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Changelog#

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 history on NAVis' Github repository.

dev#

Date: ongoing

Improvements#
Fixes#
  • fix issue when plotting skeleton where the soma has no radius
  • read_precomputed will now also look for .ngmesh files when given a folder to search

To install the current dev version of NAVis:

pip uninstall navis -y
pip install git+https://github.com/navis-org/navis@master

Version 1.10.0#

Date: 06/02/25

Improvements#
  • made reading neurons from .tar archives much faster
  • read_swc now works if additional columns are present
Fixes#
  • opacity parameter plot3d now works correctly when using the plotly backend
  • fixed an issue with Elastix transforms on Windows machines
  • fixes for navis.longest_neurite when from_root=False
  • fixed issues with neuPrint interface when using multiple clients
  • fixed an issue with the MICrONS interface
  • fixed an issue with mesh simplification and the pymeshlab and Blender backends (@floesche)
  • fixed two (potential) issues in navis.longest_neurite when from_root=False
  • fixed various issues related to numpy 2.0 (@floesche)

Full Changelog: v1.9.1...v1.10.0

Version 1.9.1#

Date: 24/10/24

Improvements#
  • MICrONS & H01 interfaces:
    • fetch_neurons now accepts a materialization parameter that determines which materialization version is used for synapse and nucleus queries; defaults to "auto" which means navis will try to find a materialization version matching the queried root IDs
    • fetch_neurons will now also assign soma positions for H01 neurons (see the .soma_pos neuron property)
  • CloudVolume.mesh.get_navis (see navis.patch_cloudvolume) now accepts a process (default is False) parameter that determines whether the NeuroGlancer mesh is processed (deduplication of vertices, etc.); contribute by Forrest Collman
Fixes#

Full Changelog: v1.9.0...v1.9.1

Version 1.9.0#

Date: 17/10/24

This version brings a shiny new interface to the H01 human cortex dataset and various other quality of life improvements.

Breaking#
  • The default for radius (navis.plot2d and navis.plot3d) was changed to False (from "auto"); this is to make sure that the defaults allow visualizing large numbers of skeletons, i.e. prioritizing performance over beauty
Additions#
  • New interface to the H01 dataset (by Jinhan Choi and Jakob Troidl; see the new tutorial for details)
Improvements#
  • I/O:
    • read_nrrd, read_tiff and read_mesh now use the same backend as e.g. read_swc which enables some niceties such as reading directly from URLs and archives, parallel processing, etc
    • all read_* functions now have an error parameter that can be used to skip errors
  • Image data:
  • TreeNeurons:
    • skeletons can now be initialized from a (vertices, edges) tuple - see also navis.edges2neuron
    • new property: TreeNeuron.vertices gives read-only to node (vertex) coordinates
  • VoxelNeurons:
    • new properties: VoxelNeuron.nnz and VoxelNeuron.density
  • navis.drop_fluff and navis.neuron2nx now also works with Dotprops
Experimental#
  • setting navis.config.add_units=True (default is False for the time being) will add units to certain neuron properties such as .cable_length to make them human-readable

Full Changelog: v1.8.0...v1.9.0

Version 1.8.0#

Date: 22/09/24

This version contains a major internal rework of both navis.plot2d and navis.plot3d to make them more consistent and easier to use.

