diff --git a/_sources/documentation/brainglobe-heatmap/index.md.txt b/_sources/documentation/brainglobe-heatmap/index.md.txt index 86a263b7..f50276c3 100644 --- a/_sources/documentation/brainglobe-heatmap/index.md.txt +++ b/_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, @@ -145,7 +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](../brainglobe-atlasapi/index.md). ## Contributing @@ -153,11 +149,29 @@ For more information see the API's [documentation](../brainglobe-atlasapi/index. 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" eLife 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} +} +``` diff --git a/documentation/brainglobe-heatmap/index.html b/documentation/brainglobe-heatmap/index.html index b6ef8895..3bc6a323 100644 --- a/documentation/brainglobe-heatmap/index.html +++ b/documentation/brainglobe-heatmap/index.html @@ -653,14 +653,14 @@

Installation#

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:

-
    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.
@@ -680,9 +680,8 @@ 
Slicing plane positionexamples/plan.py there’s an example showing how to use the planner:

 
import brainglobe_heatmap as bgh
 
-
 planner = bgh.plan(
-    regions,
+    values,
     position=(
         8000,
         5000,
@@ -695,7 +694,7 @@ 
Slicing plane position
 
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.

 
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:

-
f = bgh.heatmap(
+
f = bgh.Heatmap(
     values,
     position=1000,
     orientation="sagittal",  # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
@@ -707,7 +706,7 @@ 
Slicing plane position

 

 
Also, you can create a slice with a plane centered in the brain by passing position=None:

-
f = bgh.heatmap(
+
f = bgh.Heatmap(
     values,
     position=None,
     orientation="sagittal",  # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
@@ -722,8 +721,7 @@ 
Slicing plane position
 
Visualization#

 
Once happy with the position of the slicing planes, creating a visualization is as simple as:

-

-bgh.heatmap(
+
bgh.Heatmap(
     values,
     position=(
         8000,
@@ -734,7 +732,7 @@ 
Visualizationtitle="horizontal view",
     vmin=-5,
     vmax=3,
-    cmap='Red',
+    cmap='Reds',
     format="2D",
 ).show()
 

@@ -744,11 +742,9 @@ 
Visualization
 
Regions coordinates#

 
You can use brainglobe-heatmap to get the coordinates of the 2D ‘slices’ (in the 2D plane’s coordinates system):

-

-regions = ['TH', 'RSP', 'AI', 'SS', 'MO', 'PVZ', 'LZ', 'VIS', 'AUD', 'RHP', 'STR', 'CB', 'FRP', 'HIP', 'PA']
-
+
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,
@@ -763,7 +759,7 @@ 
Regions 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.

 
 

@@ -773,10 +769,27 @@ 
Contributing
 
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)
+

+

+
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}
+}
 

 

-
brainglobe-heatmap was originally developed by Federico Claudi and Luigi Petrucco, with the help of Marco Musy (the developer of vedo)

 

 
 
