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bgheatmap-0.0.3
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Brain regions heatmaps in brainrender
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bgheatmap-0.0.3 |
| نام | bgheatmap |
| نسخه کتابخانه | 0.0.3 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Federico Claudi |
| ایمیل نویسنده | - |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/bgheatmap/ |
| مجوز | - |
# BG Heatmaps
Rendering heatmaps with brainrender.
[](https://zenodo.org/badge/latestdoi/442271642)
`bgheatmap` makes it easier to create beautiful heatmaps from anatomical data mapping a scalar values for each brain region (e.g., number of labelled cells in each region) to color and creating beautiful visualizations in 3D and 2D.
### installation
`pip install bgheatmap`
## User guide
The starting point for a heatmap visualization is a `dict` assigning scalar values to a set of brain regions (identified by their acronym).
For example:
```python
regions = dict( # scalar values for each region
TH=1,
RSP=0.2,
AI=0.4,
SS=-3,
MO=2.6,
...
)
```
`bgheatmap` creates a brainrender 3D `Scene` with the given regions colored according the values in the dictionary.
Next, to create visualizations like the ones shown above, the three dimensional sceen needs to be **sliced** to expose
the relevant parts.
This is done by specifying the position and orientation of a `Plane` which cuts through the scene.
The orientation is set by the direction of a *normal vector* specified by the user.
Everything that is on the side opposite where the normal vector will be cut and discarded.
To keep a section of the 3D brain, two planes with normal vectors facing in opposite directions are used:
and everything in-between the two planes is kept as a slice.
### Slicing plane position
Finding the right position and orientation to the plane can take some tweaking. `bgheatmap` provides a `planner` class that makes the process easier by showing the position of the planes and how they intersect with the user provided regions (see image above).
In `examples/plan.py` there's an example showing how to use the `planner`:
```python
import bgheatmap as bgh
planner = bgh.plan(
regions,
position=(
8000,
5000,
5000,
),
orientation="frontal", # orientation, or 'sagittal', or 'horizontal' or a tuple (x,y,z)
thickness=2000, # thickness of the slices used for rendering (in microns)
)
```
The position of the center of the plane is given by a set of `(x, y, z)` coordinates. The orientation can be specified by a string (`frontal`, `sagittal`, `horizontal`) which will result in a standard orthogonal slice, or by a vector `(x, y, z)` with the orientation along the 3 axes.
Whe using one of the named orientation, 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(
values,
position=1000,
orientation="sagittal", # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
thickness=1000,
atlas_name="allen_cord_20um",
format='2D',
).show()
```
Also, you can create a slice with a plane centered in the brain by passing `position=None`:
```python
f = bgh.heatmap(
values,
position=None,
orientation="sagittal", # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
thickness=1000,
atlas_name="mpin_zfish_1um",
format='2D',
title='zebra fish heatmap'
).show(xlabel='AP (μm)', ylabel='DV (μm)')
```
### Visualization
Once happy with the position of the slicing planes, creating a visualization is as simple as:
```python
bgh.heatmap(
values,
position=(
8000,
5000,
5000,
),
orientation="horizontal", # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
title="horizontal view",
vmin=-5,
vmax=3,
cmap='Red',
format="2D",
).show()
```
Here, `format` spcifies if a 2D plot should be made (using `matplotlib`) or a 3D rendering instead (using `brainrender`). The `cmap` parameter specifies the colormap used and `vmin, vmax` the color range.
### Regions coordinates
You can use `bgheatmap` 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(
regions,
position=(
8000,
5000,
5000,
),
orientation="frontal", # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
)
```
## Using `bgheatmap` with other atlases.
`bgheatmap` uses `brainrender` which, in turn, uses brainglobe's `Atlas API` under the hood. That means that all of `bgheatmap`'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!
For more information see the API's [https://docs.brainglobe.info/bg-atlasapi/introduction](documentation).
# Citing bgheatmap
If you use `bgheatmap` 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
```
Bgheatmap was developed by Federico Claudi and Luigi Petrucco, with the help of Marco Musy (the developer of [`vedo`](https://github.com/marcomusy/vedo))
نیازمندی
| مقدار | نام |
|---|---|
| - | brainrender |
| - | matplotlib |
| - | numpy |
| - | myterial |
| - | rich |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl bgheatmap-0.0.3:
pip install bgheatmap-0.0.3.whl
نصب پکیج tar.gz bgheatmap-0.0.3:
pip install bgheatmap-0.0.3.tar.gz