From 3631d1bc539cfc084c1d2b2099ab19ab8288c33b Mon Sep 17 00:00:00 2001
From: Philipp Schlegel <observing@web.de>
Date: Tue, 24 Sep 2024 10:44:36 +0100
Subject: [PATCH] update tutorials: - rename tutorials from `plot_` to
 `tutorial_` - add tutorial on plotting cortical cell types - fix some broken
 links

---
 docs/api.md                                   |  14 +-
 docs/changelog.md                             |   2 +-
 ...eletons.py => tutorial_io_00_skeletons.py} |   2 +-
 ..._io_meshes.py => tutorial_io_01_meshes.py} |   2 +-
 ...dotprops.py => tutorial_io_02_dotprops.py} |   2 +-
 ..._io_pickle.py => tutorial_io_04_pickle.py} |   0
 ...intro.py => tutorial_plotting_00_intro.py} |   2 +-
 ...lors.py => tutorial_plotting_01_colors.py} |   2 +-
 ...tting_1d.py => tutorial_plotting_02_1d.py} |   0
 ...g_dend.py => tutorial_plotting_03_dend.py} |   0
 ...s.py => tutorial_plotting_04_skeletons.py} |   2 +-
 ...depth.py => tutorial_plotting_05_depth.py} |   0
 .../1_plotting/tutorial_plotting_06_cortex.py | 255 ++++++++++++++++++
 ...g_xkcd.py => tutorial_plotting_07_xkcd.py} |   0
 ...te.py => tutorial_morpho_00_manipulate.py} |   2 +-
 ...alyze.py => tutorial_morpho_01_analyze.py} |   6 +-
 ...on.py => tutorial_interfaces_00_neuron.py} |   0
 ...2.py => tutorial_interfaces_01_neuron2.py} |   2 +-
 ...r.py => tutorial_interfaces_02_blender.py} |   0
 ...rint.py => tutorial_remote_00_neuprint.py} |   0
 ...e.py => tutorial_remote_01_cloudvolume.py} |   2 +-
 ...crons.py => tutorial_remote_02_microns.py} |   2 +-
 ..._db.py => tutorial_remote_03_insect_db.py} |   0
 ...t_intro.py => tutorial_nblast_00_intro.py} |   4 +-
 ...ast_smat.py => tutorial_nblast_03_smat.py} |   0
 ...y => zzz_tutorial_nblast_01_flycircuit.py} |   0
 ...py => zzz_tutorial_nblast_02_hemibrain.py} |   0
 ...ss.py => tutorial_misc_00_multiprocess.py} |   0
 ...orms.py => tutorial_misc_01_transforms.py} |   0
 ...neurons.py => tutorial_basic_00_basics.py} |   4 +-
 ..._intro.py => tutorial_basic_01_neurons.py} |   2 +-
 ...ro.py => tutorial_basic_02_neuronlists.py} |   2 +-
 docs/index.md                                 |  18 +-
 docs/quickstart.md                            |   8 +-
 mkdocs.yml                                    |   1 +
 navis/morpho/ivscc.py                         |   6 +-
 navis/plotting/d.py                           |   2 +-
 navis/plotting/dd.py                          |   2 +-
 navis/plotting/ddd.py                         |   2 +-
 navis/plotting/flat.py                        |   4 +-
 tests/test_tutorials.py                       |   2 +-
 41 files changed, 305 insertions(+), 49 deletions(-)
 rename docs/examples/0_io/{plot_00_io_skeletons.py => tutorial_io_00_skeletons.py} (98%)
 rename docs/examples/0_io/{plot_01_io_meshes.py => tutorial_io_01_meshes.py} (98%)
 rename docs/examples/0_io/{plot_02_io_dotprops.py => tutorial_io_02_dotprops.py} (95%)
 rename docs/examples/0_io/{plot_04_io_pickle.py => tutorial_io_04_pickle.py} (100%)
 rename docs/examples/1_plotting/{plot_00_plotting_intro.py => tutorial_plotting_00_intro.py} (99%)
 rename docs/examples/1_plotting/{plot_01_plotting_colors.py => tutorial_plotting_01_colors.py} (99%)
 rename docs/examples/1_plotting/{plot_02_plotting_1d.py => tutorial_plotting_02_1d.py} (100%)
 rename docs/examples/1_plotting/{plot_03_plotting_dend.py => tutorial_plotting_03_dend.py} (100%)
 rename docs/examples/1_plotting/{plot_04_plotting_skeletons.py => tutorial_plotting_04_skeletons.py} (97%)
 rename docs/examples/1_plotting/{plot_05_plotting_depth.py => tutorial_plotting_05_depth.py} (100%)
 create mode 100644 docs/examples/1_plotting/tutorial_plotting_06_cortex.py
 rename docs/examples/1_plotting/{plot_07_plotting_xkcd.py => tutorial_plotting_07_xkcd.py} (100%)
 rename docs/examples/2_morpho/{plot_00_morpho_manipulate.py => tutorial_morpho_00_manipulate.py} (99%)
 rename docs/examples/2_morpho/{plot_01_morpho_analyze.py => tutorial_morpho_01_analyze.py} (97%)
 rename docs/examples/3_interfaces/{plot_00_interfaces_neuron.py => tutorial_interfaces_00_neuron.py} (100%)
 rename docs/examples/3_interfaces/{plot_01_interfaces_neuron2.py => tutorial_interfaces_01_neuron2.py} (98%)
 rename docs/examples/3_interfaces/{plot_02_interfaces_blender.py => tutorial_interfaces_02_blender.py} (100%)
 rename docs/examples/4_remote/{plot_00_remote_neuprint.py => tutorial_remote_00_neuprint.py} (100%)
 rename docs/examples/4_remote/{plot_01_remote_cloudvolume.py => tutorial_remote_01_cloudvolume.py} (97%)
 rename docs/examples/4_remote/{plot_02_remote_microns.py => tutorial_remote_02_microns.py} (99%)
 rename docs/examples/4_remote/{plot_03_remote_insect_db.py => tutorial_remote_03_insect_db.py} (100%)
 rename docs/examples/5_nblast/{plot_00_nblast_intro.py => tutorial_nblast_00_intro.py} (99%)
 rename docs/examples/5_nblast/{plot_03_nblast_smat.py => tutorial_nblast_03_smat.py} (100%)
 rename docs/examples/5_nblast/{zzz_no_plot_01_nblast_flycircuit.py => zzz_tutorial_nblast_01_flycircuit.py} (100%)
 rename docs/examples/5_nblast/{zzz_no_plot_02_nblast_hemibrain.py => zzz_tutorial_nblast_02_hemibrain.py} (100%)
 rename docs/examples/6_misc/{plot_00_misc_multiprocess.py => tutorial_misc_00_multiprocess.py} (100%)
 rename docs/examples/6_misc/{plot_01_transforms.py => tutorial_misc_01_transforms.py} (100%)
 rename docs/examples/{plot_00_basic_neurons.py => tutorial_basic_00_basics.py} (95%)
 rename docs/examples/{plot_01_neurons_intro.py => tutorial_basic_01_neurons.py} (99%)
 rename docs/examples/{plot_02_neuronlists_intro.py => tutorial_basic_02_neuronlists.py} (99%)

diff --git a/docs/api.md b/docs/api.md
index b97ced7e..897b2301 100644
--- a/docs/api.md
+++ b/docs/api.md
@@ -240,7 +240,7 @@ Properties:
 | [`NeuronList.shape`][navis.NeuronList.shape] | {{ autosummary("navis.NeuronList.shape") }} |
 | [`NeuronList.types`][navis.NeuronList.types]| {{ autosummary("navis.NeuronList.types") }} |
 
