diff --git a/docs/changelog.md b/docs/changelog.md index 67a74443..4c8aaab1 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -23,23 +23,14 @@ pip install git+https://github.com/navis-org/navis@master ## Version `1.9.1` { data-toc-label="1.9.1" } _Date: 24/10/24_ - -##### Additions -- New interface to the [H01](https://h01-release.storage.googleapis.com/landing.html) dataset by Jinhan Choi and Jakob Troidl; see the new tutorial for details - ##### Improvements -- I/O: - - [`read_nrrd`][navis.read_nrrd], [`read_tiff`][navis.read_tiff] and [`read_mesh`][navis.read_mesh] now use the same backend as e.g. [`read_swc`][navis.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: - - new function: [`navis.thin_voxels`][] can be used to thin images and `VoxelNeurons` to single-pixel width (see also below) - - new `thin` parameter for [`read_nrrd`][navis.read_nrrd], [`read_tiff`][navis.read_tiff] -- [`TreeNeurons`][navis.TreeNeuron]: - - 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`][navis.VoxelNeuron]: - - ew properties: `VoxelNeuron.nnz` and `VoxelNeuron.density` -- [`navis.drop_fluff`][] and [`navis.neuron2nx`][] now also works with [`Dotprops`][navis.Dotprops] +- 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 +- fixed a bug in [`navis.subset_neuron`][] that caused branch points to not be re-calculated **Full Changelog**: [v1.9.0...v1.9.1](https://github.com/navis-org/navis/compare/v1.9.0...v1.9.1) @@ -50,11 +41,10 @@ This version brings a shiny new interface to the [H01 human cortex](https://h01- and various other quality of life improvements. ##### Breaking -- The default for `radius` ([`navis.plot2d`][] and [`navis.plot3d`][]) was changed to `False` (from `"auto"`) to avoid running into issues - when visualizing large numbers of skeletons while using the defaults +- 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](https://h01-release.storage.googleapis.com/landing.html) dataset by Jinhan Choi and Jakob Troidl; see the new tutorial for details +- New interface to the [H01](https://h01-release.storage.googleapis.com/landing.html) dataset (by Jinhan Choi and Jakob Troidl; see the new tutorial for details) ##### Improvements - I/O: @@ -67,13 +57,13 @@ and various other quality of life improvements. - 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`][navis.VoxelNeuron]: - - ew properties: `VoxelNeuron.nnz` and `VoxelNeuron.density` + - new properties: `VoxelNeuron.nnz` and `VoxelNeuron.density` - [`navis.drop_fluff`][] and [`navis.neuron2nx`][] now also works with [`Dotprops`][navis.Dotprops] -**Full Changelog**: [v1.8.0...v1.9.0](https://github.com/navis-org/navis/compare/v1.8.0...v1.9.0) - ##### Experimental -- setting `navis.config.add_units=True` (default is `False`) will add units to certain neuron properties such as `.cable_length` to make them human-readable +- 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](https://github.com/navis-org/navis/compare/v1.8.0...v1.9.0) ## Version `1.8.0` { data-toc-label="1.8.0" } _Date: 22/09/24_