diff --git a/arborio/swcio.cpp b/arborio/swcio.cpp
index abb7296721053043e9fc738b66ffec120532aa79..69fa7833feb89dad57a60afce8bbafda56be76b5 100644
--- a/arborio/swcio.cpp
+++ b/arborio/swcio.cpp
@@ -303,7 +303,7 @@ arb::morphology load_swc_neuron(const swc_data& data) {
{soma_prox.x, soma_prox.y + soma_prox.r, soma_prox.z, soma_prox.r}, soma_tag);
return tree;
}
- // Model the soma as a 2 cylinders with total length=2*radius, extended along the y axis, centered at the sample
+ // Model the soma as a 2 cylinders with total length=2*radius, extended along the y axis, centred at the sample
auto p = tree.append(arb::mnpos, {soma_prox.x, soma_prox.y - soma_prox.r, soma_prox.z, soma_prox.r},
{soma_prox.x, soma_prox.y, soma_prox.z, soma_prox.r}, soma_tag);
tree.append(p, {soma_prox.x, soma_prox.y, soma_prox.z, soma_prox.r},
@@ -459,7 +459,7 @@ arb::morphology load_swc_allen(const swc_data& data, bool no_gaps) {
if (r.tag > 4) throw swc_unsupported_tag{r.id};
}
- // Translate the morphology so that the soma is centered at the origin (0,0,0)
+ // Translate the morphology so that the soma is centred at the origin (0,0,0)
arb::mpoint sloc{records[0].x, records[0].y, records[0].z, records[0].r};
for (auto& r: records) {
r.x -= sloc.x;
diff --git a/doc/concepts/labels.rst b/doc/concepts/labels.rst
index 62acfb136a76eba7e2e27c2d005b9b71afd3d066..cd6a394f905ba696c0ec95a7791fffd73c8774ae 100644
--- a/doc/concepts/labels.rst
+++ b/doc/concepts/labels.rst
@@ -53,7 +53,7 @@ Label types
Possible locsets might refer to:
-* The center of the soma.
+* The centre of the soma.
* The locations of inhibitory synapses.
* The tips of the dendritic tree.
diff --git a/doc/concepts/morphology.rst b/doc/concepts/morphology.rst
index b4b53a19978e8fc1290d562080a89f5e6f88f95f..a72f053e41fd71753a243de1d1840a776dc59117 100644
--- a/doc/concepts/morphology.rst
+++ b/doc/concepts/morphology.rst
@@ -32,16 +32,16 @@ proper definition for a morphology.
:align: center
**Field**, **Type**, **Description**
- ``x``, real, x coordinate of center of cable (μm).
- ``y``, real, y coordinate of center of cable (μm).
- ``z``, real, z coordinate of center of cable (μm).
+ ``x``, real, x coordinate of centre of cable (μm).
+ ``y``, real, y coordinate of centre of cable (μm).
+ ``z``, real, z coordinate of centre of cable (μm).
``radius``, real, cross sectional radius of cable (μm).
.. glossary::
segment
msegment
- A segment is a frustum (cylinder or truncated cone), with the center and radius at each
+ A segment is a frustum (cylinder or truncated cone), with the centre and radius at each
end defined by a pair of :term:`points <mpoint>`. In other words, in Arbor the radius between two points is interpolated
linearly, resulting in either a cylinder (equal radii) or truncated cone (differing radii),
centred at the line through the pair of points.
@@ -51,8 +51,8 @@ proper definition for a morphology.
:align: center
**Field**, **Type**, **Description**
- ``prox``, :term:`mpoint`, the center and radius of the proximal end.
- ``dist``, :term:`mpoint`, the center and radius of the distal end.
+ ``prox``, :term:`mpoint`, the centre and radius of the proximal end.
+ ``dist``, :term:`mpoint`, the centre and radius of the distal end.
``tag``, integer, ":term:`tag` meta-data, can be used to classify segments of the same kind (ex: soma, dendrite, but also arbitrary use-defined groups"
.. figure:: ../gen-images/term_segments.svg
@@ -677,7 +677,7 @@ Samples with the soma as a parent start new segments, that connect to the distal
or to the proximal end of the soma if they are axons or apical dendrites. Only axons, dendrites and apical dendrites
(tags 2, 3 and 4 respectively) are allowed in this interpretation, in addition to the spherical soma.
-Finally the Allen institute interpretation of SWC files centers the morphology around the soma at the origin (0, 0, 0)
+Finally the Allen institute interpretation of SWC files centres the morphology around the soma at the origin (0, 0, 0)
and all samples are translated in space towards the origin.