Breaking#
  • Plotting: the synapse_layout parameter was renamed to cn_layout (matching e.g. other parameters such as cn_colors)
  • Negative views in navis.plot2d (e.g. view=("x", "-z")) will now invert axes rather than changing the underlying data
  • Minimum version of matplotlib is now 3.9 (was 3.6)
  • The plotly backend is not part of a minimal install anymore (still installed using navis[all])
  • The Vispy backend is now deprecated and will be removed in a future release
  • Removed navis.screenshot - please use the Octarine/Vispy viewer's .screenshot() method instead
  • navis.tortuosity now calculates tortuosity as-is (i.e. without resampling) by default
Additions#
Improvements#
  • Plotting:
    • navis.plot3d:
    • legendgroup parameter (plotly backend) now also sets the legend group's title
    • new parameters for the plotly backend:
      • legend (default True): determines whether legends is shown
      • legend_orientation (default v): determines whether legend is aranged vertically (v) or horizontally (h)
      • linestyle (default -): determines line style for skeletons
    • default for radius is now "auto"
    • navis.plot2d:
    • the view parameter now also works with methods 3d and 3d_complex
    • the color_by and shade_by parameters now also work when plotting skeletons with radius=True
    • new defaults: radius="auto", alpha=1, figsize=None (use matplotlib defaults)
    • new parameters for methods 3d and 3d_complex: mesh_shade=False and non_view_axes3d
    • the scalebar and soma parameters can now also be dictionaries to style (color, width, etc) the scalebar/soma
    • the connectors parameter can now be used to show specific connector types (e.g. connectors="pre")
  • I/O:
    • read_* functions are now able to read from FTP servers (ftp://...)
    • the limit parameter used in many read_* functions can now also be a regex pattern or a slice
  • New parameter in navis.resample_skeleton: use map_column to include arbitrary columns in the resampling
  • navis.prune_twigs and navis.morpho.cable_length now accept a mask parameter
  • General improvements to docs and tutorials
Fixes#
  • Memory usage of Neuron/Lists is now correctly re-calculated when the neuron is modified
  • Various fixes and improvements for the MICrONS interface (navis.interfaces.microns)
  • navis.graph.node_label_sorting now correctly prioritizes total branch length
  • navis.TreeNeuron.simple now correctly drops soma nodes if they aren't root, branch or leaf points themselves

Full Changelog: v1.7.0...v1.8.0

Version 1.7.0#

Date: 25/07/24

Breaking#
  • Plotting: dropped the cluster parameter in favor of an improved color_by logic (see below)
Additions#
  • NAVis now uses navis-fastcore if present to dramatically speed up core functions (see updated install instructions)
  • New method navis.NeuronList.add_metadata to quickly add metadata to neurons
Improvements#
  • navis.find_soma and navis.graph.neuron2nx (used under the hood) are now much faster
  • All I/O functions such as navis.read_swc now show which file caused an error (if any); original filenames are tracked as file property
  • navis.NeuronList will only search the first 100 neurons for autocompletion to avoid freezing with large lists
  • Plotting functions: color_by now accepts either a list of labels (one per neuron) or the name of a neuron property
  • navis.subset_neuron is now faster and more memory efficient when subsetting meshes
  • navis.TreeNeuron.cable_length is now faster
  • Fixed a bug in plotting when using vertex colors
  • Fixed the progress bar in navis.interfaces.neuprint.fetch_mesh_neuron
  • Fixed a bug in navis.synblast that caused multiprocessing to fail (pickling issue with pykdtree)
  • navis.interfaces.neuprint.fetch_mesh_neuron will now ignore the lod parameter if the data source does not support it instead of breaking
  • Fixed a number of deprecation warnings in the codebase

Full Changelog: v1.6.0...v1.7.0

Version 1.6.0#

Date: 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 TreeNeuron.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
  • 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 are now faster
  • Improved logic for splitting NBLASTs across multiple cores
  • navis.xform_brain now allows specifying 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
  • 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
  • Fixed bug in navis.subset_neuron that caused connectors to be dropped when using mask
  • Fixed a bug in navis.despike_skeleton that caused the reverse argument to be ignored
  • Fixed two small bugs in navis.interfaces.neuprint.fetch_mesh_neuron

Full Changelog: v1.5.0...v1.6.0

Version 1.5.0#

Date: 27/07/23

Breaking#
  • Dropped support for Python 3.7
Additions#
  • 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
  • New NeuronList method: navis.NeuronList.set_neuron_attributes
  • New utility functions: navis.nbl.compress_scores, navis.nbl.nblast_prime
Improvements#
  • navis.xform_brain now recognizes the target template's units if available
  • 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
Fixes#
  • Various other bugfixes

