[BUG] Unable to set alpha of add_brain_region when running from Jupyter Notebook

[harshk95]

I am unable to set the alpha of the brain region added via the alpha argument. Without the argument set one can see with alpha = 1, however, for any other value of alpha, it appears as if alpha were set at 0.

This is for Brainrender v2.1.9

For example, running the example notebook workflow,

import vedo
vedo.settings.default_backend= 'vtk'

from brainrender import Scene
popup_scene = Scene(atlas_name='allen_mouse_50um', title='popup')

popup_scene.add_brain_region('VISp', alpha = 0.99)

popup_scene.render() 

yields

while running

import vedo
vedo.settings.default_backend= 'vtk'

from brainrender import Scene
popup_scene = Scene(atlas_name='allen_mouse_50um', title='popup')

popup_scene.add_brain_region('VISp', alpha = 1)

popup_scene.render() 

yields

• OS: Windows Server 2022
• Hardware specs Intel Xeon Platinum 8260, 384GB RAM

[alessandrofelder]

Hi @harshk95
Thanks for reporting - I ran 2.1.9 on my Macbook and couldn't reproduce this issue, so it might be a Windows thing - or a bug in older versions of the dependencies... not sure. With alpha=0.1 I get:

Could you try updating your brainrender and your vedo by running

pip install -U brainrender
pip install -U vedo

And let us know if you still encounter the problem, please?

If the problem persists, please post a list of your installed packages (pip list or conda list) in your environment.

[harshk95]

Hi thanks for the reply,

despite running the updates, the issue seems to persist.

Brainrender v 2.1.9
vedo v 2024.5.2

I am using the environment for a bunch of processing the end of which is a visualisation with brainrender.

conda list:

