Small changes to docs.

Author: JoeZiminski

doc/how_to/inter_session_alignment.rst

@@ -2,9 +2,9 @@ How to perform inter-session alignment
 ======================================
 
 In this how-to, we will assess and correct changes in probe position across multiple experimental sessions
-using 'inter-session alignment'.
+using `inter-session alignment`.
 
-This is often valuable chronic-recording experiments, where the goal is to track units across sessions
+This is often valuable for chronic-recording experiments, where the goal is to track units across sessions
 
 A full tutorial, including details on the many settings for this procedure, can be found `here <TODO: ADD LINK (INTERNAL)>`_.
 
@@ -14,25 +14,23 @@ Running inter-session alignment
 In SpikeInterface, it is recommended to perform inter-session alignment
 following within-session motion correction (if used) and before whitening.
 
-Preprocessed recordings should be stored in a list before being passed
-to the `session_alignment` functions:
+Preprocessed recordings should first be stored in a list:
 
 .. code:: python
 
     recordings_list = [prepro_session_1, prepro_session_2, ...]
 
 Here, we will simulate such an experiment by generating a pair of sessions in
-which the probe is displaced 200 micrometers (um) along its y-axis (depth).
+which the probe is displaced 200 micrometers (μm) along its y-axis (depth).
 
-The first step involves running all required imports:
+First, we will import all required packages and functions:
 
 .. code:: python
 
-    from spikeinterface.generation.session_displacement_generator import generate_session_displacement_recordings
+    # TODO: should add all of the below to spikeinterface.full? (CHECK)
     import spikeinterface.full as si
-    from spikeinterface.preprocessing.inter_session_alignment import (  # TODO: should add all of the below to spikeinterface.full? (CHECK)
-        session_alignment,
-    )
+    from spikeinterface.generation.session_displacement_generator import generate_session_displacement_recordings
+    from spikeinterface.preprocessing.inter_session_alignment import session_alignment
     from spikeinterface.widgets import plot_session_alignment, plot_activity_histogram_2d
     import matplotlib.pyplot as plt
 
@@ -50,14 +48,14 @@ and then generating the test recordings:
 We won't explicitly preprocess these recordings in this how-to, but you can imagine
 preprocessing steps have already been run (e.g. filtering, common reference etc.).
 
-To run inter-session alignment, we need to detect peaks and compute the peak locations,
-as the location of firing neurons are used as anchors to align the sessions.
+To run inter-session alignment, peaks must be detected and localised
+as the locations of firing neurons are used to anchor the sessions alignment.
 
 If you are **running inter-session alignment following motion correction**, the peaks will
-already be detected and localised. In this case, please jump to the
-:ref:`alignment guide <_with_motion_correction>`.
+already be detected and localised. In this case, please jump to
+:ref:`inter-session alignment after motion correction <with_motion_correction>`.
 
-In this section we will imagine motion correction was not run, so we need to compute the peaks:
+In this section we will assume motion correction was not run, so we need to compute the peaks:
 
 .. code:: python
 
@@ -81,7 +79,7 @@ The peak locations (before correction) can be visualised with the plotting funct
 
 Now, we are ready to perform inter-session alignment. There are many options associated
 with this method—the simplest way to edit these is to fetch the default options
-using the getter function as below:
+with the getter function and make select changes as required:
 
 .. code:: python
 
@@ -95,7 +93,7 @@ using the getter function as below:
         estimate_histogram_kwargs=estimate_histogram_kwargs
     )
 
-To assess the performance of inter-session alignment, `plot_session_alignment()`
+To assess the performance of inter-session alignment, ``plot_session_alignment()``
 will plot both the original and corrected recordings:
 
 .. code:: python
@@ -120,10 +118,10 @@ Inter-session alignment after motion correction
 
 If motion correction has already been performed, it is possible to reuse the
 previously computed peaks and peak locations, avoiding the need for re-computation.
-We will use the special function `align_sessions_after_motion_correction()` for this case.
+We will use the special function` `align_sessions_after_motion_correction()`` for this case.
 
-Critically, the last preprocessing step prior to inter-session alignment should be motion correction,
-so the correction for inter-session displacement will be **added directly to the motion correction**.
+Critically, the last preprocessing step prior to inter-session alignment should be motion correction.
+This ensures the correction for inter-session alignment will be **added directly to the motion correction**.
 This is beneficial as it avoids interpolating the data (i.e. shifting the traces) more than once.
 
 .. admonition:: Warning
@@ -144,9 +142,9 @@ This is beneficial as it avoids interpolating the data (i.e. shifting the traces
         assert isinstance(recording, InterpolateMotionRecording)  # error if not true
 
     ``align_sessions_after_motion_correction()`` will raise an error if the passed recordings
-    are not all `InterpolateMotionRecordings`.
+    are not all ``InterpolateMotionRecordings``.
 
-Again, let's create some test data. We can create a recording with motion errors,
+Let's first create some test data. We can create a recording with motion errors,
 then split it in two to simulate two separate sessions:
 
 .. code:: python
@@ -176,10 +174,9 @@ Next, motion correction is performed, storing the results in a list:
         motion_info_list.append(motion_info)
 
 Now, we are ready to use ``align_sessions_after_motion_correction()``
-to align the motion-corrected sessions.
-
-This function should always be used for aligning motion-corrected sessions,
-as it ensures the alignment parameters are properly matched.
+to align the motion-corrected sessions. This function should always be used
+for aligning motion-corrected sessions, as it ensures the alignment
+parameters are properly matched.
 
 We can pass any arguments directly to ``align_sessions`` using the ``align_sessions_kwargs`` argument: