Bug when running 3D inference tutorial #37
Description
I tried to run napari-empanada following the tutorial https://empanada.readthedocs.io/en/latest/tutorials/3d_tutorial.html#d-inference-tutorial
I installed it on windows 11 with the GPU support:
conda create -y -n empanada -c conda-forge python=3.9
conda activate empanada
conda install pyqt
pip install "napari[all]"
conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia
pip install empanada-napari=1.1.1I started napari, started the plugin 3D inference, loaded the image Hela Cell FibSEM ( https://www.dropbox.com/s/2gu3go2puzc47ip/hela_cell_em.tif?dl=0 ) and pressed "Run 3D inference" and get the following error logs:
napari
ImportError: _multiarray_umath failed to import
C:\Users\u0094799\.conda\envs\empanada\lib\site-packages\torch\_subclasses\functional_tensor.py:258: UserWarning: Failed to initialize NumPy: CPU dispatcher tracer already initlized (Triggered internally at C:\cb\pytorch_1000000000000\work\torch\csrc\utils\tensor_numpy.cpp:84.)!
Running without zarr storage directory, this may use a lot of memory!
Predicting xy...
0%| | 0/256 [00:00<?, ?it/s]
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
File ~\.conda\envs\empanada\lib\site-packages\superqt\utils\_qthreading.py:613, in create_worker.<locals>.reraise(e=RuntimeError('Numpy is not available'))
612 def reraise(e):
--> 613 raise e
e = RuntimeError('Numpy is not available')
File ~\.conda\envs\empanada\lib\site-packages\superqt\utils\_qthreading.py:175, in WorkerBase.run(self=<napari._qt.qthreading.FunctionWorker object>)
173 warnings.filterwarnings("always")
174 warnings.showwarning = lambda *w: self.warned.emit(w)
--> 175 result = self.work()
self = <napari._qt.qthreading.FunctionWorker object at 0x0000021E8C513940>
176 if isinstance(result, Exception):
177 if isinstance(result, RuntimeError):
178 # The Worker object has likely been deleted.
179 # A deleted wrapped C/C++ object may result in a runtime
180 # error that will cause segfault if we try to do much other
181 # than simply notify the user.
File ~\.conda\envs\empanada\lib\site-packages\superqt\utils\_qthreading.py:354, in FunctionWorker.work(self=<napari._qt.qthreading.FunctionWorker object>)
353 def work(self) -> _R:
--> 354 return self._func(*self._args, **self._kwargs)
self._func = <function volume_inference_widget.<locals>.stack_inference at 0x0000021E28751DC0>
self = <napari._qt.qthreading.FunctionWorker object at 0x0000021E8C513940>
self._args = (<empanada_napari.inference.Engine3d object at 0x0000021E8C516FD0>, <class 'numpy.ndarray'> (256, 256, 256) uint8, 'xy')
self._kwargs = {}
File ~\.conda\envs\empanada\lib\site-packages\empanada_napari\_volume_inference.py:27, in volume_inference_widget.<locals>.stack_inference(engine=<empanada_napari.inference.Engine3d object>, volume=<class 'numpy.ndarray'> (256, 256, 256) uint8, axis_name='xy')
25 @thread_worker
26 def stack_inference(engine, volume, axis_name):
---> 27 stack, trackers = engine.infer_on_axis(volume, axis_name)
volume = <class 'numpy.ndarray'> (256, 256, 256) uint8
axis_name = 'xy'
engine = <empanada_napari.inference.Engine3d object at 0x0000021E8C516FD0>
28 trackers_dict = {axis_name: trackers}
29 return stack, axis_name, trackers_dict
File ~\.conda\envs\empanada\lib\site-packages\empanada_napari\inference.py:513, in Engine3d.infer_on_axis(self=<empanada_napari.inference.Engine3d object>, volume=<class 'numpy.ndarray'> (256, 256, 256) uint8, axis_name='xy')
510 matcher_proc.start()
512 print(f'Predicting {axis_name}...')
--> 513 for batch in tqdm(dataloader, total=len(dataloader)):
dataloader = <torch.utils.data.dataloader.DataLoader object at 0x0000021E8C509A90>
514 image = batch['image']
515 size = batch['size']
File ~\.conda\envs\empanada\lib\site-packages\tqdm\std.py:1181, in tqdm.__iter__(self=<tqdm.std.tqdm object>)
1178 time = self._time
1180 try:
-> 1181 for obj in iterable:
iterable = <torch.utils.data.dataloader.DataLoader object at 0x0000021E8C509A90>
1182 yield obj
1183 # Update and possibly print the progressbar.
