diff --git a/README.md b/README.md index 95a1ed5..487d1ed 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ # brainreg brainreg is an update to [amap](https://github.com/SainsburyWellcomeCentre/amap_python) (which is itself a port -of the [original Java software](https://www.nature.com/articles/ncomms11879)) to include multiple registration backends, and to support the many atlases provided by [bg-atlasapi](https://github.com/brainglobe/bg-atlasapi). +of the [original Java software](https://www.nature.com/articles/ncomms11879)) to include multiple registration backends, and to support the many atlases provided by [brainglobe-atlasapi](https://github.com/brainglobe/brainglobe-atlasapi). It also comes with an optional [napari plugin](https://github.com/brainglobe/brainreg-napari) if you'd rather use brainreg with through graphical interface. Documentation for both the command-line tool and graphical interface can be found [here](https://brainglobe.info/documentation/brainreg/index.html). diff --git a/brainreg/core/backend/niftyreg/run.py b/brainreg/core/backend/niftyreg/run.py index 10187de..1c0d970 100644 --- a/brainreg/core/backend/niftyreg/run.py +++ b/brainreg/core/backend/niftyreg/run.py @@ -4,7 +4,7 @@ import brainglobe_space as bg import numpy as np -from bg_atlasapi import BrainGlobeAtlas +from brainglobe_atlasapi import BrainGlobeAtlas from brainglobe_utils.general.system import delete_directory_contents from brainglobe_utils.image.scale import scale_and_convert_to_16_bits from brainglobe_utils.image_io import load_any, to_tiff diff --git a/brainreg/core/main.py b/brainreg/core/main.py index 615b1f0..35f81db 100644 --- a/brainreg/core/main.py +++ b/brainreg/core/main.py @@ -1,7 +1,7 @@ import logging import brainglobe_space as bg -from bg_atlasapi import BrainGlobeAtlas +from brainglobe_atlasapi import BrainGlobeAtlas from brainglobe_utils.general.system import get_num_processes from brainglobe_utils.image_io import load_any diff --git a/brainreg/napari/register.py b/brainreg/napari/register.py index e4674f9..c780bdc 100644 --- a/brainreg/napari/register.py +++ b/brainreg/napari/register.py @@ -8,8 +8,8 @@ import brainglobe_space as bg import napari import numpy as np -from bg_atlasapi import BrainGlobeAtlas -from bg_atlasapi.list_atlases import descriptors, utils +from brainglobe_atlasapi import BrainGlobeAtlas +from brainglobe_atlasapi.list_atlases import descriptors, utils from brainglobe_napari_io.brainmapper.brainmapper_reader_dir import ( load_registration, ) diff --git a/brainreg/napari/util.py b/brainreg/napari/util.py index fbfcd88..af19a0d 100644 --- a/brainreg/napari/util.py +++ b/brainreg/napari/util.py @@ -4,7 +4,7 @@ import brainglobe_space as bg import numpy as np import skimage.transform -from bg_atlasapi import BrainGlobeAtlas +from brainglobe_atlasapi import BrainGlobeAtlas from brainglobe_utils.general.system import get_num_processes from tqdm import tqdm diff --git a/pyproject.toml b/pyproject.toml index c53b373..36d091c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ classifiers = [ ] requires-python = ">=3.9" dependencies = [ - "bg-atlasapi", + "brainglobe-atlasapi>=2.0.1", "brainglobe-space>=1.0.0", "brainglobe-utils>=0.4.0", "fancylog", diff --git a/tests/test_brainreg_napari.py b/tests/test_brainreg_napari.py index 210972c..fdd5ac7 100644 --- a/tests/test_brainreg_napari.py +++ b/tests/test_brainreg_napari.py @@ -1,6 +1,6 @@ import napari import pytest -from bg_atlasapi import BrainGlobeAtlas +from brainglobe_atlasapi import BrainGlobeAtlas from brainreg.napari.register import ( add_registered_image_layers,