m2m_crossing_finder

Find crossing regions (ROIs) between Allen Mouse Brain Connectivity experiments. Experiments are found by search in the Allen Mouse Brain Connectivity API giving two or three MI-Brain voxel coordinates.

Generate projection density maps for each experiment. Maps are downloaded from the Allen Mouse Brain Connectivity API.

Generate a RGB projection density volume combining each experiments founded. (–red, –green, –blue). At least two colors (coordinates) are mandatory.

Generate a mask at crossing regions if projection density is superior to threshold (–threshold) for each experiment founded. Masks are download from Allen Mouse Brain Altas.

Generate a json file enumarating each crossing regions.

All files are stored in a same folder.

Important: Select the same resolution as your matrix We higly recommend to work with high resolution (starting from 50) in order to search experiments more precisely.

2 colors:

Injection coordinate search: (–injection)
>>> m2m_crossing_finder.py path/to/.mat path/to/ref.nii.gz
    resolution --red x y z --green x y z --injection --dir dir
Spatial search: (–spatial):
>>> m2m_crossing_finder.py path/to/.mat path/to/ref.nii.gz
    resolution --red x y z --green x y z --spatial --dir dir
3 colors:
>>> m2m_crossing_finder.py path/to/.mat path/to/ref.nii.gz
    resolution --red x y z --green x y z --blue x y z --injection --dir dir

usage: m2m_crossing_finder.py [-h] --red RED RED RED --green GREEN GREEN GREEN
                              [--blue BLUE BLUE BLUE]
                              (--injection | --spatial)
                              [--threshold THRESHOLD] [-d DIR] [-c] [-f]
                              file_mat reference {25,50,100}

Positional Arguments

file_mat

Path to transform matrix (.mat)

reference

Path to reference volume (.nii.gz)

res

Possible choices: 25, 50, 100

Resolution of the Allen files Please use the same resolution as the transformation matrix.

Named Arguments

--red

MI-Brain voxels coordinates of first experiment. First experiment will be colored in red.

--green

MI-Brain voxels coordinates of second experiment. Second experiment will be colored in green.

--blue

MI-Brain voxels coordinates of third experiment. Third experiment will be colored in blue.

--injection

Use experiment_injection_coordinate_search to find experiments. https://allensdk.readthedocs.io/en/latest/allensdk.api.queries.mouse_connectivity_api.html

Default: False

--spatial

Use experiment_spatial_search to find experiments. https://allensdk.readthedocs.io/en/latest/allensdk.api.queries.mouse_connectivity_api.html

Default: False

--threshold

Combined projection density threshold for finding masks of crossing ROIs. Threshold is 0.10 by default. –threshold <value> will set threshold to value.

Default: 0.1

-d, --dir

Path of the ouptut file directory is . by default. Using –dir <dir> will change the output file’s directory or create a new one if does not exits.

Default: “.”

-c, --nocache

Update the Allen Mouse Brain Connectivity Cache

Default: False

-f

Force overwriting of the output files.

Default: False

Author : Mahdi