Navis

_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](https://github.com/navis-org/navis/compare/v1.3.1...v1.4.0)

_Date: 10/06/22_

Fixes
- Various bugs fixed

**Full Changelog**: [v1.3.0...v1.3.1](https://github.com/navis-org/navis/compare/v1.3.0...v1.3.1)

_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](https://github.com/navis-org/navis/compare/v1.2.1...v1.3.0)

_Date: 25/02/22_

Fixes
- Hot fix for `navis.split_axon_dendrite`

**Full Changelog**: [v1.2.0...v1.2.1](https://github.com/navis-org/navis/compare/v1.2.0...v1.2.1)

_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](https://github.com/navis-org/navis/compare/v1.1.0...v1.2.0)

_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](https://github.com/navis-org/navis/compare/v1.0.0...v1.1.0)