brainreg
brainreg is an update to amap (itself a port of the original Java software) to include multiple registration backends, and to support the many atlases provided by bg-atlasapi.
Documentation can be found here.
Details
The aim of brainreg is to register the template brain (e.g. from the Allen Reference Atlas) to the sample image. Once this is complete, any other image in the template space can be aligned with the sample (such as region annotations, for segmentation of the sample image). The template to sample transformation can also be inverted, allowing sample images to be aligned in a common coordinate space.
To do this, the template and sample images are filtered, and then registered in a three step process (reorientation, affine registration, and freeform registration.) The resulting transform from template to standard space is then applied to the atlas.
Full details of the process are in the
original aMAP paper.
Installation
pip install brainreg
Usage
Basic usage
brainreg /path/to/raw/data /path/to/output/directory -x 2 -y 2 -z 5
Arguments
Mandatory
- Path to the directory of the images. (Can also be a text file pointing to the files)
- Output directory for all intermediate and final results
You must also specify the pixel sizes, see Specifying pixel size
Additional options
-dor--downsamplePaths to N additional channels to downsample to the same coordinate space.--sort-input-fileIf set to true, the input text file will be sorted using natural sorting. This means that the file paths will be sorted as would be expected by a human and not purely alphabetically
Misc options
--n-free-cpusThe number of CPU cores on the machine to leave unused by the program to spare resources.--debugDebug mode. Will increase verbosity of logging and save all intermediate files for diagnosis of software issues.
Atlas
By default, brainreg will use the 25um version of the Allen Mouse Brain Atlas. To use another atlas (e.g. for another species, or another resolution), you must use the --atlas flag, followed by the string describing the atlas, e.g.:
--atlas allen_mouse_50um
To find out which atlases are available, once brainreg is installed, please run brainglobe list. The name of the resulting atlases is the string to pass with the --atlas flag.
Registration backend
To change the registration algorithm used, use the --backend flag. The default is niftyreg as that is currently the only option.
Input data orientation
If your data does not match the brainglobe default orientation (the origin voxel is the most anterior, superior, left-most voxel, then you must specify the orientation by using the --orientation flag. What follows must be a string in the bg-space "initials" form, to describe the origin voxel.
If the origin of your data (first, top left voxel) is the most posterior, superior, left part of the brain, then the orientation string would be "psl" (posterior, superior, left), and you would use:
--orientation psl
Registration options
To change how the actual registration performs, see Registration parameters
Full command-line arguments are available with brainreg -h, but please
get in touch if you have any questions.
2 maintainers
Release files for brainreg 0.0.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| brainreg-0.0.2.tar.gz | 16.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| brainreg-0.0.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 36.4 kB
Release files / brainreg-0.0.2.tar.gz
| Download URL | brainreg-0.0.2.tar.gz |
|---|---|
| Size | 16.7 kB |
| Tags | Source |
|
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Release files / brainreg-0.0.2-py3-none-any.whl
| Download URL | brainreg-0.0.2-py3-none-any.whl |
|---|---|
| Size | 19.8 kB |
| Tags | Python 3 |
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twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/49.2.0.post20200714 requests-toolbelt/0.9.1 tqdm/4.47.0 CPython/3.6.10
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