GitBook: [master] 19 pages and 3 assets modified

README.md

@@ -1,38 +1,17 @@
-# brainrender-docs
+# Introduction
 
-<p>
-  <img style="width:100%; maring:0px; padding:0px; background-color:rgb(240, 240, 240); border-radius:12px" src="data/overview/aba.png">
-</p>
-
-----
-&nbsp;  
+![](.gitbook/assets/aba.png)
 
 ## Welcome to the `brainrender` docs
 
-<p style="background-color:rgb(240, 240, 240); padding:8px; border-radius:8px;">
-
-brainrender is a python package for the visualization of three dimensional neuroanatomical data. 
-It can be used to render data from publicly available dataset (e.g. Allen Brain atlas) as well as user generated experimental data. 
-The goal of brainrender is to faciliate the exploration and dissemination of neuroanatomical data by providing a user-friendly platform to create high-quality 3D renderings. 
-
-</p>
-
-&nbsp;  
+ brainrender is a python package for the visualization of three dimensional neuroanatomical data. It can be used to render data from publicly available dataset \(e.g. Allen Brain atlas\) as well as user generated experimental data. The goal of brainrender is to faciliate the exploration and dissemination of neuroanatomical data by providing a user-friendly platform to create high-quality 3D renderings.
 
-When developing `brainrender` we aimed to create a flexible and easy-to-use tool for the neuroscience community to use for all their rendering needs. 
+When developing `brainrender` we aimed to create a flexible and easy-to-use tool for the neuroscience community to use for all their rendering needs.
 
 For this reason:
- * we've build upon (brainglobe)[linkmissing]'s atlas API, ensuring that you can use `brainrender` to visualise data from a wide range of species. 
- * we've created a simple and intuitive interface to download and render data from publicly available datasets like the Allen Mouse Connectome and Janelia's Mouse Light projects.
- * we've built a ton of functionality into `brainrender` to ensure that we can cover all of your visualisation needs. If we missed something, and you'd like to see a new feature added, get in touch on [github](https://github.com/BrancoLab/BrainRender)!
- * we're using `vedo`, a powerful `vtk`-based rendering package in python. `vedo`'s flexibility ensures that you can render in brainrender any 3d object you can put into a `.obj` or `.stl` file. It's therefore easier than ever to add your custom experimental implant to the renderings. 
-
-
-
-
 
+* we've build upon \(brainglobe\)\[linkmissing\]'s atlas API, ensuring that you can use `brainrender` to visualise data from a wide range of species. 
+* we've created a simple and intuitive interface to download and render data from publicly available datasets like the Allen Mouse Connectome and Janelia's Mouse Light projects.
+* we've built a ton of functionality into `brainrender` to ensure that we can cover all of your visualisation needs. If we missed something, and you'd like to see a new feature added, get in touch on [github](https://github.com/BrancoLab/BrainRender)!
+* we're using `vedo`, a powerful `vtk`-based rendering package in python. `vedo`'s flexibility ensures that you can render in brainrender any 3d object you can put into a `.obj` or `.stl` file. It's therefore easier than ever to add your custom experimental implant to the renderings. 
 
-<!-- `brainrender` can be used to create:
- * [beautiful]() renderings of neuroanatomical data
- * <a href='01-overview/regions.html' target='_blank'> interactive </a> 3d renderings to quickly share your data with collaborators and colleagues.
- * videos and animations to showcase the intricate details of the neuroanatomy of you -->

SUMMARY.md

@@ -1,21 +1,25 @@
-# Summary
+# Table of contents
+
+* [Introduction](README.md)
 
 ## Overview
 
-* [Introduction](README.md)
-
-* [gallery](01-overview/gallery.md)
-* [code examples](01-overview/examples.md)
+* [Introduction](overview/readme.md)
+* [gallery](overview/gallery.md)
+* [code examples](overview/examples.md)
 
 ## Installation
-* [installing brainrender](02-installation/installation.md)
+
+* [installing brainrender](installation/installation.md)
 
 ## Usage
-* [overview](03-usage/overview.md)
-* [the Atlas class](03-usage/atlas.md)
-* [the Scene class](03-usage/scene.md)
 
+* [overview](usage/overview.md)
+* [the Atlas class](usage/atlas.md)
+* [the Scene class](usage/scene.md)
+
+---
 
