brainglobe
[BUG] Unable to set alpha of add_brain_region when running from Jupyter Notebook
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
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.
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
Hi @harshk95, it looks like brainrender hasn't been updated. Was your conda environment activated when you ran the installation command?
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
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)
Hi, sorry for the delay. Returning to this, when the same environment is run from another system the commands run as expected. It might have to do with the specs of the computer and/or GPU. This is in case it helps troubleshoot. We have not done extensive tests to see which systems give this issue, but if we do figure out some pattern we could report it.
Sure, if you report any observed patterns that could help, so you're more than welcome to!