Version 1: changes to registration and segmentation tools

brainreg and brainreg-napari

The previously separate packages brainreg and brainreg-napari have now been combined into a single package that keeps the brainreg name. This (new) brainreg package contains two submodules; brainreg.core whose contents are equivalent to the (old) brainreg package, and brainreg.napari that handles the napari widget. The 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 brainreg. 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 brainreg.napari.

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

Command-line executable

The command-line executable has retained the name brainreg and has undergone no usability changes.

napari plugin

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 brainreg (from brainreg-napari) accordingly.

brainreg-segment

This package has been renamed brainglobe-segmentation. 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_segment to 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 brainreg:

pip uninstall brainreg-segment

however, brainreg-segment is still required by cellfinder versions <=v1.0.0.