1184 # Note: does not call self.update(1) for speed optimisation.
File ~\.conda\envs\empanada\lib\site-packages\torch\utils\data\dataloader.py:630, in _BaseDataLoaderIter.__next__(self=<torch.utils.data.dataloader._SingleProcessDataLoaderIter object>)
627 if self._sampler_iter is None:
628 # TODO(https://github.com/pytorch/pytorch/issues/76750)
629 self._reset() # type: ignore[call-arg]
--> 630 data = self._next_data()
self = <torch.utils.data.dataloader._SingleProcessDataLoaderIter object at 0x0000021E98B7EFD0>
631 self._num_yielded += 1
632 if self._dataset_kind == _DatasetKind.Iterable and \
633 self._IterableDataset_len_called is not None and \
634 self._num_yielded > self._IterableDataset_len_called:
File ~\.conda\envs\empanada\lib\site-packages\torch\utils\data\dataloader.py:673, in _SingleProcessDataLoaderIter._next_data(self=<torch.utils.data.dataloader._SingleProcessDataLoaderIter object>)
671 def _next_data(self):
672 index = self._next_index() # may raise StopIteration
--> 673 data = self._dataset_fetcher.fetch(index) # may raise StopIteration
index = [0]
self = <torch.utils.data.dataloader._SingleProcessDataLoaderIter object at 0x0000021E98B7EFD0>
self._dataset_fetcher = <torch.utils.data._utils.fetch._MapDatasetFetcher object at 0x0000021E98B7EFA0>
674 if self._pin_memory:
675 data = _utils.pin_memory.pin_memory(data, self._pin_memory_device)
File ~\.conda\envs\empanada\lib\site-packages\torch\utils\data\_utils\fetch.py:52, in _MapDatasetFetcher.fetch(self=<torch.utils.data._utils.fetch._MapDatasetFetcher object>, possibly_batched_index=[0])
50 data = self.dataset.__getitems__(possibly_batched_index)
51 else:
---> 52 data = [self.dataset[idx] for idx in possibly_batched_index]
self = <torch.utils.data._utils.fetch._MapDatasetFetcher object at 0x0000021E98B7EFA0>
self.dataset = <empanada.data.volume_dataset.VolumeDataset object at 0x0000021E8C509D30>
possibly_batched_index = [0]
53 else:
54 data = self.dataset[possibly_batched_index]
File ~\.conda\envs\empanada\lib\site-packages\torch\utils\data\_utils\fetch.py:52, in <listcomp>(.0=<list_iterator object>)
50 data = self.dataset.__getitems__(possibly_batched_index)
51 else:
---> 52 data = [self.dataset[idx] for idx in possibly_batched_index]
self = <torch.utils.data._utils.fetch._MapDatasetFetcher object at 0x0000021E98B7EFA0>
self.dataset = <empanada.data.volume_dataset.VolumeDataset object at 0x0000021E8C509D30>
idx = 0
53 else:
54 data = self.dataset[possibly_batched_index]
File ~\.conda\envs\empanada\lib\site-packages\empanada\data\volume_dataset.py:51, in VolumeDataset.__getitem__(self=<empanada.data.volume_dataset.VolumeDataset object>, idx=0)
48 assert (image.shape[0] * self.scale) >= h
49 assert (image.shape[1] * self.scale) >= w
---> 51 image = self.tfs(image=image)['image']
image = <class 'numpy.ndarray'> (256, 256) uint8
self = <empanada.data.volume_dataset.VolumeDataset object at 0x0000021E8C509D30>
self.tfs = <empanada_napari.utils.Preprocessor object at 0x0000021E98B65670>
53 return {'index': idx, 'image': image, 'size': (h, w)}
