unravel.image_tools package

• unravel.image_tools.img_math module
  • Usage to add two .nii.gz images [and apply a mask]:
  • Usage multiply three images and save as Zarr:
  • Usage to binarize an image and set to 8 bit:
  • Usage to save as a series of TIFFs after applying upper and lower thresholds:
  • parse_args()
  • apply_operation()
  • apply_mask()
  • threshold_image()
  • main()
• unravel.image_tools.avg module
  • Usage:
  • parse_args()
  • main()
• unravel.image_tools.bbox module
  • Usage:
  • parse_args()
  • main()
• unravel.image_tools.extend module
  • parse_args()
  • extend_one_side_3d_array()
  • main()
• unravel.image_tools.max module
  • Usage:
  • parse_args()
  • find_max_intensity()
  • main()
• unravel.image_tools.pad module
  • Usage:
  • parse_args()
  • main()
• unravel.image_tools.resample module
  • Usage:
  • Usage for isotropic resampling:
  • Usage for anisotropic resampling:
  • Usage for resampling by scale factor:
  • Usage to resample using a reference image:
  • parse_args()
  • main()
• unravel.image_tools.spatial_averaging module
  • Usage:
  • parse_args()
  • spatial_average_3D()
  • apply_2D_mean_filter()
  • spatial_average_2D()
  • main()
• unravel.image_tools.DoG module
  • Usage:
  • parse_args()
  • load_tif()
  • difference_of_gaussians()
  • save_tif()
  • main()
• unravel.image_tools.rb module
  • Usage:
  • parse_args()
  • load_tif()
  • rolling_ball_subtraction()
  • save_tif()
  • main()
• unravel.image_tools.transpose_axes module
  • Usage:
  • parse_args()
  • transpose_img()
  • main()
• unravel.image_tools.unique_intensities module
  • Usage for printing all non-zero intensities:
  • Usage for printing the number of voxels for each intensity that is present:
  • Usage for printing unique intensities w/ a min cluster size > 100 voxels:
  • parse_args()
  • main()
• unravel.image_tools.modify_labels module
  • Usage:
  • Usage to mask a region w/ multiple labels:
  • parse_args()
  • set_labels()
  • retain_labels()
  • main()
• unravel.image_tools.filter_objects_by_size module
  • Usage:
  • parse_args()
  • main()
• unravel.image_tools.smooth module
  • Usage:
  • parse_args()
  • smooth_w_sigma_in_mm()
  • smooth_w_sigma_in_voxels()
  • smooth_image()
  • main()
• unravel.image_tools.invert module
  • Usage:
  • parse_args()
  • invert_img()
  • main()
• unravel.image_tools.dilate module
  • Usage:
  • parse_args()
  • main()
• unravel.image_tools.means_in_mask module
  • Usage:
  • parse_args()
  • main()
• unravel.image_tools.atlas package
  • unravel.image_tools.atlas.relabel_nii module
    • Usage:
    • parse_args()
    • main()
  • unravel.image_tools.atlas.wireframe module
    • Usage:
    • parse_args()
    • process_intensity()
    • generate_wireframe()
    • main()