Version 1: changes to registration and segmentation tools#
The previously separate packages
brainreg-napari have now been combined into a single package that keeps the
brainreg package contains two submodules;
brainreg.core whose contents are equivalent to the (old)
brainreg package, and
brainreg.napari that handles the napari widget.
brainreg.napari module is optional and needs to be specified at install if you are not intending to install it via the BrainGlobe version 1 package.
If you were previously using brainreg in your scripts and have updated to version 1, you will now need to use
brainreg.core instead of
However, the internal structure of the
core submodule has been retained, so updating your scripts should be a case of replacing “
brainreg” with “
brainreg.core” across your codebase.
Similarly, if you were ever importing
brainreg_napari into your Python scripts, you will need to replace all occurrences of this with
If you are installing
brainreg as part of the brainglobe version 1 package, the napari plugin will be automatically included and you won’t need to do anything else to install the plugin.
Otherwise, to install the napari plugin, you will need to install
brainreg with it’s optional napari dependency via pip (recommended)
python -m pip install brainreg[napari]
or alternatively via conda
conda install brainreg
After updating, you may want to remove the now deprecated
brainreg-napari package from your environment if it still persists;
pip uninstall brainreg-napari # If you originally installed via pip conda remove brainreg-napari # If you originally installed via conda
The command-line executable has retained the name
brainreg and has undergone no usability changes.
When loading the plugin in napari, you will now find it listed under the plugins menu as “
Atlas Registration (brainreg)” rather than “
Atlas Registration (brainreg-napari)”.
If you have external scripts that reply on the internal name of the plugin, you will need to update these to
This package has been renamed
Beyond this renaming, there have been no internal changes to the package, so you may continue to use it as previously.
However, you will need to switch all occurrences of
brainglobe_segmentation in your Python scripts.
If you want to install the package standalone (without using BrainGlobe version 1 or through installing
brainreg) then we recommend you
pip install the package into your environment:
pip install brainglobe-segmentation
If you have
brainreg-segment in your environment, you may wish to remove it as it will no longer be needed by
pip uninstall brainreg-segment
brainreg-segment is still required by