ccf_streamlines.dataset.upscale_ish_volume#

ccf_streamlines.dataset.upscale_ish_volume(volume, orig_voxel_size=200, target_voxel_size=10, target_volume_shape=(1320, 800, 1140), rotate_axes=True)#

Upscale a lower-resolution ISH volume for projection.

Parameters

  • volume (array) – Array of ISH expression data

  • orig_voxel_size (int, default 200) – Size in microns of voxels of original data

  • target_voxel_size (int, default 10) – Size of microns of voxels in desired volume

  • target_volume_shape (tuple, default (1320, 800, 1140)) – Shape of target upscaled volume

  • rotate_axes (bool, default True) – Whether to swap the x and z axes of the input volume. Volumes downloaded directly from the ISH atlas API have the anterior-posterior axis in the z-axis and the left-right axis in the x-axis, while the CCFv3 has those swapped. The default assumes that the input volume has not been adjusted to match the CCF yet.

Returns

upscaled_volume – Upscaled ISH expression data

Return type

array