File ~\.conda\envs\empanada\lib\site-packages\empanada_napari\utils.py:163, in Preprocessor.__call__(self=<empanada_napari.utils.Preprocessor object>, image=<class 'numpy.ndarray'> (256, 256) float32)
161 max_value = np.iinfo(image.dtype).max
162 image = normalize(image, self.mean, self.std, max_pixel_value=max_value)
--> 163 return {'image': to_tensor(image)}
image = <class 'numpy.ndarray'> (256, 256) float32
File ~\.conda\envs\empanada\lib\site-packages\empanada_napari\utils.py:148, in to_tensor(img=<class 'numpy.ndarray'> (256, 256) float32)
146 def to_tensor(img):
147 # move channel dim from last to first
--> 148 tensor = torch.from_numpy(img[None])
img = <class 'numpy.ndarray'> (256, 256) float32
149 return tensor
RuntimeError: Numpy is not availableconda list
>conda list
# packages in environment at C:\Users\u0094799\.conda\envs\empanada:
#
# Name Version Build Channel
alabaster 0.7.16 pypi_0 pypi
albumentations 1.3.1 pypi_0 pypi
alembic 1.13.3 pypi_0 pypi
aniso8601 9.0.1 pypi_0 pypi
annotated-types 0.7.0 pypi_0 pypi
app-model 0.2.8 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
asttokens 2.4.1 pypi_0 pypi
attrs 24.2.0 pypi_0 pypi
babel 2.16.0 pypi_0 pypi
blas 1.0 mkl conda-forge
blinker 1.8.2 pypi_0 pypi
brotli-python 1.1.0 py39ha51f57c_2 conda-forge
build 1.2.2 pypi_0 pypi
bzip2 1.0.8 h2466b09_7 conda-forge
ca-certificates 2024.8.30 h56e8100_0 conda-forge
cachetools 5.5.0 pypi_0 pypi
cachey 0.2.1 pypi_0 pypi
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py39ha55e580_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 pypi_0 pypi
cloudpickle 3.0.0 pypi_0 pypi
colorama 0.4.6 pypi_0 pypi
comm 0.2.2 pypi_0 pypi
connected-components-3d 3.18.0 pypi_0 pypi
contourpy 1.2.1 pypi_0 pypi
cuda-cccl 12.6.77 0 nvidia
cuda-cccl_win-64 12.6.77 0 nvidia
cuda-cudart 11.8.89 0 nvidia
cuda-cudart-dev 11.8.89 0 nvidia
cuda-cupti 11.8.87 0 nvidia
cuda-libraries 11.8.0 0 nvidia
cuda-libraries-dev 11.8.0 0 nvidia
cuda-nvrtc 11.8.89 0 nvidia
cuda-nvrtc-dev 11.8.89 0 nvidia
cuda-nvtx 11.8.86 0 nvidia
cuda-profiler-api 12.6.77 0 nvidia
cuda-runtime 11.8.0 0 nvidia
cuda-version 12.6 3 nvidia
cycler 0.12.1 pypi_0 pypi
cztile 0.1.2 pypi_0 pypi
dask 2024.8.0 pypi_0 pypi
databricks-sdk 0.33.0 pypi_0 pypi
debugpy 1.8.6 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
deprecated 1.2.14 pypi_0 pypi
docker 7.1.0 pypi_0 pypi
docstring-parser 0.16 pypi_0 pypi
docutils 0.17.1 pypi_0 pypi
empanada-dl 0.1.7 pypi_0 pypi
empanada-napari 1.1.1 pypi_0 pypi
et-xmlfile 1.1.0 pypi_0 pypi
exceptiongroup 1.2.2 pypi_0 pypi
executing 2.1.0 pypi_0 pypi
fasteners 0.19 pypi_0 pypi
filelock 3.16.1 pyhd8ed1ab_0 conda-forge
flask 3.0.3 pypi_0 pypi
flexcache 0.3 pypi_0 pypi
flexparser 0.3.1 pypi_0 pypi
fonttools 4.54.1 pypi_0 pypi
freetype 2.12.1 hdaf720e_2 conda-forge
freetype-py 2.5.1 pypi_0 pypi
fsspec 2024.9.0 pypi_0 pypi
gitdb 4.0.11 pypi_0 pypi
gitpython 3.1.43 pypi_0 pypi
glib 2.82.1 h7025463_0 conda-forge
glib-tools 2.82.1 h4394cf3_0 conda-forge
google-auth 2.35.0 pypi_0 pypi
graphene 3.3 pypi_0 pypi