NEURON interpretation:
diff --git a/doc/concepts/recipe.rst b/doc/concepts/recipe.rst
index 3883309f6f4817355f884973b6309eafded8b6b3..95250eedff22908b43080378e2f00538f09fc39e 100644
--- a/doc/concepts/recipe.rst
+++ b/doc/concepts/recipe.rst
@@ -100,7 +100,7 @@ runtime execution environment.
During model building, the recipe is queried first by a load balancer,
then later when building the low-level cell groups and communication network.
-The cell-centered recipe interface, whereby cell and network properties are
+The cell-centred recipe interface, whereby cell and network properties are
specified "per-cell", facilitates this.
The steps of building a simulation from a recipe are:
diff --git a/doc/math/model/formulation.tex b/doc/math/model/formulation.tex
index d3eba7a64c4bdf8ad8bcb0da402f9bde9513da3e..8db5184e38e84b3904ce9d86b03eb3ec6a69580d 100644
--- a/doc/math/model/formulation.tex
+++ b/doc/math/model/formulation.tex
@@ -275,7 +275,7 @@ Furthermore, because $\alpha_{i,j} > 0$, the linear system is diagonally dominan
\subsubsection{The Soma}
%-------------------------------------------------------------------------------
We model the soma as a sphere with a centre $\vv{x}_s$ and a radius $r_s$.
-The soma is conceptually treated as the center of the cell: the point from which all other parts of the cell branch.
+The soma is conceptually treated as the centre of the cell: the point from which all other parts of the cell branch.
It requires special treatment, because of its size relative to the radius of the dendrites and axons that branch off from it.
Though the soma is usually visualized as a sphere, it is \emph{worth noting} that Neuron models the soma as a cylinder
@@ -306,7 +306,7 @@ This effectivly of ``collapses'' the node that defines the start of dendrites at
This requires a little slight of hand when loading the cell description from file (for example a \verb!.swc! file).
In such file formats there would be 5 points used to describe the cell in \fig{fig:soma}:
\begin{itemize}
- \item 1 to describe the center of the soma.
+ \item 1 to describe the centre of the soma.
\item 2 for each dendrite: 1 describing where the dendrite is attached to the soma, and 1 for the terminal end.
\end{itemize}
However, in the mathematical formulation there are only 3 values that are solved for: the soma and one for each of the dendrites.
diff --git a/doc/python/morphology.rst b/doc/python/morphology.rst
index 1dc0d9136c10bb27b3d04924b0c700f4bbf2f4b6..ef9eabb5be25c60ffb973f76d29bb67f128db841 100644
--- a/doc/python/morphology.rst
+++ b/doc/python/morphology.rst
@@ -375,8 +375,8 @@ Cell morphology
Loads the :class:`morphology` from an SWC file according to the AllenDB and Sonata's SWC specifications.
Specifically:
- * The first sample (the root) is treated as the center of the soma.
- * The morphology is translated such that the soma is centered at (0,0,0).
+ * The first sample (the root) is treated as the centre of the soma.
+ * The morphology is translated such that the soma is centred at (0,0,0).
* The first sample has tag 1 (soma).
* All other samples have tags 2, 3 or 4 (axon, apic and dend respectively)
@@ -385,14 +385,14 @@ Cell morphology
used to enforce this requirement.
Arbor does not support modelling the soma as a sphere, so a cylinder with length
- equal to the soma diameter is used. The cylinder is centered on the origin, and
+ equal to the soma diameter is used. The cylinder is centred on the origin, and
aligned along the z axis.
Axons and apical dendrites are attached to the proximal end of the cylinder, and
dendrites to the distal end, with a gap between the start of each branch and the
end of the soma cylinder to which it is attached.
:param str filename: the name of the SWC file.
- :param bool no_gaps: enforce that distance between soma center and branches attached to soma is the soma radius.
+ :param bool no_gaps: enforce that distance between soma centre and branches attached to soma is the soma radius.
:rtype: morphology
.. py:class:: place_pwlin
diff --git a/doc/tutorial/single_cell_recipe.rst b/doc/tutorial/single_cell_recipe.rst
index dc1f7e7b7eda528b4d3a87a266da3e360c9c5ce4..b806c07a7b03551d8b7694309a404e3fec7359a7 100644
--- a/doc/tutorial/single_cell_recipe.rst
+++ b/doc/tutorial/single_cell_recipe.rst
@@ -29,16 +29,16 @@ We can immediately paste the cell description code from the
tree = arbor.segment_tree()
tree.append(arbor.mnpos, arbor.mpoint(-3, 0, 0, 3), arbor.mpoint(3, 0, 0, 3), tag=1)
- # (2) Define the soma and its center
+ # (2) Define the soma and its midpoint
labels = arbor.label_dict({'soma': '(tag 1)',
- 'center': '(location 0 0.5)'})
+ 'midpoint': '(location 0 0.5)'})
# (3) Create cell and set properties
decor = arbor.decor()
decor.set_property(Vm=-40)
decor.paint('"soma"', 'hh')
- decor.place('"center"', arbor.iclamp( 10, 2, 0.8))
- decor.place('"center"', arbor.spike_detector(-10))
+ decor.place('"midpoint"', arbor.iclamp( 10, 2, 0.8))
+ decor.place('"midpoint"', arbor.spike_detector(-10))
cell = arbor.cable_cell(tree, labels, decor)
The recipe
@@ -123,7 +123,7 @@ Step **(4.7)** returns the properties that will be applied to all cells of that
More methods can be overridden if your model requires that, see :class:`arbor.recipe` for options.