-Please see the [tutorial on ``NeuronList``](../generated/gallery/plot_02_neuronlists_intro/) for more
+Please see the [tutorial on ``NeuronList``](../generated/gallery/tutorial_basic_02_neuronlists_intro/) for more
 information, including how to index them.
 
 ## Visualization
@@ -428,7 +428,7 @@ like to know which part of a neuron is inside a certain brain region.
 ## Transforming and Mirroring
 
 Functions to transform spatial data, e.g. move neurons from one brain space to
-another. Check out the [tutorials](../generated/gallery/6_misc/plot_01_transforms/) for examples on how to
+another. Check out the [tutorials](../generated/gallery/6_misc/tutorial_misc_01_transforms/) for examples on how to
 use them.
 
 High-level functions:
@@ -606,7 +606,7 @@ imported explicitly as they are not imported at top level.
 ### NEURON simulator
 
 Functions to facilitate creating models of neurons/networks. Please see
-the [tutorials](../generated/gallery/3_interfaces/plot_00_interfaces_neuron/) for examples.
+the [tutorials](../generated/gallery/3_interfaces/tutorial_interfaces_00_neuron/) for examples.
 
 _Not imported at top level! Must be imported explicitly:_
 
@@ -734,12 +734,12 @@ These are the additional functions added by {{ navis }}:
 | [`neuprint.fetch_skeletons()`][navis.interfaces.neuprint.fetch_skeletons] | {{ autosummary("navis.interfaces.neuprint.fetch_skeletons") }} |
 | [`neuprint.fetch_mesh_neuron()`][navis.interfaces.neuprint.fetch_mesh_neuron] | {{ autosummary("navis.interfaces.neuprint.fetch_mesh_neuron") }} |
 
-Please also check out the [tutorials](../generated/gallery/4_remote/plot_00_remote_neuprint/) for examples of how to fetch and work with data from neuPrint.
+Please also check out the [tutorials](../generated/gallery/4_remote/tutorial_remote_00_neuprint/) for examples of how to fetch and work with data from neuPrint.
 
 ### InsectBrain DB API
 
 Set of functions to grab data from [InsectBrain](https://www.insectbraindb.org)
-which hosts some neurons and standard brains (see [tutorials](../generated/gallery/4_remote/plot_03_remote_insect_db/)).
+which hosts some neurons and standard brains (see [tutorials](../generated/gallery/4_remote/tutorial_remote_03_insect_db/)).
 
 _Not imported at top level! Must be imported explicitly:_
 
@@ -763,7 +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_02_interfaces_blender/) for an introduction of how to use {{ navis }} in
+See the [tutorials](../generated/gallery/3_interfaces/tutorial_interfaces_02_blender/) for an introduction of how to use {{ navis }} in
 Blender.
 
 _Not imported at top level! Must be imported explicitly:_
@@ -864,7 +864,7 @@ from navis.interfaces import microns
 | [`microns.fetch_neurons()`][navis.interfaces.microns.fetch_neurons] | {{ autosummary("navis.interfaces.microns.fetch_neurons") }} |
 | [`microns.get_somas()`][navis.interfaces.microns.get_somas] | {{ autosummary("navis.interfaces.microns.get_somas") }} |
 
-Please also see the [MICrONS tutorial](../generated/gallery/4_remote/plot_02_remote_microns/).
+Please also see the [MICrONS tutorial](../generated/gallery/4_remote/tutorial_remote_02_microns/).
 
 
 ### R interface
diff --git a/docs/changelog.md b/docs/changelog.md
index 62eb06a5..42f99171 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -37,7 +37,7 @@ more consistent and easier to use.
 
 ##### Additions
 - Added [Octarine](https://github.com/schlegelp/octarine) as the default backend for plotting from terminal
-- New Function: [`navis.ivscc_features`][] computes some basic ICSCC features
+- New Function: [`navis.ivscc_features`][] computes some basic IVSCC features
 - New function: [`navis.graph.skeleton_adjacency_matrix`][] computes the node adjacency for skeletons
 - New function: [`navis.graph.simplify_graph`][] simplifies skeleton graphs to only root, branch and leaf nodes while preserving branch length (i.e. weights)
 - New [`NeuronList`][navis.NeuronList] method: [`get_neuron_attributes`][navis.NeuronList.get_neuron_attributes] is analagous to `dict.get`
diff --git a/docs/examples/0_io/plot_00_io_skeletons.py b/docs/examples/0_io/tutorial_io_00_skeletons.py
similarity index 98%
rename from docs/examples/0_io/plot_00_io_skeletons.py
rename to docs/examples/0_io/tutorial_io_00_skeletons.py
index 3bd20181..af1c196a 100644
--- a/docs/examples/0_io/plot_00_io_skeletons.py
+++ b/docs/examples/0_io/tutorial_io_00_skeletons.py
@@ -176,7 +176,7 @@
 # %%
 # There are a few other ways to construct a [`navis.TreeNeuron`][] (e.g. using a graph) - see the docstring for details.
 #
-# Also note that all {{ navis }} neurons can be stored to disk using `pickle` - see the [pickling tutorial](../plot_04_io_pickle).
+# Also note that all {{ navis }} neurons can be stored to disk using `pickle` - see the [pickling tutorial](../tutorial_io_04_pickle).
 #
 # Hopefully the above has given you some entry points on how to load your data. See also the [I/O API reference](../../../api.md#importexport).
 #
diff --git a/docs/examples/0_io/plot_01_io_meshes.py b/docs/examples/0_io/tutorial_io_01_meshes.py
similarity index 98%
rename from docs/examples/0_io/plot_01_io_meshes.py
rename to docs/examples/0_io/tutorial_io_01_meshes.py
index a9ab8151..ab87ed9c 100644
--- a/docs/examples/0_io/plot_01_io_meshes.py
+++ b/docs/examples/0_io/tutorial_io_01_meshes.py
@@ -119,7 +119,7 @@
 #     [`navis.Volume`][] for details.
 #
 # This tutorial has hopefully given you some entry points on how to load your data. See also the [I/O API reference](../../../api.md#importexport).
-# Also note that all {{ navis }} neurons can be stored to disk using ``pickle`` - see the [pickling tutorial](../plot_04_io_pickle).
+# Also note that all {{ navis }} neurons can be stored to disk using ``pickle`` - see the [pickling tutorial](../tutorial_io_04_pickle).
 #
 # Please also keep in mind that you can also convert one neuron type into another - for example by skeletonizing [`MeshNeurons`][navis.MeshNeuron]
 # (see also the API reference on [neuron conversion](../../../api.md#converting-between-types)).
\ No newline at end of file
diff --git a/docs/examples/0_io/plot_02_io_dotprops.py b/docs/examples/0_io/tutorial_io_02_dotprops.py
similarity index 95%
rename from docs/examples/0_io/plot_02_io_dotprops.py
rename to docs/examples/0_io/tutorial_io_02_dotprops.py
index e2029941..cab0166d 100644
--- a/docs/examples/0_io/plot_02_io_dotprops.py
+++ b/docs/examples/0_io/tutorial_io_02_dotprops.py
@@ -77,4 +77,4 @@
 
