unravel.abca.merfish.merfish_cells_to_nii module#

Use abca_merfish_cells_to_nii or mc from UNRAVEL to convert ABCA MERFISH cells to a .nii.gz 3D image.

Prereqs:

  • merfish_cluster or merfish_filter to generate filtered cell data.

Usage:#

abca_merfish_cells_to_nii -i path/filtered_cells.csv -r path/to/reference.nii.gz [-b] [-o path/to/output.nii.gz] [-v]

unravel.abca.merfish.merfish_cells_to_nii.parse_args()[source]#
unravel.abca.merfish.merfish_cells_to_nii.merfish_cells_to_img(cell_df, img, xy_res, z_res)[source]#

Convert MERFISH cell metadata into a 3D image by marking voxel positions of cells.

Parameters:

  • cell_df (pd.DataFrame) – DataFrame containing filtered cell metadata with reconstructed coordinates.

  • img (np.ndarray) – An empty 3D NumPy array shaped like the reference .nii.gz image.

  • xy_res (float) – Resolution of the x-y plane in microns (µm).

  • z_res (float) – Resolution of the z-plane in microns (µm).

Returns:

A 3D image where cell positions are marked with 1.

Return type:

np.ndarray

unravel.abca.merfish.merfish_cells_to_nii.main()[source]#