-Step **(5)** instantiates the recipe with the cable cell described earlier, and a single voltage probe located at "center".
+Step **(5)** instantiates the recipe with the cable cell described earlier, and a single voltage probe located at "midpoint".
The context and domain decomposition
------------------------------------
diff --git a/example/lfp/neuron_lfp_example.py b/example/lfp/neuron_lfp_example.py
index 1d1023ac427c3afc1688311e783f0e2388a71de1..c3db1fdada5775eb7d80b885a3b2eeb13092f679 100755
--- a/example/lfp/neuron_lfp_example.py
+++ b/example/lfp/neuron_lfp_example.py
@@ -13,7 +13,7 @@ import numpy as np
class Cell:
"""
- Cell class that handles interactions with NEURON. It finds the center position
+ Cell class that handles interactions with NEURON. It finds the centre position
of each cellular compartment (cell.xmid, cell.ymid, cell.zmid), and the transmembrane currents
cell.imem
"""
@@ -186,7 +186,7 @@ class Cell:
self.yend = yendvec
self.zend = zendvec
- # Calculates the center position of each compartment (segment)
+ # Calculates the centre position of each compartment (segment)
self.xmid = 0.5 * (self.xstart + self.xend)
self.ymid = 0.5 * (self.ystart + self.yend)
self.zmid = 0.5 * (self.zstart + self.zend)
@@ -233,7 +233,7 @@ class ExtElectrode:
Calculates 'mapping' of size (number of electrodes) * (number of cell compartments)
Extracellular potential can then be calculated as
:param cell: class containing x,y,z-positions (um) of each
- compartment (segment) center as cell.xmid, cell.ymid, cell.zmid
+ compartment (segment) centre as cell.xmid, cell.ymid, cell.zmid
"""
self.mapping = np.zeros((self.num_elecs, cell.totnsegs))
diff --git a/python/morphology.cpp b/python/morphology.cpp
index fb999543fe493d9cb5f51312cff24e2ab84afaf1..06100d9f41884b1187d07dfa162eac2330d381fb 100644
--- a/python/morphology.cpp
+++ b/python/morphology.cpp
@@ -77,7 +77,7 @@ void register_morphology(py::module& m) {
.def_readonly("y", &arb::mpoint::y, "Y coordinate [μm].")
.def_readonly("z", &arb::mpoint::z, "Z coordinate [μm].")
.def_readonly("radius", &arb::mpoint::radius,
- "Radius of cable at sample location centered at coordinates [μm].")
+ "Radius of cable at sample location centred at coordinates [μm].")
.def(py::self==py::self)
.def("__str__",
[](const arb::mpoint& p) {
@@ -281,8 +281,8 @@ void register_morphology(py::module& m) {
"filename"_a, "no_gaps"_a=false,
"Generate a morphology from an SWC file following the rules prescribed by AllenDB\n"
" and Sonata. Specifically:\n"
- "* The first sample (the root) is treated as the center of the soma.\n"
- "* The first morphology is translated such that the soma is centered at (0,0,0).\n"
+ "* The first sample (the root) is treated as the centre of the soma.\n"
+ "* The first morphology is translated such that the soma is centred at (0,0,0).\n"
"* The first sample has tag 1 (soma).\n"
"* All other samples have tags 2, 3 or 4 (axon, apic and dend respectively)\n"
"SONATA prescribes that there should be no gaps, however the models in AllenDB\n"
@@ -290,7 +290,7 @@ void register_morphology(py::module& m) {
"used to enforce this requirement.\n"
"\n"
"Arbor does not support modelling the soma as a sphere, so a cylinder with length\n"
- "equal to the soma diameter is used. The cylinder is centered on the origin, and\n"
+ "equal to the soma diameter is used. The cylinder is centred on the origin, and\n"
"aligned along the z axis.\n"
"Axons and apical dendrites are attached to the proximal end of the cylinder, and\n"
"dendrites to the distal end, with a gap between the start of each branch and the\n"