graphql-core 3.2.4 pypi_0 pypi
graphql-relay 3.2.0 pypi_0 pypi
greenlet 3.1.1 pypi_0 pypi
gst-plugins-base 1.24.7 hb0a98b8_0 conda-forge
gstreamer 1.24.7 h5006eae_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
heapdict 1.0.1 pypi_0 pypi
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
hsluv 5.0.4 pypi_0 pypi
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 75.1 he0c23c2_0 conda-forge
idna 3.10 pyhd8ed1ab_0 conda-forge
imagecodecs 2024.9.22 pypi_0 pypi
imagehash 4.3.1 pypi_0 pypi
imageio 2.35.1 pypi_0 pypi
imagesize 1.4.1 pypi_0 pypi
importlib-metadata 8.4.0 pypi_0 pypi
importlib-resources 6.4.5 pypi_0 pypi
in-n-out 0.2.1 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
itsdangerous 2.2.0 pypi_0 pypi
jedi 0.19.1 pypi_0 pypi
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 pypi_0 pypi
jsonschema 4.23.0 pypi_0 pypi
jsonschema-specifications 2023.12.1 pypi_0 pypi
jupyter-client 8.6.3 pypi_0 pypi
jupyter-core 5.7.2 pypi_0 pypi
kiwisolver 1.4.7 pypi_0 pypi
krb5 1.21.3 hdf4eb48_0 conda-forge
lazy-loader 0.4 pypi_0 pypi
lcms2 2.16 h67d730c_0 conda-forge
lerc 4.0.0 h63175ca_0 conda-forge
libblas 3.9.0 1_h8933c1f_netlib conda-forge
libcblas 3.9.0 5_hd5c7e75_netlib conda-forge
libclang13 19.1.0 default_ha5278ca_0 conda-forge
libcublas 11.11.3.6 0 nvidia
libcublas-dev 11.11.3.6 0 nvidia
libcufft 10.9.0.58 0 nvidia
libcufft-dev 10.9.0.58 0 nvidia
libcurand 10.3.7.77 0 nvidia
libcurand-dev 10.3.7.77 0 nvidia
libcusolver 11.4.1.48 0 nvidia
libcusolver-dev 11.4.1.48 0 nvidia
libcusparse 11.7.5.86 0 nvidia
libcusparse-dev 11.7.5.86 0 nvidia
libdeflate 1.21 h2466b09_0 conda-forge
libffi 3.4.2 h8ffe710_5 conda-forge
libglib 2.82.1 h7025463_0 conda-forge
libhwloc 2.11.1 default_h8125262_1000 conda-forge
libiconv 1.17 hcfcfb64_2 conda-forge
libintl 0.22.5 h5728263_3 conda-forge
libintl-devel 0.22.5 h5728263_3 conda-forge
libjpeg-turbo 3.0.0 hcfcfb64_1 conda-forge
liblapack 3.9.0 5_hd5c7e75_netlib conda-forge
libnpp 11.8.0.86 0 nvidia
libnpp-dev 11.8.0.86 0 nvidia
libnvjpeg 11.9.0.86 0 nvidia
libnvjpeg-dev 11.9.0.86 0 nvidia
libogg 1.3.5 h2466b09_0 conda-forge
libpng 1.6.44 h3ca93ac_0 conda-forge
libsqlite 3.46.1 h2466b09_0 conda-forge
libtiff 4.7.0 hb151862_0 conda-forge
libuv 1.49.0 h2466b09_0 conda-forge
libvorbis 1.3.7 h0e60522_0 conda-forge
libwebp-base 1.4.0 hcfcfb64_0 conda-forge
libxcb 1.16 h013a479_1 conda-forge
libxml2 2.12.7 h0f24e4e_4 conda-forge
libzlib 1.3.1 h2466b09_2 conda-forge
llvmlite 0.42.0 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
m2w64-gcc-libgfortran 5.3.0 6 conda-forge
m2w64-gcc-libs 5.3.0 7 conda-forge
m2w64-gcc-libs-core 5.3.0 7 conda-forge
m2w64-gmp 6.1.0 2 conda-forge
m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge
magicgui 0.9.1 pypi_0 pypi
mako 1.3.5 pypi_0 pypi
markdown 3.7 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 2.1.5 py39ha55e580_1 conda-forge
matplotlib 3.8.4 pypi_0 pypi
matplotlib-inline 0.1.7 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
mkl 2023.1.0 h6a75c08_48682 conda-forge
mlflow 2.16.2 pypi_0 pypi