 # %%
 # There is no established format to store dotprops. But like all other neuron types in navis, you can pickle data for later (re)use
-# - see the [pickling tutorial](../plot_04_io_pickle). See also the [I/O API reference](../../../api.md#importexport).
+# - see the [pickling tutorial](../tutorial_io_04_pickle). See also the [I/O API reference](../../../api.md#importexport).
diff --git a/docs/examples/0_io/plot_04_io_pickle.py b/docs/examples/0_io/tutorial_io_04_pickle.py
similarity index 100%
rename from docs/examples/0_io/plot_04_io_pickle.py
rename to docs/examples/0_io/tutorial_io_04_pickle.py
diff --git a/docs/examples/1_plotting/plot_00_plotting_intro.py b/docs/examples/1_plotting/tutorial_plotting_00_intro.py
similarity index 99%
rename from docs/examples/1_plotting/plot_00_plotting_intro.py
rename to docs/examples/1_plotting/tutorial_plotting_00_intro.py
index 865c8d50..a1e9f397 100644
--- a/docs/examples/1_plotting/plot_00_plotting_intro.py
+++ b/docs/examples/1_plotting/tutorial_plotting_00_intro.py
@@ -290,7 +290,7 @@
 #
 # Above we demo'ed making a little GIF using matplotlib. While that's certainly fun, it's not
 # very high production value. For high quality videos and renderings I recommend you check out
-# the tutorial on navis' [Blender interface](../3_interfaces/plot_01_interfaces.blender). Here's a little taster:
+# the tutorial on navis' [Blender interface](../3_interfaces/tutorial_interfaces_02_blender). Here's a little taster:
 #
 #  <iframe width="560" height="315" src="https://www.youtube.com/embed/wl3sFG7WQJc" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 #
diff --git a/docs/examples/1_plotting/plot_01_plotting_colors.py b/docs/examples/1_plotting/tutorial_plotting_01_colors.py
similarity index 99%
rename from docs/examples/1_plotting/plot_01_plotting_colors.py
rename to docs/examples/1_plotting/tutorial_plotting_01_colors.py
index fec9c8ea..5f42be3d 100644
--- a/docs/examples/1_plotting/plot_01_plotting_colors.py
+++ b/docs/examples/1_plotting/tutorial_plotting_01_colors.py
@@ -5,7 +5,7 @@
 This tutorial demonstrates how to adjust colors in NAVis plots.
 
 By now, you should already have a basic understanding on how to plot neurons in {{ navis }} (2d vs 3d plots, the various
-backends and plotting methods, etc.) - if not, check out the [plotting tutorial](../plot_00_plotting_intro).
+backends and plotting methods, etc.) - if not, check out the [plotting tutorial](../tutorial_plotting_00_intro).
 
 In this tutorial we will focus on how to finetune these plots by changing colors :rainbow:. We will demonstrate
 this using `matplotlib` ([`plot2d`][navis.plot2d]) and `plotly` ([`plot3d`][navis.plot3d]) but everything shown here
diff --git a/docs/examples/1_plotting/plot_02_plotting_1d.py b/docs/examples/1_plotting/tutorial_plotting_02_1d.py
similarity index 100%
rename from docs/examples/1_plotting/plot_02_plotting_1d.py
rename to docs/examples/1_plotting/tutorial_plotting_02_1d.py
diff --git a/docs/examples/1_plotting/plot_03_plotting_dend.py b/docs/examples/1_plotting/tutorial_plotting_03_dend.py
similarity index 100%
rename from docs/examples/1_plotting/plot_03_plotting_dend.py
rename to docs/examples/1_plotting/tutorial_plotting_03_dend.py
diff --git a/docs/examples/1_plotting/plot_04_plotting_skeletons.py b/docs/examples/1_plotting/tutorial_plotting_04_skeletons.py
similarity index 97%
rename from docs/examples/1_plotting/plot_04_plotting_skeletons.py
rename to docs/examples/1_plotting/tutorial_plotting_04_skeletons.py
index e74d75ff..250ed31a 100644
--- a/docs/examples/1_plotting/plot_04_plotting_skeletons.py
+++ b/docs/examples/1_plotting/tutorial_plotting_04_skeletons.py
@@ -5,7 +5,7 @@
 In this example we will demonstrate various ways to fine-tune plots with skeletons.
 
 By now, you should already have a basic understanding on how to plot neurons in {{ navis }} (2d vs 3d plots, the various
-backends and plotting methods, etc.) - if not, check out the [plotting tutorial](../plot_00_plotting_intro).
+backends and plotting methods, etc.) - if not, check out the [plotting tutorial](../tutorial_plotting_00_intro).
 