-* [publicly available datasets](03-usage/public.md)
-* [user-generated data](03-usage/user.md)
+* [publicly available datasets](public.md)
+* [user-generated data](user.md)
 

02-installation/installation.md → installation/installation.md

@@ -1,25 +1,34 @@
-# Installation
+# installing brainrender
+
 ## Environment
-To install `brainrender`, you need a python environment with a `python > 2.7` and `python < 3.8` (so `3.6` or `3.7` ideally). If you don't have a python environment ready, you can [crate one](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) with anaconda. 
+
+To install `brainrender`, you need a python environment with a `python > 2.7` and `python < 3.8` \(so `3.6` or `3.7` ideally\). If you don't have a python environment ready, you can [crate one](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) with anaconda.
 
 ## Basic installation
+
 Installing `brainrender` is as simple as:
-```
+
+```text
 pip install brainrender
-``` 
-(Make sure to have your anaconda environment active when running `pip install)
+```
 
+\(Make sure to have your anaconda environment active when running \`pip install\)
 
 ## Advanced installation
+
 If you want the most recent version of `brainrender`'s code, perhaps to help developing it, you can either clone/fork the [github repository](https://github.com/BrancoLab/BrainRender) or you can get it directly from github with:
-```
+
+```text
 pip install -U git+https://github.com/BrancoLab/BrainRender.git
 ```
 
 ### Testing installation
-To quickly check that everything worked for your installation, try creating a brainrender scene directly from the terminal. 
-```
+
+To quickly check that everything worked for your installation, try creating a brainrender scene directly from the terminal.
+
+```text
   brainrender TH STR -c
 ```
 
-This will show a scene based on the `allen mouse atlas` showing the thalamus and the striatum.
+This will show a scene based on the `allen mouse atlas` showing the thalamus and the striatum.
+

overview/examples.md

@@ -0,0 +1,4 @@
+# code examples
+
+to do add overview of available examples
+

overview/gallery.md

@@ -0,0 +1,4 @@
+# gallery
+
+to add - a gallery of images created with brainrend
+

overview/readme.md

@@ -0,0 +1,17 @@
+# Introduction
+
+![](../.gitbook/assets/aba.png)
+
+## Welcome to the `brainrender` docs
+
+ brainrender is a python package for the visualization of three dimensional neuroanatomical data. It can be used to render data from publicly available dataset \(e.g. Allen Brain atlas\) as well as user generated experimental data. The goal of brainrender is to faciliate the exploration and dissemination of neuroanatomical data by providing a user-friendly platform to create high-quality 3D renderings.
+
+When developing `brainrender` we aimed to create a flexible and easy-to-use tool for the neuroscience community to use for all their rendering needs.
+
+For this reason:
+
+* we've build upon \(brainglobe\)\[linkmissing\]'s atlas API, ensuring that you can use `brainrender` to visualise data from a wide range of species. 
+* we've created a simple and intuitive interface to download and render data from publicly available datasets like the Allen Mouse Connectome and Janelia's Mouse Light projects.
+* we've built a ton of functionality into `brainrender` to ensure that we can cover all of your visualisation needs. If we missed something, and you'd like to see a new feature added, get in touch on [github](https://github.com/BrancoLab/BrainRender)!
+* we're using `vedo`, a powerful `vtk`-based rendering package in python. `vedo`'s flexibility ensures that you can render in brainrender any 3d object you can put into a `.obj` or `.stl` file. It's therefore easier than ever to add your custom experimental implant to the renderings. 
+

public.md

@@ -0,0 +1,4 @@
+# publicly available datasets
+
+publicly available datasets, including brainglobe's atlases
+

usage/atlas.md

@@ -0,0 +1,4 @@
+# the Atlas class
+
+the atlas class and methods
+

03-usage/overview.md → usage/overview.md

@@ -1 +1,4 @@
-general intro to the Atlas and Scene classes. The types of data and visualisation etc...
+# overview
+
+general intro to the Atlas and Scene classes. The types of data and visualisation etc...
+

usage/scene.md

@@ -0,0 +1,4 @@
+# the Scene class
+
+the scene class and methods
+

03-usage/user.md → user.md

@@ -1 +1,4 @@
-user generated content, cells, probes... integration with neuro and cellfinder etc..
+# user-generated data
+
+user generated content, cells, probes... integration with neuro and cellfinder etc..
+