Full Changelog: v1.4.0...v1.5.0

Version 1.4.0#

Date: 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
Additions#
  • New function: navis.read_tiff to read image stacks from TIFF files
  • New utility function: navis.nbl.extract_matches
Improvements#
  • NBLASTs: single progress bar instead of one for each process
  • New via parameter for navis.xform_brain
  • 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
Fixes#
  • Tons of bug fixes

Full Changelog: v1.3.1...v1.4.0

Version 1.3.1#

Date: 10/06/22

Fixes#
  • Various bugs fixed

Full Changelog: v1.3.0...v1.3.1

Version 1.3.0#

Date: 10/05/22

Breaking#
  • As of this version pip install navis won't install a vispy backend
Additions#
  • New interface to fetch data from Virtual Fly Brain: navis.interfaces.vfb
  • Tools to build custom NBLAST score matrices
  • Bayesian implementation of the network traversal model: navis.models.network_models.BayesianTraversalModel
  • New morphometrics functions: navis.segment_analysis & navis.form_factor
  • New function to write meshes: navis.write_mesh
Improvements#
  • NBLASTs: new approx_nn parameter
  • Example neurons now come with some meta data
Fixes#
  • Lots of fixes and improvements in particular for I/O-related functions

Full Changelog: v1.2.1...v1.3.0

Version 1.2.1#

Date: 25/02/22

Fixes#
  • Hot fix for navis.split_axon_dendrite

Full Changelog: v1.2.0...v1.2.1

Version 1.2.0#

Date: 24/02/22

Additions#
  • 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
  • Added a new interface with the Allen Cell Types Atlas
Improvements#
  • Improvements to various functions: e.g. navis.bending_flow, navis.synapse_flow_centrality, navis.split_axon_dendrite, navis.longest_neurite
  • navis.write_nrrd and navis.read_nrrd can now be used to write/read Dotprops to/from NRRD files
  • navis.read_swc now accepts a limit parameter that enables reading on the first N neurons
  • navis.nblast (and variants) now accept a precision parameter
  • navis.simplify_mesh (and therefore navis.downsample_neuron with skeletons) now uses the pyfqmr if present
  • Improved the interface to Neuromorpho
Fixes#
  • Myriads of small and big bugfixes

Full Changelog: v1.1.0...v1.2.0

Version 1.1.0#

Date: 18/11/21

Additions#
  • New function: navis.sholl_analysis
  • Plotly is now correctly chosen as default backend in Google colab
Fixes#
  • Fixed a critical bug with plotting skeletons with plotly 5.4.0