 We will focus on how to finetune [`plot2d`][navis.plot2d] plots because `matplotlib` is much more flexible than the
 [`plot3d`][navis.plot3d] backends when it comes to rendering lines. That said: some of the things we show here will also
diff --git a/docs/examples/1_plotting/plot_05_plotting_depth.py b/docs/examples/1_plotting/tutorial_plotting_05_depth.py
similarity index 100%
rename from docs/examples/1_plotting/plot_05_plotting_depth.py
rename to docs/examples/1_plotting/tutorial_plotting_05_depth.py
diff --git a/docs/examples/1_plotting/tutorial_plotting_06_cortex.py b/docs/examples/1_plotting/tutorial_plotting_06_cortex.py
new file mode 100644
index 00000000..3a5adbaf
--- /dev/null
+++ b/docs/examples/1_plotting/tutorial_plotting_06_cortex.py
@@ -0,0 +1,255 @@
+"""
+Cortical Neurons
+================
+
+This tutorial demonstrates how to plot cortical neurons.
+
+
+In this exercise we will visualize morphological data from ["Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells"](https://www.cell.com/cell/pdf/S0092-8674(20)31254-X.pdf)
+by Gouwens, Sorensen _et al._, Cell (2020). Specifically, we will re-create a plot similar to their
+[Figure 4A](https://www.cell.com/cms/10.1016/j.cell.2020.09.057/asset/c684cc3f-ee17-4a36-98c9-e464a7ce8063/main.assets/gr4_lrg.jpg).
+
+For brevity, we will use some fixed cell IDs and properties from the dataset. These were taken from the
+[`20200711_patchseq_metadata_mouse.csv`](https://brainmapportal-live-4cc80a57cd6e400d854-f7fdcae.divio-media.net/filer_public/5e/2a/5e2a5936-61da-4e09-b6da-74ab97ce1b02/20200711_patchseq_metadata_mouse.csv)
+file provided alongside the supplementary material of the paper:
+
+"""
+
+# %%
+
+# The cell IDs we will use (it's the first 5 in the meta data file)
+ids = [601506507, 601790961, 601803754, 601808698, 601810307]
+
+# The normalized soma depths for these cells (also from the meta data file)
+soma_depths = [0.36101451, 0.62182935, 0.16423996, 0.48303029, 0.2956563]
+
+# %%
+# ## Part I: Loading and Aligning Neurons
+#
+# First we need to load the neurons. Here, we will take them straight from their FTP server but you can of course download them first
+# and load then from disk!
+
+import navis
+
+nl = navis.read_swc(
+    "ftp://download.brainlib.org:8811/biccn/zeng/pseq/morph/200526/",
+    limit=[f"{i}_transformed.swc" for i in ids],  #  Load only the files we need
+    fmt="{name,id:int}_transformed.swc",  # Parse the name and id from the file name
+)
+
+# %%
+# To make our lives a bit easier, we will attach the soma depth to the neurons as metadata:
+
+nl.set_neuron_attributes(
+    soma_depths,
+    name="cell_soma_normalized_depth",
+    register=True
+    )
+
+nl
+
+# %%
+# Next, we need to align the neurons according to their soma depth! The normalized `cell_soma_normalized_depth` should
+# map to a physical range of `0` to `922.5861720311` microns.
+#
+# Let's demo with one neuron before we run this for all neurons:
+
+# Grab one of the neurons
+n = nl[0]
+
+# This is the normalized soma depth:
+print(f"Normalized soma depth: {n.cell_soma_normalized_depth}")
+
+# %%
+# The physical soma depth is simply the normalized depth multiplied by the total depth of the cortex.
+# Note that we're positioning from the bottom - i.e. 922.586 will be at the surface and 0 at the bottom!
+# This is to make our lifes easier when it comes to plotting: the origin in `matplotlib`
+# figures is in the bottom left corner.
+
+phys_y = (1 - n.cell_soma_normalized_depth) * 922.5861720311
+print(f"Physical soma depth: {phys_y}")
+
+# Current soma
+print(f"Current soma coordinates: {n.soma_pos[0]}")
+
+# %%
+# We will now offset the neuron such that the soma is at `(0, 589.519, 0)`:
+
+# %%
+offset = [0, phys_y, 0] - n.soma_pos[0]
+offset
+
+# %%
+# Moving or scaling neurons in {{ navis }} is super straight forward: adding, subtracting, dividing or multiplying neurons by a number or an
+# `[x, y, z]` vector will change their coordinates:
+
+# Move the neuron to the new centered position
+n += offset
+
+# Check the that the soma is now in the correct position
+n.soma_pos[0]
+
+# %%
+# That looks good! Let's do it for all neurons:
+
+# %%
+for n in nl:
+    phys_y = (1 - n.cell_soma_normalized_depth) * 922.5861720311
+    offset = [0, phys_y, 0] - n.soma_pos[0]
+    n += offset
+
+# %%
+# Check that all soma positions are correct:
+nl.soma_pos.reshape(-1, 3)
+
+# %% [markdown]
+# ## Part II: Plotting
+#
+# Now that we have loaded and aligned the neurons, let's recreate a plot similar to those in Figure 4A:
+
+def plot_neurons(to_plot, color="purple", axon_color="magenta", offset=500):
+    """Plot all neurons of a given transcriptomic type.
+
+    Parameters
+    ----------
+    neurons : NeuronList
+        The aligned neurons to plot.
+    color : str
+        The color of the dendrites.
+    axon_color : str
+        The color of the axon.
+    offset : int
+        The offset between neurons along the x-axis.
+
+    Returns
+    -------
+    fig, ax
+        The matplotlib figure and axis.
+
+    """
+    # Offset the neurons along the x-axis so that they don't overlap
+    to_plot = [n + [offset * i, 0, 0] for i, n in enumerate(to_plot)]
+
+    # The SWC files for this dataset include a `label` column which
+    # indicates the compartment type:
+    # 1 = soma
+    # 2 = axon
+    # 3 = dendrites
+    # We will use this `label` to color the neurons' compartments.
+
+    # Here we define a color palette for the compartments:
+    compartment_palette = {1: color, 2: axon_color, 3: color}
+
+    # Plot the neuron
+    fig, ax = navis.plot2d(
+        to_plot,
+        radius=False,
+        lw=1.5,
+        soma=dict(
+            fc="black",  # soma fill color
+            ec="white",  # highlight the soma with a white outline
+            radius=10,   # override the default soma radius
+        ),
+        color_by="label",  # color by `label` column in node table
+        palette=compartment_palette,
+        figsize=(
+            len(to_plot) * 2,
+            10,
+        ),  # scale the figure size with the number of neurons
+        method="2d",
+    )
+
