Viewer`: press B to show a bounding box moved tests from Travis to Github Actions (this now also includes testing tutorial notebooks) a great many small and big bug fixes
0.5.2	02/02/21	new functions: `navis.xform()`, `navis.write_precomputed()` `navis.downsample_neuron()` now also works on `Dotprops` Neurons: - connectors are now included in bounding boxes NeuronLists: - added progress bar for division / multiplication
0.5.1	10/01/21	a couple under-the-hood improvements and bugfixes
0.5.0	05/01/21	new functions for transforming spatial data (locations, neurons, etc) between brain spaces: `navis.xform_brain()` transforms data from one space to another `navis.mirror_brain()` mirrors data about given axis see the new tutorials for explanations low-level interfaces to work with affine, H5-, CMTK- and thin plate spline transforms de-cluttered top level namespace: some more obscure functions are now only available through modules
0.4.3	22/12/20	more small bug fixes
0.4.2	22/12/20	some small bug fixes
0.4.1	06/12/20	hotfix for critical bug in NBLAST
0.4.0	06/12/20	native implementation of NBLAST: `navis.nblast()` and `navis.nblast_allbyall()`! new parameter `navis.plot3d()` (plotly backend) with `hover_id=True` will show node IDs on hover `navis.Volume.resize()` has now `inplace=False` as default
0.3.4	24/11/20	improved `navis.Dotprops`: more control over generation in `navis.make_dotprops()` `navis.Dotprops` now play nicely with R interface
0.3.3	23/11/20	new module: `models` for modelling networks and neurons new functions `navis.resample_along_axis()`, `navis.insert_nodes()`, `navis.remove_nodes()` full rework of `navis.Dotprops`: make them a subclass of BaseNeuron implement `nat:dotprops` in `navis.make_dotprops()` added `navis.read_nrrd()` and `navis.write_nrrd()` side-effect: renamed `navis.from_swc` -> `read_swc` and `navis.to_swc` -> `write_swc` improved conversion between nat and navis `Dotprops` full rework of topology-related functions: `navis.strahler_index()`, `navis.segregation_index()`, `navis.bending_flow()`, `navis.synapse_flow_centrality()` and `navis.split_axon_dendrite()` now work better, faster and more accurately. See their docs for details. new function: `navis.arbor_segregation_index()` new `color_by` and `shade_by` parameters for `plot3d` and `plot2d` that lets you color/shade a neuron by custom properties (e.g. by Strahler index or compartment) neurons are now more memory efficient: pandas “categoricals” are used for connector and node “type” and “label” columns add a `.memory_usage` method analogous to that of `pandas.DataFrames` `navis.NeuronList` can now be pickled! made `navis.Viewer` faster `navis.prune_twigs()` can now (optionally) prune by exactly the desired length improved `navis.NeuronList.apply` small bugfixes and improvements
0.3.2	18/10/20	`navis.plot2d()` and `navis.plot3d()` now accept `trimesh.Trimesh` directly `navis.in_volume()` now works with any mesh-like object, not just `navis.Volumes` lots of small bugfixes and improvements
0.3.1	07/10/20	new function `navis.rewire_skeleton()` improve `navis.heal_skeleton()` and `navis.stitch_skeletons()`: now much much faster `navis.reroot_skeleton()` can now reroot to multiple roots in one go `navis.plot3d()` now accepts a `soma` argument improved caching for neurons improved multiplication/division of neurons faster `r.nblast` and `r.nblast_allbyall` `r.xform_brain` now also adjusts the soma radius `neuprint.fetch_skeletons` now returns correct soma radius lots of small bugfixes
0.3.0	06/10/20	started module to manipulate mesh data: see `navis.simplify_mesh()` improved interfaces with R NBLAST and `xform_brain` improved attribute caching for neurons
0.2.3	06/09/20	new Neuron property `.label` that if present will be used for plot legends new function for R interface: `navis.interfaces.r.load_rda()` Blender interface: improved scatter plot generation
0.2.2	15/08/20	new `plot3d` parameter: with plotly backend, use `fig` to add data to existing plotly figure new `plot3d` parameter: with vispy backend, use `center=False` to not re-center camera on adding new data new `r.mirror_brain` parameter: use e.g. `via='FCWB'` if source space does not have mirror transform new `NeuronList` method: `append()` works like `list.append()` first implementation of smarter (re-)calculation of temporary Neuron properties using `.is_stale` property Neurons can now be multiplied/divided by array/list of x/y/z coordinates for non-isometric transforms fix issues with newer rpy2 versions various improvements and bug fixes
0.2.1	20/07/20	new `plot3d` parameter: with plotly backend, use `radius=True` plots TreeNeurons with radius new `plot2d` parameter: `orthogonal=False` sets view to perspective various improvements to e.g. `nx2neuron
0.2.0	29/06/20	new neuron class `MeshNeuron` that consists of vertices and faces new `TreeNeuron` property `.volume` we now use ncollpyde for ray casting (intersections) clean-up in neuromorpho interface fix bugs in `Volume` pickling new example data from the Janelia hemibrain data set breaking changes: :func:`~navis.nx2neuron` now returns a `TreeNeuron` instead of a `DataFrame`
0.1.16	26/05/20	many small bugfixes
0.1.15	15/05/20	improvements to R and Blender interface improved loading from SWCs (up to 2x faster) TreeNeurons: allow rerooting by setting the `.root` attribute
0.1.14	05/05/20	emergency fixes for 0.1.13
0.1.13	05/05/20	new function `navis.vary_color()` improvements to Blender interface and various other functions
0.1.12	02/04/20	`Volume` is now sublcass of `trimesh.Trimesh`
0.1.11	28/02/20	removed hard-coded swapping and translation of axes in the Blender interface improved `navis.stitch_neurons`: much faster now if you have iGraph fixed errors when using multiprocessing (e.g. in `NeuronList.apply`) fixed bugs in `navis.downsample_neuron()`
0.1.10	24/02/20	fixed bugs in Blender interface introduced in 0.1.9
0.1.9	24/02/20	removed hard-coded swapping and translation of axes in the Blender interface fixed bugs in `stitch_neurons`
0.1.8	21/02/20	Again lots of fixed bugs Blame myself for not keeping track of changes
0.1.0	23/05/19	Made lots of fixes Promised myself to be better at tracking changes
0.0.1	29/01/19	First commit, lots to fix.