Actor
classes for many commonly-used data types: Actors. However, before you can use brainrender to visualize your data, you'll have to load and process them to put them into a format that brainrender accepts. These are the main steps you'll have to undertake to visualize your data.Scene.add()
accepts paths to files and takes care of loading/rendering them..csv
and .h5
files, numpy for .npy
etc..swc
files. Brainrender's Neuron
class can load morphology data directly from this file format, but head to morphapi for more details about to load and process neuron morphology data..npy
files, tiffiles
for .tiff
etc. Brainglobe provides a general purpuse software tool for loading and saving image data: imio. You can use imio to load most types of data (e.g. .npy
, .tiff
, .nifti
etc) :.npy
file, brainrender's Volume actor can load the file directly:vedo
provides code to go from volumes to meshes:Volume
class: .json
and loaded with pandas's read_json
function. Data should be organized in a hierarchical structure with two main entries (points
and lines
) denoting the injection points and the coordinates of points along each "line" of the streamlines. Each line should be a list of dictionaries with "x", "y" and "z" coordinates.