Full Changelog: v1.0.0...v1.1.0

Version 1.0.0#

Date: 11/11/21

Breaking#
  • navis.MeshNeuron: __getattr__ does not search trimesh representation anymore
  • NBLASTs: queries/targets now MUST be navis.Dotprops (no more automatic conversion, use navis.make_dotprops)
  • Renamed functions to make it clear they work only on TreeNeurons:
  • smooth_neuron navis.smooth_skeleton
  • reroot_neuron navis.reroot_skeleton
  • rewire_neuron navis.rewire_skeleton
  • despike_neuron navis.despike_skeleton
  • average_neurons navis.average_skeletons
  • heal_fragmented_neuron navis.heal_skeleton
  • stitch_neurons navis.stitch_skeletons
  • cut_neuron navis.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 navis.synapse_similarity
    • renamed cluster_by_connectivity navis.connectivity_similarity
    • renamed sparseness navis.connectivity_sparseness
    • renamed navis.write_google_binary navis.write_precomputed
  • navis.geodesic_matrix renamed parameter tn_ids from_
Additions & Improvements#
  • navis.NeuronList.apply() now allows omitting failures
  • navis.VoxelNeuron:
    • new class representing neurons as voxels
    • new (experimental) class representing neurons as voxels
    • navis.read_nrrd now returns VoxelNeuron instead of Dotprops by default
    • currently works with only a selection of functions
  • navis.TreeNeuron:
    • can now be initialized directly with skeletor.Skeleton
    • new method: navis.TreeNeuron.snap
  • navis.MeshNeuron:
    • navis.in_volume, navis.subset_neuron and navis.break_fragments now work on MeshNeurons
    • new properties: .skeleton, .graph and .igraph
    • new methods: navis.MeshNeuron.skeletonize and navis.MeshNeuron.snap
    • can now be initialized with skeletor.Skeleton and (vertices, faces) tuple
    • plotting: color_by parameter now works with MeshNeurons
  • navis.Dotprops:
    • new property: .sampling_resolution (used e.g. for scaling vectors for plotting)
    • new method: navis.Dotprops.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 (navis.read_swc & navis.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 navis.write_precomputed
    • new function: navis.read_precomputed
  • Plotting:
    • new function navis.plot_flat plots neurons as dendrograms
    • navis.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 navis.plot2d and navis.plot3d: use clusters=[0, 0, 0, 1, 1, ...] to assigns clusters and have them automatically coloured accordingly
    • navis.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
  • navis.make_dotprops now accepts parallel=True parameter for parallel processing
  • navis.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: navis.read_mesh and navis.write_mesh
  • New function navis.read_nmx reads pyKNOSSOS files
  • New function navis.smooth_mesh smoothes meshes and MeshNeurons
  • Improved/updated the InsectBrain DB interface (see the tutorial)
  • Under-the-hood fixes and improvements to: navis.plot2d, navis.split_axon_dendrite, navis.tortuosity, navis.resample_skeleton, navis.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 navis.cable_overlap
Fixes#
  • Under-the-hood fixes and improvements

Full Changelog: v0.6.0...v1.0.0

Version 0.6.0#

Date: 12/05/21

Additions#
  • new functions: navis.prune_at_depth, navis.read_rda, navis.cell_body_fiber
  • new functions to map units into neuron space: BaseNeuron.map_units and navis.to_neuron_space
Improvements#
  • 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
  • navis.nblast_smart: drop quantile and add score criterion
  • 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
  • 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
Fixes#
  • fixed navis.guess_radius
  • fixed NBLAST progress bars in notebook environments
  • fixed a couple bugs with CMTK transforms

Full Changelog: v0.5.3...v0.6.0

Version 0.5.3#

Date: 10/04/21

Additions#
  • new functions: navis.nblast_smart, navis.synblast, navis.symmetrize_brain
  • navis.plot2d: rasterize=True will rasterize neurons (but not axes or labels) to help keep file sizes low
  • navis.plot3d (plotly): hover_name=True will show neuron names on hover
Improvements#
  • 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)
Fixes#
  • a great many small and big bug fixes

Full Changelog: v0.5.2...v0.5.3

Version 0.5.2#

Date: 02/02/21

Additions#
  • new functions: navis.xform, navis.write_precomputed
Improvements#
  • navis.downsample_neuron now also works on Dotprops
  • Neurons: connectors are now included in bounding box calculations
  • NeuronLists: added progress bar for division / multiplication

Full Changelog: v0.5.1...v0.5.2

Version 0.5.1#

Date: 10/01/21

Fixes#
  • Various under-the-hood improvements and bugfixes

Full Changelog: v0.5.0...v0.5.1

Version 0.5.0#

Date: 05/01/21

Additions#
  • 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
Improvements#
  • de-cluttered top level namespace: some more obscure functions are now only available through modules

Full Changelog: v0.4.3...v0.5.0

Version 0.4.3#

Date: 22/12/20

Fixes#
  • Small bugfixes

Full Changelog: v0.4.2...v0.4.3

Version 0.4.2#

Date: 22/12/20

Fixes#
  • Small bugfixes

Full Changelog: v0.4.1...v0.4.2

Version 0.4.1#

Date: 06/12/20

Fixes#
  • Critical bugfix in NBLAST

Full Changelog: v0.4.0...v0.4.1

Version 0.4.0#

Date: 06/12/20

Additions#
  • 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

Full Changelog: v0.3.4...v0.4.0

Version 0.3.4#

Date: 24/11/20

Improvements#
  • improved navis.Dotprops:
  • more control over generation in navis.make_dotprops
  • navis.Dotprops now play nicely with R interface

