CLARITY whole-brain registration to Allen Atlas

The registration workflow relies on an autofluorescence channel input (tiff files), and can perform whole-brain or hemisphere registrations to the Allen Atlas.

This workflow performs the following tasks:

1. Sets orientation of input data using a GUI

2. Converts TIFF to NII

3. Registers CLARITY data (down-sampled images) to Allen Reference mouse brain Atlas

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

5. Warps the higher-resolution CLARITY to Allen space (if chosen)

6. Test data

7. A test dataset (CLARITY autofluorescence channel) for registration is found here under data: https://www.dropbox.com/sh/i9swdedx7bsz1s8/AABpDmmN1uqPz6qpBLYLtt8va

Main outputs

File	Description
reg_final/clar_allen_space.nii.gz	CLARITY data in Allen reference space
reg_final/clar_downsample_res{vox}um.nii.gz	CLARITY data downsampled and oriented to ‘standard’
reg_final/annotation_hemi_{hemi}_{vox}um_clar_downsample.nii.gz	Allen labels registered to downsampled CLARITY
reg_final/annotation_hemi_{hemi}_{vox}um_clar_vox.tif	Allen labels registered to oriented CLARITY
reg_final/annotation_hemi_{hemi}_{vox}um_clar.tif	Allen labels registered to original (full-resolution) CLARITY

GUI

Run:

$ miraclGUI

and choose CLARITY-Allen Registration from the Workflows tab:

Or run:

$ miracl flow reg_clar

Choose the input tiff folder with the auto fluorescence channel from the pop-up menu:

The following GUI will appear which opens the data and lets you set its orientation manually:

You can navigate through the data using the bar bellow, by specifying the slice number or using the arrows:

First choose the data plane (axial, coronal or sagittal):

Then choose the orientation at the top and right of the image:

Next, choose the orientation for scrolling through the slices (going into the page), can confirm the orientation by changing the image number at the bottom (enter higher number and press Enter), or using the Next or Prev image buttons:

Finally close the GUI:

Next, set the tiff conversion parameters:

Conversion parameters description:

Parameter	Description Default
out nii	Output nifti name	clarity
downsample ratio	Downsample factor for conversion	5
channel #	Number for extracting single channel from multiple channel data (leave blank if single channel data/tiff files)	0
channel prefix	String before channel number in file name (leave blank if single channel). For example, if tiff file name has _C001_.tif for channel 1 and _C002_.tif for channel 2, to choose channel 1 if it’s the auto fluorescence channel: Chan number would be: 1 Chan prefix would be: C00	Channel prefix not invoked if not provided
channel name	Output channel name	eyfp
in-plane res	Original resolution in x-y plane in um	5
z res	Thickness (z-axis resolution/spacing between slices) in um	5
center	Center of nifti file	0 0 0

Next, choose the registration options:

Registration parameters description:

Parameter	Description	Default
Hemi	Warp Allen labels with hemisphere split (Left labels are different from Right labels) or combined (Left and Right lables are the same i.e. mirrored). Accepted inputs are: combined split	combined
Labels resolution [vox]	Voxel size/resolution of labels in um accepted inputs are: 10, 25 or 50	10
olfactory bulb	If olfactory bulb is included in the dataset. Accepted inputs are: 0 (not included) 1 (included)	0
Side	Only if registering hemisphere, else leave blank. Accepted inputs are: rh (right hemisphere) lh (left hemisphere)	None

Command-line

Usage:

$ miracl flow reg_clar -f [ Tiff folder ]

Example:

$ miracl flow reg_clar  -f my_tifs -n "-d 5 -ch autofluo" -r "-o ARS -m combined -v 25"

Arguments (required):

f. Input Clarity tif dir/folder

Optional arguments (remember the quotes):

Conversion to nii (invoked by -n " "):

d.  [ Downsample ratio (default: 5) ]
cn. [ chan # for extracting single channel from multiple channel data (default: 0) ]
cp. [ chan prefix (string before channel number in file name). ex: C00 ]
ch. [ output chan name (default: eyfp) ]
vx. [ original resolution in x-y plane in um (default: 5) ]
vz. [ original thickness (z-axis resolution / spacing between slices) in um (default: 5) ]
c.  [ nii center (default: 5.7 -6.6 -4) corresponding to Allen atlas nii template ]

Registration (invoked by -r " "):

o. Orient code (default: ALS)
   to orient nifti from original orientation to "standard/Allen" orientation
m. Warp allen labels with hemisphere split (Left different than Right labels) or combined (L & R same labels / Mirrored)
   accepted inputs are: <split> or <combined>  (default: combined)
v. Labels voxel size/Resolution of labels in um
   accepted inputs are: 10, 25 or 50  (default: 10)
l. image of input Allen Labels to warp (default: annotation_hemi_split_10um.nii.gz - which are at a resolution of 0.01mm/10um)
   input could be at a different depth than default labels
   If l. is specified (m & v cannot be specified)

Visualize results

Run:

$ miracl reg check

Usage:

$ miracl reg check -f [ reg_final_folde r] -v [ visualization_software ] -s [ reg_space_(clarity_or_allen) ]

Example:

$ miracl reg check -f reg_final -v itk -s clarity

Arguments:

Required:

  -f, Input final registration folder

Optional:

  -v, Visualization software: itkSNAP 'itk' (default) or freeview 'free'
  -s, Registration Space of results: clarity (default) or allen