CLARITY-Allen registration

This function will do the following:

1. Registers CLARITY data (down-sampled images) to Allen Reference mouse brain atlas

2. Warps Allen annotations to the original high-res CLARITY space

3. Warps the higher-resolution CLARITY to Allen space

GUI

To open the main registration menu, open MIRACL’s main menu first by running:

$ miraclGUI

MIRACL’s main menu will open:

Select the Registration tab on the left for the main registration menu.

The main registration window will look like this:

From here you can select CLARITY-Allen to start the registration. The Reg options menu will open:

Tip

To open the above Reg options menu directly, run: $ miracl reg clar_allen

The registration will be run on downsampled CLARITY Nii images. You can provide the folder containing these files in the first field. This parameter is required to run the registration. You can use MIRACL's conversion methods to create the downsampled files if you do not have them yet.

Flag	Parameter	Description	Default
-i	Input down-sampled CLARITY Nii	Preferably auto-fluorescence channel data (or Thy1_EYFP if no auto chan). File name should have **x_down like 05x_down (meaning 5x downsampled). Example: combined split	Required. Script exits with error 1 if not provided.

All remaining parameters are optional. If left blank, their respective default values will be used:

Flag	Parameter	Description	Default
-r	Output directory	Directory the output (results) will be written to.	<working_directory>/reg_final
-o	Orient code	Code to orient nifti from original orientation to ‘standard/Allen’ orientation.	ALS
-m	Labels hemi	Chose to register to one or both hemispheres. Warps Allen labels with hemisphere split (L differ from R labels) or combined (L and R have the same labels i.e. are mirroed). Accepted inputs are: combined split	combined
-v	Labels resolution [vox]	Labels voxel size/resolution in um. Accepted inputs are: 10 25 50	10
-b	Olfactory bulb included	Specify whether the olfactory bulb is included in brain. Accepted inputs are: 0 (not included) 1 (included)	0
-s	Side	Provide this parameter if you are only registering one hemisphere instead of the whole brain. Accepted inputs are: rh (right hemisphere) lh (left hemisphere)	None
-p	Extra int correct	If utilfn intensity correction has already been run, skip correction inside registration. Accepted inputs are: 0 (don’t skip) 1 (skip)	0

After providing the parameters click Enter to save them and Run to start the registration process.

Once the registration is done the final files will be located in the output folder (default: <working_directory>/reg_final). Files created in intermediate steps will be located in a folder called <working_directory>/clar_allen_reg.

Command-line

The command-line version has additional functionality that is not included in the GUI version:

-l, input Allen labels to warp: input labels could be at a different depth than default labels.
    -m and -v flags cannot be used if this parameter is specified manually (default: annotation_hemi_combined_10um.nii.gz)
-a, input custom Allen atlas: for example for registering sections
-f, save mosaic figure (.png) of Allen labels registered to CLARITY (default: 1).
-w, warp high-res clarity to Allen space (default: 0).

Attention

Note that the above listed -i parameter (input down-sampled CLARITY Nii) is also required for the command-line

Usage:

$ miracl reg clar_allen -i [ input_clarity_nii_folder ] -o [ orientation_code ] -m [ hemispheres ] -v [ labels_resolution ] -l [ input_labels ] -s [ side_if_hemisphere_only ] -b [ olfactory_buld_included ]

Example:

$ miracl reg clar_allen -i downsampled_niftis/SHIELD_03x_down_autoflor_chan.nii.gz -o ARI -m combined -b 1

Jupyter notebook

An accompanying Jupyter notebook for this tutorial can be found here.