docs: various small fixes

README.md

@@ -8,13 +8,13 @@ NAVis is a Python 3 library for **N**euron **A**nalysis and **Vis**ualization.
 Visit our documentation [here](https://navis-org.github.io/navis/ "NAVis Documentation")!
 
 ## Features
-* **polyglot**: work and convert between neuron skeletons, meshes, dotprops and images
-* **visualize**: 2D (matplotlib) and 3D (vispy, plotly or k3d)
+* **polyglot**: work with and convert between neuron skeletons, meshes, dotprops and images
+* **visualize**: 2D (matplotlib) and 3D (octarine, vispy, plotly or k3d) plots
 * **process**: skeletonization, meshing, smoothing, repair, downsampling, etc.
 * **morphometrics**: Strahler analysis, cable length, volume, tortuosity and more
 * **similarity**: compare & cluster by morphology (e.g. NBLAST, persistence or form factor) or connectivity metrics
 * **transform**: move data between template brains (built-in support for HDF5, CMTK, Elastix and landmark-based transforms)
-* **interface**: load neurons directly from [neuPrint](https://neuprint.janelia.org), [neuromorpho.org](http://neuromorpho.org) and other data sources
+* **interface**: load neurons directly from [neuPrint](https://neuprint.janelia.org), [neuromorpho.org](http://neuromorpho.org) and other remote data repositories
 * **model** neurons and networks using the *NEURON* simulator
 * **render**: use Blender 3D for high quality [visualizations](https://youtu.be/wl3sFG7WQJc)
 * **R** neuron libraries: interfaces with [nat](https://github.com/jefferis/nat), [rcatmaid](https://github.com/jefferis/rcatmaid), [elmr](https://github.com/jefferis/elmr) and more
@@ -27,7 +27,7 @@ Visit our documentation [here](https://navis-org.github.io/navis/ "NAVis Documen
 See the [documentation](http://navis.readthedocs.io/ "NAVis ReadTheDocs") for detailed installation instructions, tutorials and examples. For the impatient:
 
 ```sh
-pip3 install 'navis[all]'
+pip3 install "navis[all]"
 ```
 
 which includes all optional extras providing features and/or performance improvements.

docs/api.md

@@ -20,7 +20,7 @@ This API reference is a more or less complete account of the primary functions:
 
 1. [Neuron- and NeuronList functions and methods](#neurons-neuronlists)
 2. [Functions for visualization](#visualization)
-3. [Manipulate or analyze neuron morphology](#morphometrics)
+3. [Manipulate or analyze neuron morphology](#neuron-morphology)
 4. [Transforming and mirroring data](#transforming-and-mirroring)
 5. [Analyze connectivity](#connectivity)
 6. [Import/Export](#importexport)
@@ -233,8 +233,8 @@ Properties:
 |----------|-------------|
 | [`NeuronList.bbox`][navis.NeuronList.bbox] | {{ autosummary("navis.NeuronList.bbox") }} |
 | [`NeuronList.empty`][navis.NeuronList.empty] | {{ autosummary("navis.NeuronList.empty") }} |
-| [`NeuronList.id`] | An array with the IDs of the neurons contained in the list. |
-| [`NeuronList.idx`] | An indexer similar to pandas' `iloc` that accepts neuron IDs. |
+| [`NeuronList.id`][navis.NeuronList.id] | An array with the IDs of the neurons contained in the list. |
+| [`NeuronList.idx`][navis.NeuronList.idx] | An indexer similar to pandas' `iloc` that accepts neuron IDs. |
 | [`NeuronList.is_degenerated`][navis.NeuronList.is_degenerated] | {{ autosummary("navis.NeuronList.is_degenerated") }} |
 | [`NeuronList.is_mixed`][navis.NeuronList.is_mixed] | {{ autosummary("navis.NeuronList.is_mixed") }} |
 | [`NeuronList.shape`][navis.NeuronList.shape] | {{ autosummary("navis.NeuronList.shape") }} |
@@ -370,7 +370,6 @@ NBLAST and related functions:
 | [`navis.nblast_smart`][navis.nblast_smart] | {{ autosummary("navis.nblast_smart") }} |
 | [`navis.nblast_allbyall`][navis.nblast_allbyall] | {{ autosummary("navis.nblast_allbyall") }} |
 | [`navis.nblast_align`][navis.nblast_align] | {{ autosummary("navis.nblast_align") }} |
-| [`navis.vxnblast`][navis.vxnblast] | {{ autosummary("navis.vxnblast") }} |
 | [`navis.synblast`][navis.synblast] | {{ autosummary("navis.synblast") }} |
 | [`navis.persistence_distances`][navis.persistence_distances] | {{ autosummary("navis.persistence_distances") }} |
 
@@ -476,6 +475,12 @@ So to register and use a new transform you would look something like this:
 >>> xf = navis.xform_brain(data, 'brainA', 'brainB')
 ```
 
+You can check which transforms are registered like so:
+
+``` python
+>>> navis.transforms.registry.summary()  # this outputs a dataframe
+```
+
 These are the methods and properties of ``registry``:
 
 | Method   | Description |
@@ -758,7 +763,7 @@ from navis.interfaces import insectbrain_db
 Functions to be run inside [Blender 3D](https://www.blender.org/) and import
 CATMAID data (see Examples). Please note that this requires Blender >2.8 as
 earlier versions are shipped with older Python versions not supported by {{ navis }}.
-See the [tutorials](../generated/gallery/3_interfaces/plot_01_interfaces_blender/) for an introduction of how to use {{ navis }} in
+See the [tutorials](../generated/gallery/3_interfaces/plot_02_interfaces_blender/) for an introduction of how to use {{ navis }} in
 Blender.
 
 _Not imported at top level! Must be imported explicitly:_

docs/changelog.md

@@ -62,8 +62,8 @@ more consistent and easier to use.
     - 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`
+    - `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.cable_length`][] now accept a `mask` parameter
 - General improvements to docs and tutorials

docs/index.md

@@ -48,7 +48,7 @@ morphology. It stands on the shoulders of the excellent
 
     ---
 
-    Generate beautiful publication-ready 2D (matplotlib) and 3D (octarine,
+    Generate beautiful, publication-ready 2D (matplotlib) and 3D (octarine,
     vispy or plotly) [figures](generated/gallery/#plotting).
 
 -   :material-progress-wrench:{ .lg .middle } __Processing__
@@ -61,7 +61,7 @@ morphology. It stands on the shoulders of the excellent
 
     ---
 
-    Uses compiled Rust code under-the-hood. Also scale thanks to
+    Uses compiled Rust code under-the-hood and
     out-of-the-box support for [multiprocessing](generated/gallery/6_misc/plot_00_misc_multiprocess).
 
 -   :material-lightbulb-group:{ .lg .middle } __Clustering__
@@ -75,7 +75,7 @@ morphology. It stands on the shoulders of the excellent
     ---
 
     Fully featured [transform system](generated/gallery/5_transforms/plot_00_transforms) to move neurons between brain spaces.
-    We support e.g. CMTK or Elastix.
+    We support CMTK, Elastix, landmark-based transforms and more!
 
 -   :octicons-file-directory-symlink-24:{ .lg .middle } __Import/Export__