Full Changelog: v0.3.3...v0.3.4

Version 0.3.3#

Date: 23/11/20

Additions#
  • 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)
Improvements#
  • 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
Fixes#
  • small bugfixes and improvements

Full Changelog: v0.3.2...v0.3.3

Version 0.3.2#

Date: 18/10/20

Improvements#
  • navis.plot2d and navis.plot3d now accept trimesh.Trimesh directly
  • navis.in_volume now works with any mesh-like object, not just navis.Volumes
Fixes#
  • lots of small bugfixes and improvements

Full Changelog: v0.3.1...v0.3.2

Version 0.3.1#

Date: 07/10/20

Additions#
  • new function navis.rewire_skeleton
Improvements#
  • navis.heal_skeleton and navis.stitch_skeletons are 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
Fixes#
  • lots of small bugfixes

Full Changelog: v0.3.0...v0.3.1

Version 0.3.0#

Date: 06/10/20

Additions#
  • Started module to manipulate mesh data (see e.g. navis.simplify_mesh)
Improvements#
  • Improved interfaces with R NBLAST and xform_brain
  • Improved attribute caching for neurons

Full Changelog: v0.2.3...v0.3.0

Version 0.2.3#

Date: 06/09/20

Additions#
  • New Neuron property .label that if present will be used for plot legends
  • New function for R interface: navis.interfaces.r.load_rda
Improvements#
  • Blender interface: improved scatter plot generation

Version 0.2.2#

Date: 15/08/20

Additions#
  • 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
Fixes#
  • Fix issues with newer rpy2 versions
  • Various improvements and bug fixes

Version 0.2.1#

Date: 20/04/20

Additions#
  • New plot3d parameter: with plotly backend, use radius=True plots TreeNeurons with radius
  • New plot2d parameter: orthogonal=False sets view to perspective
Improvements#
  • Various improvements to e.g. nx2neuron

Version 0.2.0#

Date: 29/06/20

Breaking#
  • navis.nx2neuron now returns a navis.TreeNeuron instead of a DataFrame
Additions#
  • New neuron class navis.MeshNeuron
  • New navis.TreeNeuron property .volume
  • New example data from the Janelia hemibrain data set
Improvements#
  • Clean-up in neuromorpho interface
  • We now use ncollpyde for ray casting (intersections)
Fixes#
  • Fix bugs in navis.Volume pickling

Version 0.1.16#

Date: 26/05/20

Fixes#
  • Many small bugfixes

Version 0.1.15#

Date: 15/05/20

Improvements#
  • Improvements to R and Blender interface
  • Improved loading from SWCs (up to 2x faster)
  • TreeNeurons: allow rerooting by setting the .root attribute

Version 0.1.14#

Date: 05/05/20

Fixes#
  • Emergency fixes for critical bugs

Version 0.1.13#

Date: 05/05/20

Additions#
  • new function: navis.vary_color
Improvements#
  • improvements to Blender interface and various other functions

Version 0.1.12#

Date: 02/04/20

Imnprovements#
  • navis.Volume is now sublcass of trimesh.Trimesh

Version 0.1.11#

Date: 28/02/20

Improvements#
  • improved navis.stitch_neurons: much faster now if you have iGraph
Fixes#
  • fixed errors when using multiprocessing (e.g. in NeuronList.apply)
  • fixed bugs in navis.downsample_neuron

Version 0.1.10#

Date: 24/02/20

Fixes#
  • Fixed bugs in Blender interface introduced in 0.1.9

Version 0.1.9#

Date: 24/02/20

Fixes#
  • Removed hard-coded swapping and translation of axes in the Blender interface
  • Fixed bugs in navis.stitch_neurons

Version 0.1.8#

Date: 21/02/20

Fixes#
  • Again lots of fixed bugs

Version 0.1.0#

Date: 23/05/19

Fixes#
  • Many small bugfixes

Version 0.0.1#

Date: 29/01/19

Fixes#
  • First commit, lots to fix.