Fixed spelling, grammatical and formatting errors, and removed empty …

…code box. (#335) * Fixed spelling, grammatical and formatting errors in markdown text. * Removed empty code box at the end. (Should it contain code to return side name instead of number, as written in the text above it?) * Update tutorials/Atlas API usage.ipynb Co-authored-by: Adam Tyson <[email protected]> * Update tutorials/Atlas API usage.ipynb Co-authored-by: Adam Tyson <[email protected]> * Update tutorials/Atlas API usage.ipynb Co-authored-by: Adam Tyson <[email protected]> * Update tutorials/Atlas API usage.ipynb Co-authored-by: Adam Tyson <[email protected]> * Added Adam's changes and added subheadings for unlabelled code block below --------- Co-authored-by: Adam Tyson <[email protected]>
brainglobe · Aug 2, 2024 · c0f7e3d · c0f7e3d
1 parent 38ffcc7
commit c0f7e3d
Showing 1 changed file with 23 additions and 23 deletions.
diff --git a/tutorials/Atlas API usage.ipynb b/tutorials/Atlas API usage.ipynb
@@ -11,14 +11,14 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "## 0. Creating a `BrainGlobeAtlas` object and list availabe options"
+                "## 0. Creating a `BrainGlobeAtlas` object and listing available options"
             ]
         },
         {
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "To instantiate a `BrainGlobeAtlas` object, we need to instantiate it with the atlas name. The first time we use it, a version of this atlas files will be downloaded from the [remote GIN repository](http://gin.g-node.org/brainglobe/atlases) and stored on your local machine (by default, in .../Users/username/.brainglobe):"
+                "To instantiate a `BrainGlobeAtlas` object, we need to instantiate it with the atlas name. The first time we use it, a version of this atlas will be downloaded from the [remote GIN repository](http://gin.g-node.org/brainglobe/atlases) and stored on your local machine (by default, in .../Users/username/.brainglobe):"
             ]
         },
         {
@@ -211,7 +211,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "### 1.1 Anatomical, annotation and hemispheres stack"
+                "### 1.1 Reference, annotation and hemispheres stack"
             ]
         },
         {
@@ -227,7 +227,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "Anatomical reference:"
+                "Reference stack:"
             ]
         },
         {
@@ -252,7 +252,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "Annotations stack:"
+                "Annotation stack:"
             ]
         },
         {
@@ -273,6 +273,13 @@
                 "    axs[i].set_xlabel(labels[1])\n"
             ]
         },
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "Hemispheres stack:"
+            ]
+        },
         {
             "cell_type": "code",
             "execution_count": null,
@@ -301,7 +308,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "The atlas comes with the description of a hierarchy of brain structures. To have an overview:"
+                "The atlas comes with a description of the hierarchy of brain structures. To have an overview:"
             ]
         },
         {
@@ -1273,15 +1280,15 @@
             "source": [
                 "---\n",
                 "**NOTE**: \n",
-                "the levels of the hierarchy depends on the underlying atlas, so we cannot ensure the goodness and consistency of their hierarchy three.\n",
+                "The levels of the hierarchy depend on the underlying atlas, so we cannot ensure the goodness and consistency of their hierarchy tree.\n",
                 "---"
             ]
         },
         {
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "There is an higher level description of the structures hierarchy that is built using the [treelib](https://treelib.readthedocs.io/en/latest/) package, and is available as: "
+                "There is a higher level description of the structures hierarchy that is built using the [treelib](https://treelib.readthedocs.io/en/latest/) package, and is available as: "
             ]
         },
         {
@@ -1308,7 +1315,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "For most applications though the methods described above and the list path of each region should be enough to query the hierarchy without additional layers of complication."
+                "For most applications though, the methods described above and the list path of each region should be sufficient to query the hierarchy without additional layers of complication."
             ]
         },
         {
@@ -1322,9 +1329,9 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "The `get_structure_mask` method returns a mask volume where all voxels belonging to an area or to the descendants of that area are non zero. All other voxels are zero. We will generate the structure mask for primary visual cortex to see how this works. \n",
+                "The `get_structure_mask` method returns a mask volume where all voxels belonging to an area or to the descendants of that area are non-zero. All other voxels are zero. We will generate the structure mask for the primary visual cortex to see how this works. \n",
                 "\n",
-                "Primary visual cortex (`VISp`) has an ID value of `385` but no voxels in the annotation image actually have that value:"
+                "Primary visual cortex (`VISp`) has an ID value of `385`, but no voxels in the annotation image actually have that value:"
             ]
         },
         {
@@ -1375,7 +1382,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "The reason no VISp voxels exist is because the annotation volume is segmented more finely. In this case `VISp` is divided into cortical layers and it is IDs associated with these layers that are present in the annotation volume."
+                "The reason no VISp voxels exist is because the annotation volume is segmented more finely. In this case `VISp` is divided into cortical layers and the IDs associated with these layers are the ones that are present in the annotation volume."
             ]
         },
         {
@@ -1460,7 +1467,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "So lets use `get_structure_mask` to return a mask volume that retains only `VISp`."
+                "So let's use `get_structure_mask` to return a mask volume that retains only `VISp`."
             ]
         },
         {
@@ -1490,7 +1497,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "The `root` node encompases the whole brain and we can use this to provide a background image for the above area."
+                "The `root` node encompasses the whole brain and we can use this to provide a background image for the above area."
             ]
         },
         {
@@ -1654,7 +1661,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "A very similar method can be used for hemispheres. 0 correspond to outside the brain, a,d 1 and 2 to left and right hemispheres - but we can just ask for the side name instead of the number:"
+                "A very similar method can be used for hemispheres. 0 corresponds to outside the brain, and 1 and 2 to left and right hemispheres respectively - but we can just ask for the hemisphere name instead of the number:"
             ]
         },
         {
@@ -1682,13 +1689,6 @@
                 "# Now print side string\n",
                 "print(\"By :\", bg_atlas.hemisphere_from_coords((5000, 4000, 3000), microns=True))"
             ]
-        },
-        {
-            "cell_type": "code",
-            "execution_count": null,
-            "metadata": {},
-            "outputs": [],
-            "source": []
         }
     ],
     "metadata": {
@@ -1707,7 +1707,7 @@
             "name": "python",
             "nbconvert_exporter": "python",
             "pygments_lexer": "ipython3",
-            "version": "3.8.10"
+            "version": "3.12.4"
         }
     },
     "nbformat": 4,