absl-py 2.1.0 pypi_0 pypi
affinewarp 0.1.0 pypi_0 pypi
aiohappyeyeballs 2.4.0 pypi_0 pypi
aiohttp 3.10.5 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
alabaster 0.7.16 pypi_0 pypi
allensdk 2.16.2 pypi_0 pypi
anndata 0.10.9 pypi_0 pypi
annotated-types 0.7.0 pypi_0 pypi
anyio 4.4.0 pypi_0 pypi
app-model 0.2.8 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
apptools 5.3.0 pypi_0 pypi
argon2-cffi 23.1.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
argschema 3.0.4 pypi_0 pypi
array-api-compat 1.8 pypi_0 pypi
arrow 1.3.0 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
asttokens 2.4.1 pypi_0 pypi
async-lru 2.0.4 pypi_0 pypi
async-timeout 4.0.3 pypi_0 pypi
attrs 24.2.0 pypi_0 pypi
babel 2.16.0 pypi_0 pypi
bctpy 0.6.1 pypi_0 pypi
beautifulsoup4 4.12.3 pypi_0 pypi
bleach 6.1.0 pypi_0 pypi
blosc2 2.5.1 pypi_0 pypi
boto3 1.35.10 pypi_0 pypi
botocore 1.35.10 pypi_0 pypi
brainglobe 1.1.0 pypi_0 pypi
brainglobe-atlasapi 2.0.6 pypi_0 pypi
brainglobe-heatmap 0.5.3 pypi_0 pypi
brainglobe-napari-io 0.3.4 pypi_0 pypi
brainglobe-segmentation 1.2.4 pypi_0 pypi
brainglobe-space 1.0.2 pypi_0 pypi
brainglobe-utils 0.5.0 pypi_0 pypi
brainreg 1.0.9 pypi_0 pypi
brainrender 2.1.9 pypi_0 pypi
brainrender-napari 0.0.3 pypi_0 pypi
bs4 0.0.2 pypi_0 pypi
build 1.2.1 pypi_0 pypi
ca-certificates 2024.8.30 h56e8100_0 conda-forge
cachetools 5.5.0 pypi_0 pypi
cachey 0.2.1 pypi_0 pypi
ccf-streamlines 1.1.4 pypi_0 pypi
cebra 0.4.0 pypi_0 pypi
cellfinder 1.3.0 pypi_0 pypi
certifi 2024.8.30 pypi_0 pypi
cffi 1.17.0 pypi_0 pypi
charset-normalizer 3.3.2 pypi_0 pypi
click 8.1.7 pypi_0 pypi
cloudpickle 3.0.0 pypi_0 pypi
cmcrameri 1.9 pypi_0 pypi
colorama 0.4.6 pypi_0 pypi
comm 0.2.2 pypi_0 pypi
configobj 5.0.8 pypi_0 pypi
contourpy 1.3.0 pypi_0 pypi
cuda-version 11.0 h6b8d8af_3 conda-forge
cudatoolkit 11.0.3 hd336c7a_13 conda-forge
cupy 12.1.0 py39h58dc777_0 conda-forge
cycler 0.12.1 pypi_0 pypi
dask 2024.8.0 pypi_0 pypi
debugpy 1.8.5 pypi_0 pypi
decorator 4.4.2 pypi_0 pypi
defusedxml 0.7.1 pypi_0 pypi
distro 1.9.0 pypi_0 pypi
docstring-parser 0.16 pypi_0 pypi
docutils 0.21.2 pypi_0 pypi
envisage 7.0.3 pypi_0 pypi
exceptiongroup 1.2.2 pypi_0 pypi
executing 2.1.0 pypi_0 pypi
fancylog 0.4.2 pypi_0 pypi
fasteners 0.19 pypi_0 pypi
fastjsonschema 2.20.0 pypi_0 pypi
fastrlock 0.8.2 py39h99910a6_2 conda-forge
ffmpeg-python 0.2.0 pypi_0 pypi
filelock 3.15.4 pypi_0 pypi
flexcache 0.3 pypi_0 pypi
flexparser 0.3.1 pypi_0 pypi
fonttools 4.53.1 pypi_0 pypi
fqdn 1.5.1 pypi_0 pypi
freetype-py 2.5.1 pypi_0 pypi
frozenlist 1.4.1 pypi_0 pypi
fsspec 2024.6.1 pypi_0 pypi
future 1.0.0 pypi_0 pypi
