brainreg
brainreg copied to clipboard
brainglobe
Automated 3D brain registration with support for multiple species and atlases.
for issue #84, PR #91 changes the flags to -a and --additional. However, it would be preferable to remove this flag and for brainreg to accept N images, and use...
Currently the preprocessing is hard coded. There should be options for different types of filters etc to allow systematic optimisation
Installing brainreg brings in 3.4GB of dependencies, as measured by my virtualenv folder's size. I see many things I don't think(?!) I need for a simple registration - e.g. ipython,...
When registering data with Elastix the transform parameters are saved to disk and it is possible to use the `transformix` command to rapidly apply these parameters to a new volume....
Add `--pre-processing` command line option, which accepts strings such as 'fmost', 'none', 'default'. Add pre-processing functions specifically for fMOST datasets, which remove horizontal stripes and background.
Passing e.g. `-d image2.tiff` gives output such as `downsampled_image2.tiff.tiff` and `downsampled_standard_image2.tiff.tiff`.
A number of issues lead to unhelpful error messages (e.g. [this one](https://forum.image.sc/t/brainreg-could-not-broadcast-input-array-from-shape-error/69169) and [this one](https://forum.image.sc/t/valueerror-brainreg/64171)). These should be caught, and more useful information presented to the user.
Now NityReg is on conda, we should be able to more easily support macOS. This would require: - [ ] Supporting system installations of NityReg (rather than the packaged binaries)...
Metadata
Owner
Metadata
Automated 3D brain registration with support for multiple species and atlases.