atlas

Atlas Mouse Brain

Require optional dependency bg-atlasapi.

Install

pip install bg-atlasapi

Commandline options

use --atlas to specific which atlases. You can use bg_atlasapi.show_atlases() to show all available atlases. For the mouse brain atlases, you can give --atlas=25 to specific use allen_mouse_25um atlas.

For the first running, it needs to download the corresponding atlas for a while.

By default, the atlas view will show once the correspond package is installed. If no, use --view=atlas in command-line.

Application View

Once bg-atlasapi installed, you can find a brain slice shown in the middle figure.

Controls

Moving

On Figure toolbar , select .

Use mouse cursor to drag the image. You can see a boundary of image is following your movement. Once you release the mouse button, the atlas image will update to the new position.
Other controls
- Slice view: change between coronal, sagittal and transverse.
- Slice plane: change the slice plane.
- Shear: change the horizontal or vertical plane difference.
- Rotation: rotate the image. (we rotate the content of the image instead of the image due to the technique issue.)
- Scaling: scale the image.
- Masking: add color shadow on the corresponding regions.

Configurations

It is saved in the configuration besides a corresponding channelmap file. It is looked like:

{
  "AtlasBrainView": {
    "atlas_brain": "allen_mouse_25um",
    "brain_slice": "coronal",
    "slice_plane": 264,
    "slice_rot_w": 0,
    "slice_rot_h": 0,
    "image_dx": 0.0,
    "image_dy": 0.0,
    "image_sx": 1.0,
    "image_sy": 1.0,
    "image_rt": 0.0
  }
}