get-annotations 0.1.2 pypi_0 pypi
git 2.45.2 haa95532_0
glymur 0.13.6 pypi_0 pypi
google 3.0.0 pypi_0 pypi
greenlet 3.0.3 pypi_0 pypi
h11 0.14.0 pypi_0 pypi
h5py 3.11.0 pypi_0 pypi
hdmf 3.14.3 pypi_0 pypi
heapdict 1.0.1 pypi_0 pypi
hsluv 5.0.4 pypi_0 pypi
httpcore 1.0.5 pypi_0 pypi
httpx 0.27.2 pypi_0 pypi
idna 3.8 pypi_0 pypi
imagecodecs 2024.6.1 pypi_0 pypi
imageio 2.35.1 pypi_0 pypi
imageio-ffmpeg 0.5.1 pypi_0 pypi
imagesize 1.4.1 pypi_0 pypi
imbalanced-learn 0.12.3 pypi_0 pypi
imio 0.3.1 pypi_0 pypi
importlib-metadata 8.4.0 pypi_0 pypi
importlib-resources 6.4.4 pypi_0 pypi
in-n-out 0.2.1 pypi_0 pypi
iniconfig 2.0.0 pypi_0 pypi
intel-openmp 2024.2.1 h57928b3_1083 conda-forge
ipykernel 6.29.5 pypi_0 pypi
ipython 8.18.1 pypi_0 pypi
ipywidgets 8.1.5 pypi_0 pypi
isoduration 20.11.0 pypi_0 pypi
jax 0.4.30 pypi_0 pypi
jaxlib 0.4.30 pypi_0 pypi
jaxopt 0.8.3 pypi_0 pypi
jedi 0.19.1 pypi_0 pypi
jinja2 3.1.4 pypi_0 pypi
jmespath 1.0.1 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
json5 0.9.25 pypi_0 pypi
jsonpointer 3.0.0 pypi_0 pypi
jsonschema 4.23.0 pypi_0 pypi
jsonschema-specifications 2023.12.1 pypi_0 pypi
jupyter-client 8.6.2 pypi_0 pypi
jupyter-core 5.7.2 pypi_0 pypi
jupyter-events 0.10.0 pypi_0 pypi
jupyter-lsp 2.2.5 pypi_0 pypi
jupyter-server 2.14.2 pypi_0 pypi
jupyter-server-terminals 0.5.3 pypi_0 pypi
jupyterlab 4.2.5 pypi_0 pypi
jupyterlab-pygments 0.3.0 pypi_0 pypi
jupyterlab-server 2.27.3 pypi_0 pypi
jupyterlab-widgets 3.0.13 pypi_0 pypi
k3d 2.16.1 pypi_0 pypi
keras 3.5.0 pypi_0 pypi
kiwisolver 1.4.5 pypi_0 pypi
lazy-loader 0.4 pypi_0 pypi
legacy-api-wrap 1.4 pypi_0 pypi
libblas 3.9.0 23_win64_mkl conda-forge
libcblas 3.9.0 23_win64_mkl conda-forge
libhwloc 2.11.1 default_h8125262_1000 conda-forge
libiconv 1.17 hcfcfb64_2 conda-forge
liblapack 3.9.0 23_win64_mkl conda-forge
libxml2 2.12.7 h0f24e4e_4 conda-forge
libzlib 1.3.1 h2466b09_1 conda-forge
literate-dataclasses 0.0.6 pypi_0 pypi
llvmlite 0.43.0 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
loguru 0.7.2 pypi_0 pypi
lxml 5.3.0 pypi_0 pypi
magicgui 0.9.1 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 2.1.5 pypi_0 pypi
marshmallow 3.22.0 pypi_0 pypi
matplotlib 3.9.2 pypi_0 pypi
matplotlib-inline 0.1.7 pypi_0 pypi
matplotlib-venn 1.1.1 pypi_0 pypi
mayavi 4.8.2 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
meshio 5.3.5 pypi_0 pypi
mistune 3.0.2 pypi_0 pypi
mkl 2024.1.0 h66d3029_694 conda-forge
ml-dtypes 0.4.0 pypi_0 pypi
morphapi 0.2.5 pypi_0 pypi
morphio 3.3.9 pypi_0 pypi
moviepy 1.0.3 pypi_0 pypi
mpmath 1.3.0 pypi_0 pypi
msgpack 1.0.8 pypi_0 pypi
