deploy: f992318

_sources/documentation/brainglobe-heatmap/index.md.txt

@@ -20,14 +20,14 @@ 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.
@@ -56,9 +56,8 @@ In `examples/plan.py` there's an example showing how to use the `planner`:
 ```python
 import brainglobe_heatmap as bgh
 
-
 planner = bgh.plan(
-    regions,
+    values,
     position=(
         8000,
         5000,
@@ -74,7 +73,7 @@ The position of the center of the plane is given by a set of `(x, y, z)` coordin
 When using one of the named orientations, you don't need to pass a whole set of `(x, y, z)` coordinates for the plane center. A single value is sufficient as the other two won't affect the plane position:
 
 ```python
-f = bgh.heatmap(
+f = bgh.Heatmap(
     values,
     position=1000,
     orientation="sagittal",  # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
@@ -88,7 +87,7 @@ f = bgh.heatmap(
 Also, you can create a slice with a plane centered in the brain by passing `position=None`:
 
 ```python
-f = bgh.heatmap(
+f = bgh.Heatmap(
     values,
     position=None,
     orientation="sagittal",  # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
@@ -104,8 +103,7 @@ f = bgh.heatmap(
 Once happy with the position of the slicing planes, creating a visualization is as simple as:
 
 ```python
-
-bgh.heatmap(
+bgh.Heatmap(
     values,
     position=(
         8000,
@@ -116,7 +114,7 @@ bgh.heatmap(
     title="horizontal view",
     vmin=-5,
     vmax=3,
-    cmap='Red',
+    cmap='Reds',
     format="2D",
 ).show()
 ```
@@ -128,11 +126,9 @@ Here, `format` specifies if a 2D plot should be made (using `matplotlib`) or a 3
 You can use `brainglobe-heatmap` to get the coordinates of the 2D 'slices' (in the 2D plane's coordinates system):
 
 ```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,
@@ -145,19 +141,37 @@ 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](../brainglobe-atlasapi/index.md).
 
 ## Contributing
 
 Contributions to `brainglobe-heatmap` are more than welcome. Please see the [Developer's guide](https://github.com/brainglobe/.github/blob/main/CONTRIBUTING.md).
 
 ## Citing `brainglobe-heatmap`
-
 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:
+```
+Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T.W., Portugues, R.,  Branco, T. (2021) "Visualizing anatomically registered data with Brainrender&quot; <i>eLife</i> 2021;10:e65751 [doi.org/10.7554/eLife.65751](https://doi.org/10.7554/eLife.65751)
 ```
 
-`brainglobe-heatmap` was originally developed by Federico Claudi and Luigi Petrucco, with the help of Marco Musy (the developer of [`vedo`](https://github.com/marcomusy/vedo))
+BibTeX:
+
+``` bibtex
+@article{Claudi2021,
+author = {Claudi, Federico and Tyson, Adam L. and Petrucco, Luigi and Margrie, Troy W. and Portugues, Ruben and Branco, Tiago},
+doi = {10.7554/eLife.65751},
+issn = {2050084X},
+journal = {eLife},
+pages = {1--16},
+pmid = {33739286},
+title = {{Visualizing anatomically registered data with brainrender}},
+volume = {10},
+year = {2021}
+}
+```