Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add brainmapper example script #359

Merged
merged 1 commit into from
May 29, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
36 changes: 36 additions & 0 deletions examples/brainmapper.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
"""
Visualise the output from brainmapper. Cells transformed to atlas space can
be found at brainmapper_output/points/points.npy.

For more details on brainmapper, please see:
https://brainglobe.info/documentation/brainglobe-workflows/brainmapper/index.html
"""

from pathlib import Path

from myterial import orange
from rich import print

from brainrender.scene import Scene
from brainrender.actors import Points
from brainrender import settings

settings.SHADER_STYLE = "plastic"

cells_path = Path(__file__).parent.parent / "resources" / "points.npy"

print(f"[{orange}]Running example: {Path(__file__).name}")

# Create a brainrender scene
scene = Scene(title="brainmapper cells")

# Create points actor
cells = Points(cells_path, radius=45, colors="palegoldenrod", alpha=0.8)

# Visualise injection site
scene.add_brain_region("VISp", color="mediumseagreen", alpha=0.6)

# Add cells
scene.add(cells)

scene.render()
Binary file added resources/points.npy
Binary file not shown.
Loading