Visualization Functions

transbrain.vis.map_phenotype_to_nifti(phenotype_df, atlas_dict)[source]

Map phenotype values to a mouse atlas and create a NIfTI image.

Parameters:

  • phenotype_df (pd.DataFrame) – DataFrame with ‘Phenotype’ column and anatomical names as index.

  • atlas_dict (dict) – Dictionary with ‘info_table’ (mapping anatomical names to atlas indices) and ‘atlas’ (NIfTI image of the mouse brain atlas).

Returns:

NIfTI image with phenotype values mapped to atlas regions.

Return type:

phenotype_img (nib.Nifti1Image)

transbrain.vis.plot_mouse_phenotype(phenotype_img, coor=[1.85, 0.85, -1.65, -2.15, -3.15], normalize_img=False, symmetric_cbar=True, vmax=2, threshold=0)[source]

Visualize the phenotype map and overlay contours.

Parameters:

  • phenotype_img (NIfTI image) – The phenotype image to visualize. This is a 3D NIfTI image containing the data to be plotted.

  • coor (List, optional) – Coordinates for display

  • normalize_img (bool, optional) – If True, the phenotype image will be normalized using z-score transformation. Default is False.

  • symmetric_cbar (bool, optional) – Whether to use a symmetric colorbar (True) or not (False). Default is True.

  • vmax (float, optional) – Maximum value for colormap scaling. Default is 2. This parameter defines the upper bound for the colormap range.

  • threshold (float, optional) – Threshold value for masking the image. Default is 0. Any values below this threshold will be masked (set to 0).

Returns:

This function does not return any value. It generates and displays a plot of the phenotype image with contours.

Return type:

None

transbrain.vis.plot_human_phenotype(phenotype_img, normalize_img=False, cut_coords=range(0, 50, 10), vmax=2, symmetric_cbar=True)[source]

Plots the human phenotype data on the MNI152 template.

Parameters:

  • phenotype_img (nib.Nifti1Image) – A NIfTI image containing the phenotype data to be visualized. This image will be overlaid on the MNI152 template.

  • normalize_img (bool, optional, default=False) – If True, the phenotype image will be normalized using z-score transformation before visualization.

  • cut_coords (range, optional, default=range(0, 50, 10)) – Slice coordinates at which the phenotype data will be displayed. The default is from 0 to 50 in steps of 10.

  • vmax (float, optional, default=2) – The maximum value for color intensity in the plot. This parameter controls the upper bound for the colormap range.

  • symmetric_cbar (bool, optional, default=True) – If True, the colorbar will be symmetric, with zero at the center. If False, the colorbar will scale based on the provided data.

Return type:

None

transbrain.surf.plot_surface_phenotype(vertex_data, vmax=2, thresh=0, darkness=0.6, show_boundary=True, sym_bar=True)[source]

Visualize the surface phenotype data by generating a surface map with the given input data.

Parameters:

  • vertex_data (array-like) – The input vertex data representing the surface phenotype values.

  • vmax (float, optional, default=2) – The maximum value for the color scale.

  • thresh (float, optional, default=0) – The threshold value below which data is not displayed.

  • darkness (float, optional, default=0.6) – The darkness level for the background surface. Ranges between 0 (light) and 1 (dark).

  • show_boundary (bool, optional, default=True) – Whether to show the boundary overlay on the surface map.

  • sym_bar (bool, optional, default=True) – Whether to make the colorbar symmetric around zero.

Returns:

visualize – The generated figure containing the surface phenotype visualization.

Return type:

PIL.Image.Image