multidict 6.0.5 pypi_0 pypi
myterial 1.2.1 pypi_0 pypi
namex 0.0.8 pypi_0 pypi
napari 0.5.3 pypi_0 pypi
napari-console 0.0.9 pypi_0 pypi
napari-ndtiffs 0.2.1 pypi_0 pypi
napari-plugin-engine 0.2.0 pypi_0 pypi
napari-plugin-manager 0.1.0 pypi_0 pypi
napari-svg 0.2.0 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
nbclient 0.10.0 pypi_0 pypi
nbconvert 7.16.4 pypi_0 pypi
nbformat 5.10.4 pypi_0 pypi
ndindex 1.8 pypi_0 pypi
ndx-events 0.2.0 pypi_0 pypi
nemos 0.1.6 pypi_0 pypi
nest-asyncio 1.6.0 pypi_0 pypi
networkx 3.2.1 pypi_0 pypi
neurom 3.2.11 pypi_0 pypi
nibabel 5.2.1 pypi_0 pypi
notebook-shim 0.2.4 pypi_0 pypi
npe2 0.7.7 pypi_0 pypi
nptyping 2.5.0 pypi_0 pypi
npyx 4.0.6 pypi_0 pypi
numba 0.60.0 pypi_0 pypi
numcodecs 0.12.1 pypi_0 pypi
numexpr 2.10.1 pypi_0 pypi
numpy 1.23.5 pypi_0 pypi
numpydoc 1.8.0 pypi_0 pypi
opencv-python 4.10.0.84 pypi_0 pypi
openssl 3.3.1 h2466b09_3 conda-forge
opt-einsum 3.3.0 pypi_0 pypi
optree 0.12.1 pypi_0 pypi
overrides 7.7.0 pypi_0 pypi
packaging 24.1 pypi_0 pypi
pandas 1.5.3 pypi_0 pypi
pandocfilters 1.5.1 pypi_0 pypi
parso 0.8.4 pypi_0 pypi
partd 1.4.2 pypi_0 pypi
patsy 0.5.6 pypi_0 pypi
pillow 10.4.0 pypi_0 pypi
pint 0.24.3 pypi_0 pypi
pip 24.2 py39haa95532_0
platformdirs 4.2.2 pypi_0 pypi
pluggy 1.5.0 pypi_0 pypi
pooch 1.8.2 pypi_0 pypi
proglog 0.1.10 pypi_0 pypi
prometheus-client 0.20.0 pypi_0 pypi
prompt-toolkit 3.0.47 pypi_0 pypi
psutil 6.0.0 pypi_0 pypi
psycopg2-binary 2.9.9 pypi_0 pypi
psygnal 0.11.1 pypi_0 pypi
pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge
pure-eval 0.2.3 pypi_0 pypi
py 1.11.0 pypi_0 pypi
py-cpuinfo 9.0.0 pypi_0 pypi
pyarrow 17.0.0 pypi_0 pypi
pyconify 0.1.6 pypi_0 pypi
pycparser 2.22 pypi_0 pypi
pydantic 2.8.2 pypi_0 pypi
pydantic-compat 0.1.2 pypi_0 pypi
pydantic-core 2.20.1 pypi_0 pypi
pyface 8.0.0 pypi_0 pypi
pygments 2.18.0 pypi_0 pypi
pyinspect 0.1.0 pypi_0 pypi
pymcubes 0.1.6 pypi_0 pypi
pynapple 0.6.6 pypi_0 pypi
pynndescent 0.5.13 pypi_0 pypi
pynrrd 1.0.0 pypi_0 pypi
pynwb 2.8.1 pypi_0 pypi
pyopengl 3.1.7 pypi_0 pypi
pyparsing 3.1.4 pypi_0 pypi
pyproject-hooks 1.1.0 pypi_0 pypi
pyqt5 5.15.11 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.15.0 pypi_0 pypi
pytest 8.3.2 pypi_0 pypi
python 3.9.19 h1aa4202_1
python-dateutil 2.9.0.post0 pypi_0 pypi
python-json-logger 2.0.7 pypi_0 pypi
python_abi 3.9 2_cp39 conda-forge
pytz 2024.1 pypi_0 pypi
pywin32 306 pypi_0 pypi
pywinpty 2.0.13 pypi_0 pypi
pyyaml 6.0.2 pypi_0 pypi
pyzmq 26.2.0 pypi_0 pypi
qtconsole 5.6.0 pypi_0 pypi
qtpy 2.4.1 pypi_0 pypi
referencing 0.35.1 pypi_0 pypi
requests 2.32.3 pypi_0 pypi
requests-toolbelt 1.0.0 pypi_0 pypi
