Merge pull request #66 from brainglobe/readme-updates

Fix code examples in readme

README.md

@@ -18,14 +18,14 @@ The starting point for a heatmap visualization is a `dict` assigning scalar valu
 For example:
 
 ```python
-    regions = dict(  # scalar values for each region
-        TH=1,
-        RSP=0.2,
-        AI=0.4,
-        SS=-3,
-        MO=2.6,
-        ...
-    )
+values = dict(  # scalar values for each region
+    TH=1,
+    RSP=0.2,
+    AI=0.4,
+    SS=-3,
+    MO=2.6,
+    ...
+)
 ```
 
 `brainglobe-heatmap` creates a brainrender 3D `Scene` with the given regions colored according the values in the dictionary.
@@ -55,7 +55,7 @@ import brainglobe_heatmap as bgh
 
 
 planner = bgh.plan(
-    regions,
+    values,
     position=(
         8000,
         5000,
@@ -102,7 +102,6 @@ f = bgh.Heatmap(
 Once happy with the position of the slicing planes, creating a visualization is as simple as:
 
 ```python
-
 bgh.Heatmap(
     values,
     position=(
@@ -115,7 +114,7 @@ bgh.Heatmap(
     title="horizontal view",
     vmin=-5,
     vmax=3,
-    cmap='Red',
+    cmap='Reds',
     format="2D",
 ).show()
 ```
@@ -127,11 +126,9 @@ You can use `brainglobe-heatmap` to get the coordinates of the 2D 'slices' (in t
 
 
 ```python
-
 regions = ['TH', 'RSP', 'AI', 'SS', 'MO', 'PVZ', 'LZ', 'VIS', 'AUD', 'RHP', 'STR', 'CB', 'FRP', 'HIP', 'PA']
 
-
-coordinates = bgh.get_plane_coordinates(
+coordinates = bgh.get_structures_slice_coords(
     regions,
     position=(
         8000,
@@ -144,7 +141,7 @@ coordinates = bgh.get_plane_coordinates(
 
 ## Using `brainglobe-heatmap` with other atlases.
 
-`brainglobe-heatmap` uses `brainrender` which, in turn, uses brainglobe's `Atlas API` under the hood. That means that all of `brainglobe-heatmap`'s functionality is compatible with any of the atlases supported by the atlas API. `bgh.heatmap`, `bgh.planner` and `bgh.get_plane_coordinates` all accept a `atlas_name` argument, pass the name of the atlas name you'd like to use!
+`brainglobe-heatmap` uses `brainrender` which, in turn, uses brainglobe's `Atlas API` under the hood. That means that all of `brainglobe-heatmap`'s functionality is compatible with any of the atlases supported by the atlas API. `bgh.Heatmap`, `bgh.planner` and `bgh.get_structures_slice_coords` all accept a `atlas_name` argument, pass the name of the atlas name you'd like to use!
 For more information see the API's [documentation](https://brainglobe.info/documentation/brainglobe-atlasapi/index.html).
 
 ## Seeking help or contributing
@@ -154,7 +151,7 @@ We are always happy to help users of our tools, and welcome any contributions. I
 If you use `brainglobe-heatmap` in your work, please cite it as:
 
 ```
-Federico Claudi, & Luigi Petrucco. (2022). brainglobe/bg-heatmaps: (V0.2). Zenodo. https://doi.org/10.5281/zenodo.5891814
+Federico Claudi, Adam Tyson, Luigi Petrucco, Mathieu Bourdenx, carlocastoldi, Rami Hamati, & Alessandro Felder. (2024). brainglobe/brainglobe-heatmap. Zenodo. https://doi.org/10.5281/zenodo.10375287
 ```
 
 If you use `brainrender` via `brainglobe-heatmap` (i.e. for 3D visualisation), please also cite it:
@@ -176,5 +173,4 @@ title = {{Visualizing anatomically registered data with brainrender}},
 volume = {10},
 year = {2021}
 }
-
 ```