+    # Add the layer boundaries (top bound for each layer in microns)
+    layer_bounds = {
+        "L1": 0,
+        "L2/3": 115.1112491335,
+        "L4": 333.4658190171,
+        "L5": 453.6227158132,
+        "L6": 687.6482650269,
+        "L6b": 883.1308910545,
+    }
+
+    for layer, y in layer_bounds.items():
+        y = 922.5861720311 - y  # flip the y-axis
+        # Add a dashed line
+        ax.axhline(y, color="gray", ls="--", lw=1)
+        # Add the layer name
+        ax.text(-300, y - 25, layer, color="gray", va="center", size=10)
+    # Add the bottom bound
+    ax.axhline(0, color="gray", ls="--", lw=1)
+
+    # Set the axis y limits according to the layers
+    ax.set_ylim(-10, 930)
+
+    # Hide axes
+    ax.axis("off")
+
+    return fig, ax
+
+
+fig, ax = plot_neurons(nl)
+
+# %% [markdown]
+# Next, let's calculate the distribution of cable lengths:
+#
+# We're going to be cheap here and simply generate a histogram over the node positions.
+# To make this representative, we should make sure that the number of nodes per unit of cable
+# is homogeneous across neurons. For that we will resample the neurons:
+print(
+    f"Sampling rate (nodes per micron of cable) before resampling: {nl.sampling_resolution.mean():.2f}"
+)
+
+# Resample to 2 nodes per micron
+resampled = navis.resample_skeleton(
+    nl,
+    resample_to=0.5,
+    map_columns="label",  # make sure label column is carried over
+)
+
+print(
+    f"Sampling rate (nodes per micron of cable) after resampling: {resampled.sampling_resolution.mean():.2f}"
+)
+
+# %%
+# Get the combined nodes table:
+nodes = resampled.nodes
+nodes.head()
+
+# %%
+# Now we can plot the distribution of cable lengths for the neurons of the type we're interested in:
+
+import seaborn as sns
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+
+# Plot the neurons using the function we defined earlier
+fig, ax = plot_neurons(nl)
+
+# Add a new axis to the right of the main plot
+divider = make_axes_locatable(ax)
+ax_hist = divider.append_axes("right", size=0.75, pad=0.05)
+
+# Add histograms
+# For axon:
+sns.kdeplot(
+    data=nodes[nodes.label == 2], y="y", ax=ax_hist, color="purple", linewidth=1.5
+)
+# For the rest:
+sns.kdeplot(
+    data=nodes[nodes.label != 2], y="y", ax=ax_hist, color="magenta", linewidth=1.5
+)
+
+# Add soma positions
+soma_pos = nl.soma_pos.reshape(-1, 3)
+ax_hist.scatter([0] * len(soma_pos), soma_pos[:, 1], color="black", s=10, clip_on=False)
+
+# Set same axis limits as the main plot
+ax_hist.set_ylim(-10, 930)
+
+# Hide axes
+ax_hist.set_axis_off()
+
+# %%
+# ## Acknowledgements
+#
+# We thank Staci Sorensen and Casey Schneider-Mizell from the Allen Institute for Brain Science
+# for helping with extra information and data for this tutorial!
\ No newline at end of file
diff --git a/docs/examples/1_plotting/plot_07_plotting_xkcd.py b/docs/examples/1_plotting/tutorial_plotting_07_xkcd.py
similarity index 100%
rename from docs/examples/1_plotting/plot_07_plotting_xkcd.py
rename to docs/examples/1_plotting/tutorial_plotting_07_xkcd.py
diff --git a/docs/examples/2_morpho/plot_00_morpho_manipulate.py b/docs/examples/2_morpho/tutorial_morpho_00_manipulate.py
similarity index 99%
rename from docs/examples/2_morpho/plot_00_morpho_manipulate.py
rename to docs/examples/2_morpho/tutorial_morpho_00_manipulate.py
index bd8c73e5..c83420ae 100644
--- a/docs/examples/2_morpho/plot_00_morpho_manipulate.py
+++ b/docs/examples/2_morpho/tutorial_morpho_00_manipulate.py
@@ -351,5 +351,5 @@
 # About half the presynapses are in the LH (most of the rest will be in the MB calyx). The large majority of postsynapses are
 # outside the LH in the antennal lobe where this neuron has its dendrites.
 #
-# That's it for now! Please see the [NBLAST tutorial](../../05_nblast/plot_00_nblast_intro.py) for morphological comparisons using NBLAST and the
+# That's it for now! Please see the [NBLAST tutorial](../../05_nblast/tutorial_nblast_00_intro.py) for morphological comparisons using NBLAST and the
 # [API reference](../../../api.md#neuron-morphology) for a full list of morphology-related functions.
diff --git a/docs/examples/2_morpho/plot_01_morpho_analyze.py b/docs/examples/2_morpho/tutorial_morpho_01_analyze.py
similarity index 97%
rename from docs/examples/2_morpho/plot_01_morpho_analyze.py
rename to docs/examples/2_morpho/tutorial_morpho_01_analyze.py
index 1c616d74..f61c904b 100644
--- a/docs/examples/2_morpho/plot_01_morpho_analyze.py
+++ b/docs/examples/2_morpho/tutorial_morpho_01_analyze.py
@@ -121,7 +121,7 @@
 # %%
 # ## Sholl Analysis
 #
-# For an example of a Sholl analyses, check out the [MICrONS tutorial](../4_remote/plot_02_remote_microns).
+# For an example of a Sholl analyses, check out the [MICrONS tutorial](../4_remote/tutorial_remote_02_microns).
 #
 # ## Geodesic Distances
 #
@@ -245,5 +245,5 @@
 # %%
 # As you can see in the heatmap, the dendrites and the axon nicely separate.
 #
-# That's it for now! Please see the [NBLAST tutorial](../../5_nblast/plot_00_nblast_intro) for morphological comparisons using NBLAST and
-# the :[API reference](../../../api.md) for a full list of morphology-related functions.
+# That's it for now! Please see the [NBLAST tutorial](../../5_nblast/tutorial_nblast_00_intro) for morphological comparisons using NBLAST and
+# the [API reference](../../../api.md) for a full list of morphology-related functions.
diff --git a/docs/examples/3_interfaces/plot_00_interfaces_neuron.py b/docs/examples/3_interfaces/tutorial_interfaces_00_neuron.py
similarity index 100%
rename from docs/examples/3_interfaces/plot_00_interfaces_neuron.py
rename to docs/examples/3_interfaces/tutorial_interfaces_00_neuron.py
diff --git a/docs/examples/3_interfaces/plot_01_interfaces_neuron2.py b/docs/examples/3_interfaces/tutorial_interfaces_01_neuron2.py
similarity index 98%
rename from docs/examples/3_interfaces/plot_01_interfaces_neuron2.py
rename to docs/examples/3_interfaces/tutorial_interfaces_01_neuron2.py
index d7e52b2f..ba24d546 100644
--- a/docs/examples/3_interfaces/plot_01_interfaces_neuron2.py
+++ b/docs/examples/3_interfaces/tutorial_interfaces_01_neuron2.py
@@ -4,7 +4,7 @@
 
