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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 facilitate the exploration and dissemination of neuroanatomical data by providing a user-friendly platform to create high-quality 3D renderings.** +**`brainrender` is a python package for the visualization of three dimensional neuro-anatomical data. It can be used to render data from publicly available data set \(e.g. Allen Brain atlas\) as well as user generated experimental data. The goal of `brainrender` is to facilitate the exploration and dissemination of neuro-anatomical data by providing a user-friendly platform to create high-quality 3D renderings.** @@ -16,10 +14,12 @@ While developing `brainrender` we aimed to create a flexible and easy-to-use too 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 build upon \(brainglobe\)\[linkmissing\]'s atlas API, ensuring that you can use `brainrender` to visualize 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 built a ton of functionality into `brainrender` to ensure that we can cover all of your visualization needs \(e.g. see these [images](overview/gallery.md) and [examples](overview/examples.md)\). If we missed something or you'd like to see a new feature added, get in touch on [github](https://github.com/BrancoLab/BrainRender)! +* we're using [`vedo`](https://github.com/marcomusy/vedo), a powerful vtk-based rendering package in python. `vedo`'s flexibility ensures that you can render in `brainrender` any 3d design you can put into a `.obj` or `.stl` file. It's therefore easier than ever to add your custom experimental implant to the renderings. + + #### Getting in touch diff --git a/overview/gallery.md b/overview/gallery.md index 1785f40..f9c83b8 100644 --- a/overview/gallery.md +++ b/overview/gallery.md @@ -4,5 +4,37 @@ description: Some examples of the kind of images you can create in brainrender # Gallery -to add - a gallery of images created with brainrend +![The mouse brain and skull](../.gitbook/assets/skull%20%281%29.png) + +![Labelled cells in several cortical and sub cortical areas](../.gitbook/assets/cells.png) + +![Location of an optic fiber implanted in the thalamus](../.gitbook/assets/optic_fiber.png) + +![Location of an implanted neuropixel probe in the cortex and thalamus](../.gitbook/assets/neuropixel.png) + +![The brain of Schistocerca gregaria](../.gitbook/assets/ibdb.png) + +![Gene expression levels for Cacna2d1 across the mouse cortex. ](../.gitbook/assets/gene_expr.png) + + + +![Tractography visualisation of projections to the Zona Incerta \(data: the Allen Mouse Connectome project\)](../.gitbook/assets/tractography.png) + +![Layer 5b neurons in the mouse motor cortex. Sagittal view.](../.gitbook/assets/neurons.png) + + + + + +![The C.Elegans connectome \(data courtesy of Daniel Witvliet and co-authors\)](../.gitbook/assets/celegans.png) + + + +![Streamlines visualization of projections from the motor cortex in the mouse brain](../.gitbook/assets/streamlinespretty.png) + +![Views of the human brain](../.gitbook/assets/humanbrainexp.png) + + + +