V1 -> V2
Brainrender version 2.0 was recently released. This includes a major overhaul of most of brainrender's code and the introduction of a few new features. If you have been using version 1 of brainrender, we strongly recommend upgrading to the new one with:
1
pip install brainrender -U
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However going from v1 to v2 means that some changes will be needed to make your brainrender code work.

Main changes

new Actor class

A new Actor class is introduced, everything rendered in brainrender is first converted into an instance of Actor. Different types of Actor class have been created to render different types of data:
  • brainrender.actors.Neuron is used to render neurons morphology (e.g. downloaded with morphapi)
  • brainrender.actors.Points is used to render anything that can be represented as a set of points (e.g. labelled cells from cellfinder
  • brainrender.actors.Streamlines is used to render streamlines tractography data
  • brainrender.actors.Volume renders volumetric data (e.g. gene expression)
  • Other actor classes like Cylinder, Point and Ruler can be used to render other types of data.
The introduction of these new classes implies that the workflow for rendering data in brainrender has changed a little bit. While before you would use methods like Scene.add_cells to render labelled cells, now you have to create a Points actor and add that to the scene with Scene.add. The same goes for all other types of visualizations supported by dedicated Actor classes. More details can be found in the examples at the Github repository.
If the data you want to render does not have a dedicated Actor class, you can create a vedo Mesh object from your data, as you would've done in v1, and use that to create a generic Actor object.

changes to Scene class

As state above, most of Scene's method for adding actors to your rendering have been removed. A generic Scene.add can be used to add any Actor or Mesh object to the scene, while Scene.add_brain_regions can be used specifically to add brain region meshes. Also methods to add a silhouette or a label to individual actors are supported.
Scene got a few new methods as well: remove can be used to remove an Actor from the rendering, get_actors can be used to get a handle on the actors in the scene. The slice method also replaced cut_actors_with_plane .

changes to Video and new Animation class

The VideoMaker class changed slightly. Your interaction with it will be largely unchanged, however its inner workings are now different: it uses ffmpeg instead of opencv to create and compress videos. This means that you don't need opencv anymore (yay
🎉
) however you do need to make sure that ffmpeg is installed and working correctly.
A brand new Animation class has been introduced which facilitates the creation of videos with more advanced animations, more about it in the docs and examples.

the brainrender GUI has landed

The GUI, previously developed as part of a separate python package has not been fully integrated in brainrender.

other changes

Much of the remainder of brainrender's functionality persists unchanged. Some method names might have changed however, but you should find all the info you need in the examples at the Github repository. Two more things worth noticing are:
  • The name of the camera parameters used to specify the position of custom cameras have changed
  • Some of the parameters in brainrender.settings have changed or have been removed.
Last modified 1yr ago
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Main changes