dev |
In development |
NeuronList :-
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 :-
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
__getattr__ does not search trimesh representation anymore
Dotprops :-
experimental support for non-isometric .units for neurons
- NBLASTs:
queries/targets now MUST be Dotprops - no more automatic conversion
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
- I/O to/from Google neuroglancer’s precomputed format:
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- 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
- renamed functions to make it clear they are only for
TreeNeurons : -
- removals and other renamings:
-
- transforms:
-
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 smoother 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 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
geodesic_matrix() renamed parameter tn_ids -> from_
improved cable_overlap()
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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()
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0.5.3 |
10/04/21 |
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0.5.2 |
02/02/21 |
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0.5.1 |
10/01/21 |
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0.5.0 |
05/01/21 |
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0.4.3 |
22/12/20 |
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0.4.2 |
22/12/20 |
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0.4.1 |
06/12/20 |
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0.4.0 |
06/12/20 |
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0.3.4 |
24/11/20 |
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0.3.3 |
23/11/20 |
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0.3.2 |
18/10/20 |
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0.3.1 |
07/10/20 |
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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
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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
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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
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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
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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
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0.1.16 |
26/05/20 |
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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
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0.1.14 |
05/05/20 |
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0.1.13 |
05/05/20 |
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0.1.12 |
02/04/20 |
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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()
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0.1.10 |
24/02/20 |
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0.1.9 |
24/02/20 |
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0.1.8 |
21/02/20 |
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0.1.0 |
23/05/19 |
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0.0.1 |
29/01/19 |
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