 In this tutorial you will learn to visualize a compartment neuron model.
 
-We will jump right in, so please make sure to have a look at the [introductory NEURON tutorial](../plot_00_interfaces_neuron)
+We will jump right in, so please make sure to have a look at the [introductory NEURON tutorial](../tutorial_interfaces_00_neuron)
 first.
 
 ## Setup the model
diff --git a/docs/examples/3_interfaces/plot_02_interfaces_blender.py b/docs/examples/3_interfaces/tutorial_interfaces_02_blender.py
similarity index 100%
rename from docs/examples/3_interfaces/plot_02_interfaces_blender.py
rename to docs/examples/3_interfaces/tutorial_interfaces_02_blender.py
diff --git a/docs/examples/4_remote/plot_00_remote_neuprint.py b/docs/examples/4_remote/tutorial_remote_00_neuprint.py
similarity index 100%
rename from docs/examples/4_remote/plot_00_remote_neuprint.py
rename to docs/examples/4_remote/tutorial_remote_00_neuprint.py
diff --git a/docs/examples/4_remote/plot_01_remote_cloudvolume.py b/docs/examples/4_remote/tutorial_remote_01_cloudvolume.py
similarity index 97%
rename from docs/examples/4_remote/plot_01_remote_cloudvolume.py
rename to docs/examples/4_remote/tutorial_remote_01_cloudvolume.py
index 84297ab2..d2af0ec1 100644
--- a/docs/examples/4_remote/plot_01_remote_cloudvolume.py
+++ b/docs/examples/4_remote/tutorial_remote_01_cloudvolume.py
@@ -15,7 +15,7 @@
    will to register and apply for access. Check out [FAFBseg](https://fafbseg-py.readthedocs.io) for a fairly mature interface built on
    top of {{ navis }}.
 2. [Google's flood-filling segmentation](http://fafb-ffn1.storage.googleapis.com/landing.html) of an entire *Drosophila* brain.
-3. The Allen Institute's [MICrONs datasets](https://www.microns-explorer.org/). We have a separate [tutorial](../plot_02_remote_microns) on this!
+3. The Allen Institute's [MICrONs datasets](https://www.microns-explorer.org/). We have a separate [tutorial](../tutorial_remote_02_microns) on this!
 4. The Janelia [hemibrain connectome](https://neuprint.janelia.org).
 
 `CloudVolume` supports the backends/data formats of these and many up-and-coming datasets. You can use it to query the segmentation directly,
diff --git a/docs/examples/4_remote/plot_02_remote_microns.py b/docs/examples/4_remote/tutorial_remote_02_microns.py
similarity index 99%
rename from docs/examples/4_remote/plot_02_remote_microns.py
rename to docs/examples/4_remote/tutorial_remote_02_microns.py
index ed3f55a5..ddc457f2 100644
--- a/docs/examples/4_remote/plot_02_remote_microns.py
+++ b/docs/examples/4_remote/tutorial_remote_02_microns.py
@@ -182,7 +182,7 @@
 # ## Render Videos
 #
 # Beautiful data like the MICrONS datasets lend themselves to visualizations. For making high quality videos (and renderings)
-# I recommend you check out the tutorial on navis' [Blender interface](../../../gallery/3_interfaces/plot_01_interfaces_blender).
+# I recommend you check out the tutorial on navis' [Blender interface](../../../gallery/3_interfaces/tutorial_interfaces_02_blender).
 # Here's a little taster:
 #
 #  <iframe width="560" height="315" src="https://www.youtube.com/embed/wl3sFG7WQJc" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
diff --git a/docs/examples/4_remote/plot_03_remote_insect_db.py b/docs/examples/4_remote/tutorial_remote_03_insect_db.py
similarity index 100%
rename from docs/examples/4_remote/plot_03_remote_insect_db.py
rename to docs/examples/4_remote/tutorial_remote_03_insect_db.py
diff --git a/docs/examples/5_nblast/plot_00_nblast_intro.py b/docs/examples/5_nblast/tutorial_nblast_00_intro.py
similarity index 99%
rename from docs/examples/5_nblast/plot_00_nblast_intro.py
rename to docs/examples/5_nblast/tutorial_nblast_00_intro.py
index 55eef2ab..984fefd3 100644
--- a/docs/examples/5_nblast/plot_00_nblast_intro.py
+++ b/docs/examples/5_nblast/tutorial_nblast_00_intro.py
@@ -33,7 +33,7 @@
     Importantly, these matrices were created using _Drosophila_ neurons from the [FlyCircuit](http://flycircuit.tw/) light-level dataset which
     are in microns. Consequently, you should make sure your neurons are also in micrometer units for NBLAST! If you are working on non-insect
     neurons you might have to play around with the scaling to improve results. Alternatively, you can also produce your own scoring function
-    (see [this tutorial](../plot_03_nblast_smat)).
+    (see [this tutorial](../tutorial_nblast_03_smat)).
 
 3. Produce a per-pair score:
 
@@ -205,7 +205,7 @@
 # Let's try something more elaborate and pull some hemibrain neurons from [neuPrint](https://neuprint.janelia.org/). For this you need to install the
 # `neuprint-python` package (`pip3 install neuprint-python`), make a neuPrint account and generate/set an authentication token. Sounds complicated
 # but is all pretty painless - see the [neuPrint documentation](https://connectome-neuprint.github.io/neuprint-python/docs/quickstart.html) for details.
-# There is also a separate {{ navis }} tutorial on neuprint [here](../4_remote/plot_00_remote_neuprint).
+# There is also a separate {{ navis }} tutorial on neuprint [here](../4_remote/tutorial_remote_00_neuprint).
 #
 # Once that's done we can get started by importing the neuPrint interface from {{ navis }}:
 