retry 0.9.2 pypi_0 pypi
rfc3339-validator 0.1.4 pypi_0 pypi
rfc3986-validator 0.1.1 pypi_0 pypi
rich 13.8.0 pypi_0 pypi
rpds-py 0.20.0 pypi_0 pypi
ruamel-yaml 0.18.6 pypi_0 pypi
ruamel-yaml-clib 0.2.8 pypi_0 pypi
s3transfer 0.10.2 pypi_0 pypi
scanpy 1.10.2 pypi_0 pypi
scikit-build 0.18.1 pypi_0 pypi
scikit-image 0.24.0 pypi_0 pypi
scikit-learn 1.5.1 pypi_0 pypi
scipy 1.10.0 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
semver 3.0.2 pypi_0 pypi
send2trash 1.8.3 pypi_0 pypi
session-info 1.0.0 pypi_0 pypi
setuptools 57.0.0 pypi_0 pypi
shellingham 1.5.4 pypi_0 pypi
simpleitk 2.4.0 pypi_0 pypi
simplejson 3.19.3 pypi_0 pypi
six 1.16.0 pypi_0 pypi
slurmio 0.1.1 pypi_0 pypi
sniffio 1.3.1 pypi_0 pypi
snowballstemmer 2.2.0 pypi_0 pypi
soupsieve 2.6 pypi_0 pypi
sphinx 7.4.7 pypi_0 pypi
sphinxcontrib-applehelp 2.0.0 pypi_0 pypi
sphinxcontrib-devhelp 2.0.0 pypi_0 pypi
sphinxcontrib-htmlhelp 2.1.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 2.0.0 pypi_0 pypi
sphinxcontrib-serializinghtml 2.0.0 pypi_0 pypi
sqlalchemy 2.0.32 pypi_0 pypi
sqlite 3.45.3 h2bbff1b_0
stack-data 0.6.3 pypi_0 pypi
statsmodels 0.14.2 pypi_0 pypi
stdlib-list 0.10.0 pypi_0 pypi
superqt 0.6.7 pypi_0 pypi
sympy 1.13.2 pypi_0 pypi
tables 3.9.2 pypi_0 pypi
tabulate 0.9.0 pypi_0 pypi
tbb 2021.12.0 hc790b64_4 conda-forge
tdt 0.6.6 pypi_0 pypi
terminado 0.18.1 pypi_0 pypi
threadpoolctl 3.5.0 pypi_0 pypi
tifffile 2024.8.30 pypi_0 pypi
tinycss2 1.3.0 pypi_0 pypi
tomli 2.0.1 pypi_0 pypi
tomli-w 1.0.0 pypi_0 pypi
toolz 0.12.1 pypi_0 pypi
torch 2.4.0 pypi_0 pypi
tornado 6.4.1 pypi_0 pypi
tqdm 4.66.5 pypi_0 pypi
traitlets 5.14.3 pypi_0 pypi
traits 6.4.3 pypi_0 pypi
traitsui 8.0.0 pypi_0 pypi
traittypes 0.2.1 pypi_0 pypi
treelib 1.7.0 pypi_0 pypi
triangle 20230923 pypi_0 pypi
typer 0.12.5 pypi_0 pypi
types-python-dateutil 2.9.0.20240821 pypi_0 pypi
typing-extensions 4.12.2 pypi_0 pypi
tzdata 2024a h04d1e81_0
ucrt 10.0.22621.0 h57928b3_0 conda-forge
umap-learn 0.5.6 pypi_0 pypi
uri-template 1.3.0 pypi_0 pypi
urllib3 1.26.20 pypi_0 pypi
vc 14.40 h2eaa2aa_0
vc14_runtime 14.40.33810 hcc2c482_20 conda-forge
vedo 2024.5.2 pypi_0 pypi
vispy 0.14.3 pypi_0 pypi
vs2015_runtime 14.40.33810 h3bf8584_20 conda-forge
vtk 9.3.1 pypi_0 pypi
wcwidth 0.2.13 pypi_0 pypi
webcolors 24.8.0 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.8.0 pypi_0 pypi
wheel 0.43.0 py39haa95532_0
widgetsnbextension 4.0.13 pypi_0 pypi
win32-setctime 1.1.0 pypi_0 pypi
wrapt 1.16.0 pypi_0 pypi
xarray 2023.1.0 pypi_0 pypi
xmltodict 0.13.0 pypi_0 pypi
yarl 1.9.7 pypi_0 pypi
zarr 2.18.2 pypi_0 pypi
zipp 3.20.1 pypi_0 pypi

