View Tools

The ccf2d view command provides visualization tools for examining registered brain slices overlaid with Allen Brain Atlas coordinates and annotations.

Command Usage

ccf2d view -h

options:
  -h, --help            show this help message and exit

Input/Output Options:
  -R RAW_IMAGE, --raw RAW_IMAGE
                        raw image path (after resize to allen space)
  -T TRANS_MATRIX, --trans TRANS_MATRIX
                        transform matrix (3 x 3) .mat file
  -C CCF_DATA, --ccf CCF_DATA
                        ccf transformed .mat file
  --output OUTPUT       output image path, if not specified, show image (default: None)

View Options:
  -P coronal|sagittal|transverse, --plane-type coronal|sagittal|transverse
                        cutting orientation (default: 'coronal')
  --overlay             only show image (default: False)
  --annotation ANNOTATION_REGION
                        annotation brain region (default: None)

Verbose Options:
  --print-tree          print tree for the available regions for the given source (default: False)
  --tree-init TREE_INIT
                        init region for the tree print (default: None)
  --print-name          print acronym and the corresponding name (default: False)