diff --git a/docs/examples/5_nblast/plot_03_nblast_smat.py b/docs/examples/5_nblast/tutorial_nblast_03_smat.py
similarity index 100%
rename from docs/examples/5_nblast/plot_03_nblast_smat.py
rename to docs/examples/5_nblast/tutorial_nblast_03_smat.py
diff --git a/docs/examples/5_nblast/zzz_no_plot_01_nblast_flycircuit.py b/docs/examples/5_nblast/zzz_tutorial_nblast_01_flycircuit.py
similarity index 100%
rename from docs/examples/5_nblast/zzz_no_plot_01_nblast_flycircuit.py
rename to docs/examples/5_nblast/zzz_tutorial_nblast_01_flycircuit.py
diff --git a/docs/examples/5_nblast/zzz_no_plot_02_nblast_hemibrain.py b/docs/examples/5_nblast/zzz_tutorial_nblast_02_hemibrain.py
similarity index 100%
rename from docs/examples/5_nblast/zzz_no_plot_02_nblast_hemibrain.py
rename to docs/examples/5_nblast/zzz_tutorial_nblast_02_hemibrain.py
diff --git a/docs/examples/6_misc/plot_00_misc_multiprocess.py b/docs/examples/6_misc/tutorial_misc_00_multiprocess.py
similarity index 100%
rename from docs/examples/6_misc/plot_00_misc_multiprocess.py
rename to docs/examples/6_misc/tutorial_misc_00_multiprocess.py
diff --git a/docs/examples/6_misc/plot_01_transforms.py b/docs/examples/6_misc/tutorial_misc_01_transforms.py
similarity index 100%
rename from docs/examples/6_misc/plot_01_transforms.py
rename to docs/examples/6_misc/tutorial_misc_01_transforms.py
diff --git a/docs/examples/plot_00_basic_neurons.py b/docs/examples/tutorial_basic_00_basics.py
similarity index 95%
rename from docs/examples/plot_00_basic_neurons.py
rename to docs/examples/tutorial_basic_00_basics.py
index 3e751ec2..231b01ec 100644
--- a/docs/examples/plot_00_basic_neurons.py
+++ b/docs/examples/tutorial_basic_00_basics.py
@@ -121,14 +121,14 @@
 #
 #     Find out more about the different neuron types in {{ navis }}.
 #
-#     [:octicons-arrow-right-24: Neuron types tutorial](../plot_01_neurons_intro)
+#     [:octicons-arrow-right-24: Neuron types tutorial](../tutorial_basic_01_neurons)
 #
 # -   :fontawesome-solid-list-ul:{ .lg .middle } __Lists of Neurons__
 #     ---
 #
 #     Check out the guide on lists of neurons.
 #
-#     [:octicons-arrow-right-24: NeuronLists tutorial](../plot_02_neuronlists_intro)
+#     [:octicons-arrow-right-24: NeuronLists tutorial](../tutorial_basic_02_neuronlists)
 #
 # -   :octicons-file-directory-symlink-16:{ .lg .middle } __Neuron I/O__
 #     ---
diff --git a/docs/examples/plot_01_neurons_intro.py b/docs/examples/tutorial_basic_01_neurons.py
similarity index 99%
rename from docs/examples/plot_01_neurons_intro.py
rename to docs/examples/tutorial_basic_01_neurons.py
index 9f2a6e9f..6af9139b 100644
--- a/docs/examples/plot_01_neurons_intro.py
+++ b/docs/examples/tutorial_basic_01_neurons.py
@@ -535,7 +535,7 @@
 #
 #     Check out the guide on lists of neurons.
 #
-#     [:octicons-arrow-right-24: NeuronLists tutorial](../plot_02_neuronlists_intro)
+#     [:octicons-arrow-right-24: NeuronLists tutorial](../tutorial_basic_02_neuronlists)
 #
 # -   :octicons-file-directory-symlink-16:{ .lg .middle } __Neuron I/O__
 #
diff --git a/docs/examples/plot_02_neuronlists_intro.py b/docs/examples/tutorial_basic_02_neuronlists.py
similarity index 99%
rename from docs/examples/plot_02_neuronlists_intro.py
rename to docs/examples/tutorial_basic_02_neuronlists.py
index 440a16ba..43497e7b 100644
--- a/docs/examples/plot_02_neuronlists_intro.py
+++ b/docs/examples/tutorial_basic_02_neuronlists.py
@@ -5,7 +5,7 @@
 This tutorial will show you how to use NeuronLists to efficiently work with many neurons at a time.
 
 !!! note
-    If you haven't please check out the [neuron types tutorial](../plot_01_neurons_intro) first.
+    If you haven't please check out the [neuron types tutorial](../tutorial_basic_01_neurons) first.
 
 {{ navis }} will typically collect multiple neurons into a [`navis.NeuronList`][] as container.
 This container behaves like a mix of lists, numpy arrays and pandas dataframes, and allows you
diff --git a/docs/index.md b/docs/index.md
index bc1752ff..3f103040 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -28,7 +28,7 @@ morphology. It stands on the shoulders of the excellent
 
     ---
 
-    Support for all kinds of [neuron types](generated/gallery/plot_01_neurons_intro): skeletons, meshes, dotprops and images.
+    Support for all kinds of [neuron types](generated/gallery/tutorial_basic_01_neurons): skeletons, meshes, dotprops and images.
 
 -   :material-eye:{ .lg .middle } __Exploration__
 
@@ -42,7 +42,7 @@ morphology. It stands on the shoulders of the excellent
     ---
 
     Calculate Strahler indices, cable length, volume, tortuosity, NBLAST
-    and many other [morphometrics](generated/gallery/2_morpho/plot_01_morpho_analyze).
+    and many other [morphometrics](generated/gallery/2_morpho/tutorial_morpho_01_analyze).
 
 -   :fontawesome-solid-brush:{ .lg .middle } __Visualization__
 
@@ -62,19 +62,19 @@ morphology. It stands on the shoulders of the excellent
     ---
 
     Uses compiled Rust code under-the-hood and
-    out-of-the-box support for [multiprocessing](generated/gallery/6_misc/plot_00_misc_multiprocess).
+    out-of-the-box support for [multiprocessing](generated/gallery/6_misc/tutorial_misc_00_multiprocess).
 
 -   :material-lightbulb-group:{ .lg .middle } __Clustering__
 
     ---
 
-    Cluster your neurons by e.g. morphology using [NBLAST](generated/gallery/5_nblast/plot_00_nblast_intro).
+    Cluster your neurons by e.g. morphology using [NBLAST](generated/gallery/5_nblast/tutorial_nblast_00_intro).
 
 -   :material-move-resize:{ .lg .middle } __Transforms__
 
     ---
 
-    Fully featured [transform system](generated/gallery/5_transforms/plot_00_transforms) to move neurons between brain spaces.
+    Fully featured [transform system](generated/gallery/6_misc/tutorial_misc_01_transforms) to move neurons between brain spaces.
     We support CMTK, Elastix, landmark-based transforms and more!
 
 -   :octicons-file-directory-symlink-24:{ .lg .middle } __Import/Export__
@@ -89,16 +89,16 @@ morphology. It stands on the shoulders of the excellent
     ---
 
     Load neurons straight from Allen's
-    [MICrONS](generated/gallery/4_remote/plot_02_remote_microns) datasets,
-    [neuromorpho](http://neuromorpho.org), [neuPrint](generated/gallery/4_remote/plot_00_remote_neuprint)
+    [MICrONS](generated/gallery/4_remote/tutorial_remote_02_microns) datasets,
+    [neuromorpho](http://neuromorpho.org), [neuPrint](generated/gallery/4_remote/tutorial_remote_00_neuprint)
     or any NeuroGlancer source.
 
 -   :material-connection:{ .lg .middle } __Interfaces__
 
     ---
 
-    Load neurons into [Blender 3D](generated/gallery/3_interfaces/plot_01_interfaces_blender), simulate neurons and networks using
-    [NEURON](generated/gallery/3_interfaces/plot_00_interfaces_neuron), or use the R natverse library via `rpy2`.
+    Load neurons into [Blender 3D](generated/gallery/3_interfaces/tutorial_interfaces_02_blender), simulate neurons and networks using
+    [NEURON](generated/gallery/3_interfaces/tutorial_interfaces_00_neuron), or use the R natverse library via `rpy2`.
 