diff --git a/searchindex.js b/searchindex.js
index c4620e26..a1e2a694 100644
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merged under a new name", "An Atlas for the regenerative Ambystoma mexicanum (axolotl) has been added to BrainGlobe", "A mouse brain atlas with barrel field annotations has been added to BrainGlobe", "bg-space has been renamed", "BrainGlobe version 1.1.0 is released!", "New brainmapper napari widget released", "Plans for brainrender", "An atlas for the Blind Mexican Cavefish has been added to BrainGlobe", "Cellfinder version 1.3.0 is released!", "imio will be merging into brainglobe-utils", "Blog", "An atlas for the prairie vole Microtus ochrogaster has been added to BrainGlobe", "Version 1 of brainreg and brainglobe-segmentation released", "cellfinder has moved: version 1 of brainglobe-workflows released", "cellfinder-core and cellfinder-napari have merged", "BrainGlobe is being restructured, version 1 is on it\u2019s way!", "BrainGlobe version 1 is here!", "Courses", "Whole brain microscopy analysis with BrainGlobe and napari", "December 6th 2023", "October 7th-8th 2024", "Conventions", "Developer\u2019s guide", "Introduction to the BrainGlobe codebase for developers", "Publishing new releases", "brainglobe-atlasapi", "brainglobe-meta", "brainglobe-utils", "brainglobe-workflows", "cellfinder.core", "Specific Repository Developer Documentation", "Testing", "Tooling", "Software built by the community", "Community", "Releases", "Version 1: changes to registration and segmentation tools", "Version 1: changes to the cellfinder backend and plugin", "Version 1: Cellfinder migration and brainglobe-workflows", "BrainGlobe version 1 overview", "Roadmaps", "May 2024", "November 2023", "Contact", "Adding a new atlas", "BrainGlobe Atlas API (brainglobe-atlasapi)", "Atlas details", "Command line interface", "Python API", "Using the files directly", "brainglobe-heatmap", "brainglobe-segmentation", "Analysing segmentation from other napari plugins", "Prerequisites", "brainglobe-space", "Generating Citations for BrainGlobe tools", "Image IO submodule", "brainglobe-utils", "brainmapper cell transformation widget", "Cell candidate detection", "Cell candidate classification", "Command line interface", "Data requirements", "Debugging common error messages", "brainmapper command line tool", "Output files", "Visualisation", "brainglobe-workflows", "brainreg", "Requirements", "Troubleshooting", "Command line tool", "Napari plugin", "Checking orientation", "Output files", "Registration parameters", "Visualising brainreg output", "brainrender", "Installing brainrender", "Actors", "Usage", "Scene", "Using Notebooks", "Using your own data in brainrender", "Registering data", "Videos, animations and exporting to html", "cellfinder", "Installation", "Debugging common error messages", "Troubleshooting", "Speeding up cellfinder", "cellfinder.core API", "Downloading the pre-trained model in advance", "All cell detection parameters", "Cell detection", "cellfinder napari plugin", "Generating data to retrain the cellfinder classification network", "Retraining the network for new data", "Retraining the pre-trained network", "Using supplied training data", "Documentation", "morphapi", "Downloading data", "Rendering data", "Using conda", "Setting up your GPU", "Image space definition", "Setting up", "Funders", "BrainGlobe", "Media", "People", "BrainGlobe publications", "Talks", "Exploring the numerical results", "Whole brain cell detection and registration with the brainmapper command line tool", "Running brainmapper", "Setting up", "Visualising the results", "Visualising your data in brainrender", "Detecting cells in 3D with cellfinder", "Retraining the cellfinder classification network", "Tutorials", "Download an atlas through napari", "Segmenting a 1D track", "Segmenting 2/3D structures", "Silicon probe tracking", "Aligning samples for template building", "Analyze and visualize bulk fluorescence tracing data", "Analysing brainwide distribution of cells", "Registering a whole-brain image to an atlas", "Visualise an atlas in 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cellfinder-napari have merged", "BrainGlobe is being restructured, version 1 is on it\u2019s way!", "BrainGlobe version 1 is here!", "Courses", "Whole brain microscopy analysis with BrainGlobe and napari", "December 6th 2023", "October 7th-8th 2024", "Conventions", "Developer\u2019s guide", "Introduction to the BrainGlobe codebase for developers", "Publishing new releases", "brainglobe-atlasapi", "brainglobe-meta", "brainglobe-utils", "brainglobe-workflows", "cellfinder.core", "Specific Repository Developer Documentation", "Testing", "Tooling", "Software built by the community", "Community", "Releases", "Version 1: changes to registration and segmentation tools", "Version 1: changes to the cellfinder backend and plugin", "Version 1: Cellfinder migration and brainglobe-workflows", "BrainGlobe version 1 overview", "Roadmaps", "May 2024", "November 2023", "Contact", "Adding a new atlas", "BrainGlobe Atlas API (brainglobe-atlasapi)", "Atlas details", "Command line interface", "Python API", 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cellfinder", "cellfinder.core API", "Downloading the pre-trained model in advance", "All cell detection parameters", "Cell detection", "cellfinder napari plugin", "Generating data to retrain the cellfinder classification network", "Retraining the network for new data", "Retraining the pre-trained network", "Using supplied training data", "Documentation", "morphapi", "Downloading data", "Rendering data", "Using conda", "Setting up your GPU", "Image space definition", "Setting up", "Funders", "BrainGlobe", "Media", "People", "BrainGlobe publications", "Talks", "Exploring the numerical results", "Whole brain cell detection and registration with the brainmapper command line tool", "Running brainmapper", "Setting up", "Visualising the results", "Visualising your data in brainrender", "Detecting cells in 3D with cellfinder", "Retraining the cellfinder classification network", "Tutorials", "Download an atlas through napari", "Segmenting a 1D track", "Segmenting 2/3D structures", "Silicon 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