[adamltyson]

Hi @harshk95, it looks like brainrender hasn't been updated. Was your conda environment activated when you ran the installation command?

[harshk95]

Hi @adamltyson , it was indeed in the environment. However, I had python 3.9 which was only supported by brainrender 2.1.9. I recreated the environment with python 3.10 which is required by the latest brainrender distribution, but the issue persists. Pasted below is the pip list of the environment for confirmation.

Package Version

---

absl-py 2.1.0
aiohappyeyeballs 2.4.3
aiohttp 3.10.10
aiosignal 1.3.1
alabaster 1.0.0
allensdk 2.16.2
anndata 0.10.9
annotated-types 0.7.0
anyio 4.6.2.post1
app-model 0.3.0
appdirs 1.4.4
apptools 5.3.0
argon2-cffi 23.1.0
argon2-cffi-bindings 21.2.0
argschema 3.0.4
array_api_compat 1.9
arrow 1.3.0
asciitree 0.3.3
asttokens 2.4.1
async-lru 2.0.4
async-timeout 4.0.3
attrs 24.2.0
babel 2.16.0
bctpy 0.6.1
beautifulsoup4 4.12.3
bleach 6.1.0
blosc2 2.7.1
boto3 1.35.49
botocore 1.35.49
brainglobe 1.3.1
brainglobe-atlasapi 2.0.9
brainglobe-heatmap 0.5.4
brainglobe-napari-io 0.3.4
brainglobe-segmentation 1.2.6
brainglobe_space 1.0.2
brainglobe-utils 0.6.2
brainreg 1.0.10
brainrender 2.1.15
brainrender-napari 0.0.4.post1
bs4 0.0.2
build 1.2.2.post1
cachetools 5.5.0
cachey 0.2.1
ccf_streamlines 1.1.4
cebra 0.4.0
cellfinder 1.3.3
certifi 2024.8.30
cffi 1.17.1
charset-normalizer 3.4.0
click 8.1.7
cloudpickle 3.1.0
cmcrameri 1.9
colorama 0.4.6
comm 0.2.2
configobj 5.0.9
contourpy 1.3.0
cupy 12.1.0
cycler 0.12.1
dask 2024.8.1
debugpy 1.8.7
decorator 4.4.2
defusedxml 0.7.1
distro 1.9.0
docstring_parser 0.16
docutils 0.21.2
envisage 7.0.3
exceptiongroup 1.2.2
executing 2.1.0
fancylog 0.4.3
fasteners 0.19
fastjsonschema 2.20.0
fastrlock 0.8.2
ffmpeg-python 0.2.0
filelock 3.16.1
flexcache 0.3
flexparser 0.3.1
fonttools 4.54.1
fqdn 1.5.1
freetype-py 2.5.1
frozenlist 1.5.0
fsspec 2024.10.0
future 1.0.0
Glymur 0.13.6
google 3.0.0
greenlet 3.1.1
h11 0.14.0
h5py 3.12.1
hdmf 3.14.5
HeapDict 1.0.1
hsluv 5.0.4
httpcore 1.0.6
httpx 0.27.2
idna 3.10
imagecodecs 2024.9.22
imageio 2.36.0
imageio-ffmpeg 0.5.1
imagesize 1.4.1
imbalanced-learn 0.12.4
importlib_metadata 8.5.0
importlib_resources 6.4.5
in-n-out 0.2.1
ipykernel 6.29.5
ipython 8.29.0
ipywidgets 8.1.5
isoduration 20.11.0
jax 0.4.30
jaxlib 0.4.30
jaxopt 0.8.3
jedi 0.19.1
Jinja2 3.1.4
jmespath 1.0.1
joblib 1.4.2
json5 0.9.25
jsonpointer 3.0.0
jsonschema 4.23.0
jsonschema-specifications 2024.10.1
jupyter_client 8.6.3
jupyter_core 5.7.2
jupyter-events 0.10.0
jupyter-lsp 2.2.5
jupyter_server 2.14.2
jupyter_server_terminals 0.5.3
jupyterlab 4.2.5
jupyterlab_pygments 0.3.0
jupyterlab_server 2.27.3
jupyterlab_widgets 3.0.13
k3d 2.16.1
keras 3.5.0
kiwisolver 1.4.7
lazy_loader 0.4
legacy-api-wrap 1.4
literate-dataclasses 0.0.6
llvmlite 0.43.0
locket 1.0.0
loguru 0.7.2
lxml 5.3.0
magicgui 0.9.1
markdown-it-py 3.0.0
MarkupSafe 3.0.2
marshmallow 3.23.0
matplotlib 3.9.2
matplotlib-inline 0.1.7
matplotlib-venn 1.1.1
mayavi 4.8.2
mdurl 0.1.2
meshio 5.3.5
mistune 3.0.2