 -   :material-google-circles-extended:{ .lg .middle } __Extensible__
 
diff --git a/docs/quickstart.md b/docs/quickstart.md
index 6e504b0d..93950dea 100644
--- a/docs/quickstart.md
+++ b/docs/quickstart.md
@@ -34,7 +34,7 @@ print(n)  # markdown-exec: hide
     [I/O Tutorials](../generated/gallery#import-export) to learn more!
 
 {{ navis }} represents neurons as [`navis.TreeNeuron`][], [`navis.MeshNeuron`][], [`navis.VoxelNeuron`][] or
-[`navis.Dotprops`][] - see the tutorial on [Neuron Types](../generated/gallery/plot_01_neurons_intro/)
+[`navis.Dotprops`][] - see the tutorial on [Neuron Types](../generated/gallery/tutorial_basic_01_neurons/)
 for details.
 
 In above code we asked for a skeleton, so the neuron returned is a [`TreeNeuron`][navis.TreeNeuron].
@@ -113,7 +113,7 @@ print(buffer.getvalue()) # markdown-exec: hide
 plt.close() # markdown-exec: hide
 ```
 
-See the [Lists of Neurons](../generated/gallery/plot_02_neuronlists_intro/)
+See the [Lists of Neurons](../generated/gallery/tutorial_basic_02_neuronlists/)
 tutorial for more information.
 
 ## Methods vs Functions
@@ -189,14 +189,14 @@ Note that most functions have helpful `Examples`!
 
     Find out more about the different neuron types in {{ navis }}.
 
-    [:octicons-arrow-right-24: Neuron types tutorial](../generated/gallery/plot_01_neurons_intro)
+    [:octicons-arrow-right-24: Neuron types tutorial](../generated/gallery/tutorial_basic_01_neurons)
 
 -   :material-cube:{ .lg .middle } __Lists of Neurons__
     ---
 
     Check out the guide on lists of neurons.
 
-    [:octicons-arrow-right-24: NeuronLists tutorial](../generated/gallery/plot_02_neuronlists_intro)
+    [:octicons-arrow-right-24: NeuronLists tutorial](../generated/gallery/tutorial_basic_02_neuronlists)
 
 -   :octicons-file-directory-symlink-16:{ .lg .middle } __Neuron I/O__
 
diff --git a/mkdocs.yml b/mkdocs.yml
index 018d3fd0..0f20342c 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -134,6 +134,7 @@ plugins:
               - "^__init__$"
   - glightbox
   - gallery:
+      filename_pattern: "/tutorial_"
       examples_dirs: docs/examples          # path to your example scripts
       gallery_dirs: docs/generated/gallery  # where to save generated gallery
       conf_script: docs/gallery_conf.py      # configuration script
diff --git a/navis/morpho/ivscc.py b/navis/morpho/ivscc.py
index 44984b6e..605da567 100644
--- a/navis/morpho/ivscc.py
+++ b/navis/morpho/ivscc.py
@@ -333,7 +333,7 @@ def ivscc_features(
     Parameters
     ----------
     x :                     TreeNeuron | NeuronList
-                            Neuron(s) to calculate IVCSS for.
+                            Neuron(s) to calculate IVSCC for.
     features :              Sequence[Features], optional
                             Provide specific features to calculate.
                             Must be subclasses of `BasicFeatures`.
@@ -347,8 +347,8 @@ def ivscc_features(
 
     Returns
     -------
-    ivcss :     pd.DataFrame
-                IVCSS features for the neuron(s).
+    ivscc :                 pd.DataFrame
+                            IVSCC features for the neuron(s).
 
     """
 
diff --git a/navis/plotting/d.py b/navis/plotting/d.py
index 6638bf79..2e872733 100644
--- a/navis/plotting/d.py
+++ b/navis/plotting/d.py
@@ -87,7 +87,7 @@ def plot1d(x: 'core.NeuronObject',
 
     >>> plt.close('all')
 
-    See the [`flat plotting tutorial`](generated/gallery/plotting/plot_02_plotting_1d/)
+    See the [`flat plotting tutorial`](generated/gallery/1_plotting/tutorial_plotting_02_1d/)
     for more examples.
 
     """
diff --git a/navis/plotting/dd.py b/navis/plotting/dd.py
index 14cd6e36..7d6e3b9f 100644
--- a/navis/plotting/dd.py
+++ b/navis/plotting/dd.py
@@ -344,7 +344,7 @@ def plot2d(
     >>> fig, ax = navis.plot2d(nl, method='3d', depth_coloring=True, view=('x', '-z'))
     >>> plt.show() # doctest: +SKIP
 
-    See the [plotting intro](../../../generated/gallery/1_plotting/plot_00_plotting_intro)
+    See the [plotting intro](../../generated/gallery/1_plotting/tutorial_plotting_00_intro)
     for more examples.
 
     See Also
diff --git a/navis/plotting/ddd.py b/navis/plotting/ddd.py
index 57269807..53f5f2a5 100644
--- a/navis/plotting/ddd.py
+++ b/navis/plotting/ddd.py
@@ -345,7 +345,7 @@ def plot3d(
     >>> # Clear viewer (works only with octarine and vispy)
     >>> v = navis.plot3d(nl, clear=True)
 
-    See the [plotting intro](../../../generated/gallery/1_plotting/plot_00_plotting_intro)
+    See the [plotting intro](../../generated/gallery/1_plotting/tutorial_plotting_00_intro)
     for even more examples.
 
     """
diff --git a/navis/plotting/flat.py b/navis/plotting/flat.py
index 15a10222..7ce0d39f 100644
--- a/navis/plotting/flat.py
+++ b/navis/plotting/flat.py
@@ -124,8 +124,8 @@ def plot_flat(
 
     >>> plt.close('all')
 
-    See the [plotting intro](../../../generated/gallery/1_plotting/plot_00_plotting_intro)
-    and the [neuron topology tutorial](../../../generated/gallery/1_plotting/plot_03_plotting_dend)
+    See the [plotting intro](../../generated/gallery/1_plotting/tutorial_plotting_00_intro)
+    and the [neuron topology tutorial](../../generated/gallery/1_plotting/tutorial_plotting_03_dend)
     for more examples.
 
     """
diff --git a/tests/test_tutorials.py b/tests/test_tutorials.py
index 80b232e9..3954feec 100644
--- a/tests/test_tutorials.py
+++ b/tests/test_tutorials.py
@@ -21,7 +21,7 @@
 from pathlib import Path
 from contextlib import contextmanager
 
-SKIP = ["zzz_no_plot_01_nblast_flycircuit.py", "zzz_no_plot_02_nblast_hemibrain.py"]
+SKIP = ["zzz_tutorial_nblast_01_flycircuit.py", "zzz_tutorial_nblast_02_hemibrain.py"]
 
 
 @contextmanager