ml_dtypes 0.5.0
morphapi 0.3.0
morphio 3.4.0
moviepy 1.0.3
mpmath 1.3.0
msgpack 1.1.0
multidict 6.1.0
myterial 1.2.1
namex 0.0.8
napari 0.5.4
napari-console 0.1.0
napari-ndtiffs 0.2.1
napari-plugin-engine 0.2.0
napari-plugin-manager 0.1.3
napari-svg 0.2.0
natsort 8.4.0
nbclient 0.10.0
nbconvert 7.16.4
nbformat 5.10.4
ndindex 1.9.2
ndx-events 0.2.0
nemos 0.1.6
nest-asyncio 1.6.0
networkx 3.4.2
neurom 3.2.11
nibabel 5.3.2
notebook_shim 0.2.4
npe2 0.7.7
nptyping 2.5.0
npyx 4.0.6
numba 0.60.0
numcodecs 0.13.1
numexpr 2.10.1
numpy 1.23.5
numpydoc 1.8.0
opencv-python 4.10.0.84
opt_einsum 3.4.0
optree 0.13.0
overrides 7.7.0
packaging 24.1
pandas 1.5.3
pandocfilters 1.5.1
parso 0.8.4
partd 1.4.2
patsy 0.5.6
pillow 11.0.0
Pint 0.24.3
pip 24.2
platformdirs 4.3.6
pooch 1.8.2
proglog 0.1.10
prometheus_client 0.21.0
prompt_toolkit 3.0.48
propcache 0.2.0
psutil 6.1.0
psycopg2-binary 2.9.10
psygnal 0.11.1
pure_eval 0.2.3
py 1.11.0
py-cpuinfo 9.0.0
pyarrow 18.0.0
pyconify 0.1.6
pycparser 2.22
pydantic 2.9.2
pydantic-compat 0.1.2
pydantic_core 2.23.4
pyface 8.0.0
Pygments 2.18.0
pyinspect 0.1.0
pynapple 0.7.1
pynndescent 0.5.13
pynrrd 1.0.0
pynwb 2.8.2
PyOpenGL 3.1.7
pyparsing 3.2.0
pyproject_hooks 1.2.0
PyQt5 5.15.11
PyQt5-Qt5 5.15.2
PyQt5_sip 12.15.0
python-dateutil 2.9.0.post0
python-json-logger 2.0.7
pytz 2024.2
pywin32 308
pywinpty 2.0.14
PyYAML 6.0.2
pyzmq 26.2.0
qtconsole 5.6.0
QtPy 2.4.1
referencing 0.35.1
requests 2.32.3
requests-toolbelt 1.0.0
retry 0.9.2
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rich 13.9.3
rpds-py 0.20.0
ruamel.yaml 0.18.6
ruamel.yaml.clib 0.2.12
s3transfer 0.10.3
scanpy 1.10.3
scikit-build 0.18.1
scikit-image 0.24.0
scikit-learn 1.5.2
scipy 1.10.0
seaborn 0.13.2
semver 3.0.2
Send2Trash 1.8.3
session_info 1.0.0
setuptools 57.0.0
shellingham 1.5.4
SimpleITK 2.4.0
simplejson 3.19.3
six 1.16.0
slurmio 0.1.1
sniffio 1.3.1
snowballstemmer 2.2.0
soupsieve 2.6
Sphinx 8.1.3
sphinxcontrib-applehelp 2.0.0
sphinxcontrib-devhelp 2.0.0
sphinxcontrib-htmlhelp 2.1.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 2.0.0
sphinxcontrib-serializinghtml 2.0.0
SQLAlchemy 2.0.36
stack-data 0.6.3
statsmodels 0.14.4
stdlib-list 0.11.0
superqt 0.6.7
sympy 1.13.1
tables 3.10.1
tabulate 0.9.0
tdt 0.6.6
terminado 0.18.1
threadpoolctl 3.5.0
tifffile 2024.9.20
tinycss2 1.4.0
tomli 2.0.2
tomli_w 1.1.0
toolz 1.0.0
torch 2.5.0
tornado 6.4.1
tqdm 4.66.5
traitlets 5.14.3
traits 6.4.3
traitsui 8.0.0
traittypes 0.2.1
treelib 1.7.0
triangle 20230923
typer 0.12.5
types-python-dateutil 2.9.0.20241003
typing_extensions 4.12.2
umap-learn 0.5.6
uri-template 1.3.0
urllib3 2.2.3
vedo 2024.5.2
vispy 0.14.3
vtk 9.3.1
wcwidth 0.2.13
webcolors 24.8.0
webencodings 0.5.1
websocket-client 1.8.0
wheel 0.44.0
widgetsnbextension 4.0.13
win32-setctime 1.1.0
wrapt 1.16.0
xarray 2023.1.0
yarl 1.16.0
zarr 2.18.2
zipp 3.20.2

[alessandrofelder]

Hey @harshk95
Can you run the commands below in the same notebook, and post the output, please:

print(vedo.settings)

from brainrender import settings
print(settings.ROOT_ALPHA)