mlflow-skinny 2.16.2 pypi_0 pypi
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
msys2-conda-epoch 20160418 1 conda-forge
napari 0.4.18 pypi_0 pypi
napari-console 0.1.0 pypi_0 pypi
napari-plugin-engine 0.2.0 pypi_0 pypi
napari-plugin-manager 0.1.3 pypi_0 pypi
napari-svg 0.2.0 pypi_0 pypi
nest-asyncio 1.6.0 pypi_0 pypi
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
npe2 0.7.7 pypi_0 pypi
numba 0.59.0 pypi_0 pypi
numcodecs 0.12.1 pypi_0 pypi
numpy 1.22.0 pypi_0 pypi
numpydoc 1.5.0 pypi_0 pypi
opencv-python 4.9.0.80 pypi_0 pypi
opencv-python-headless 4.9.0.80 pypi_0 pypi
openjpeg 2.5.2 h3d672ee_0 conda-forge
openpyxl 3.1.5 pypi_0 pypi
openssl 3.3.2 h2466b09_0 conda-forge
opentelemetry-api 1.27.0 pypi_0 pypi
opentelemetry-sdk 1.27.0 pypi_0 pypi
opentelemetry-semantic-conventions 0.48b0 pypi_0 pypi
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.0.3 pypi_0 pypi
parso 0.8.4 pypi_0 pypi
partd 1.4.2 pypi_0 pypi
pcre2 10.44 h3d7b363_2 conda-forge
pillow 10.4.0 py39hfa8c767_1 conda-forge
pint 0.24.3 pypi_0 pypi
pip 24.2 pyh8b19718_1 conda-forge
platformdirs 4.3.6 pypi_0 pypi
ply 3.11 pyhd8ed1ab_2 conda-forge
pooch 1.8.2 pypi_0 pypi
prompt-toolkit 3.0.48 pypi_0 pypi
protobuf 5.28.2 pypi_0 pypi
psutil 6.0.0 pypi_0 pypi
psygnal 0.11.1 pypi_0 pypi
pthread-stubs 0.4 hcd874cb_1001 conda-forge
pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge
pure-eval 0.2.3 pypi_0 pypi
pyarrow 17.0.0 pypi_0 pypi
pyasn1 0.6.1 pypi_0 pypi
pyasn1-modules 0.4.1 pypi_0 pypi
pyconify 0.1.6 pypi_0 pypi
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pydantic 1.10.18 pypi_0 pypi
pydantic-compat 0.1.2 pypi_0 pypi
pydantic-core 2.23.4 pypi_0 pypi
pygments 2.18.0 pypi_0 pypi
pyopengl 3.1.7 pypi_0 pypi
pyparsing 3.1.4 pypi_0 pypi
pyproject-hooks 1.2.0 pypi_0 pypi
pyqt 5.15.9 py39hb77abff_5 conda-forge
pyqt5-sip 12.12.2 py39h99910a6_5 conda-forge
pysocks 1.7.1 pyh0701188_6 conda-forge
python 3.9.20 hfaddaf0_1_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
python_abi 3.9 5_cp39 conda-forge
pytorch 2.4.1 py3.9_cuda11.8_cudnn9_0 pytorch
pytorch-cuda 11.8 h24eeafa_5 pytorch
pytorch-mutex 1.0 cuda pytorch
pytz 2024.2 pypi_0 pypi
pywavelets 1.4.1 pypi_0 pypi
pywin32 307 pypi_0 pypi
pyyaml 6.0.2 py39ha55e580_1 conda-forge
pyzmq 26.2.0 pypi_0 pypi
qt-main 5.15.8 h264fbc2_26 conda-forge
qtconsole 5.6.0 pypi_0 pypi
qtpy 2.4.1 pypi_0 pypi
qudida 0.0.4 pypi_0 pypi
referencing 0.35.1 pypi_0 pypi
requests 2.32.3 pyhd8ed1ab_0 conda-forge
rich 13.9.2 pypi_0 pypi
rpds-py 0.20.0 pypi_0 pypi
rsa 4.9 pypi_0 pypi
scikit-image 0.22.0 pypi_0 pypi
scikit-learn 1.5.2 pypi_0 pypi
scipy 1.11.4 pypi_0 pypi
setuptools 75.1.0 pyhd8ed1ab_0 conda-forge
shellingham 1.5.4 pypi_0 pypi
simpleitk 2.4.0 pypi_0 pypi
sip 6.7.12 py39h99910a6_0 conda-forge
six 1.16.0 pypi_0 pypi
smmap 5.0.1 pypi_0 pypi
snowballstemmer 2.2.0 pypi_0 pypi
sphinx 4.5.0 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 2.0.35 pypi_0 pypi
sqlparse 0.5.1 pypi_0 pypi
stack-data 0.6.3 pypi_0 pypi
superqt 0.6.7 pypi_0 pypi
sympy 1.13.3 pyh04b8f61_3 conda-forge
tabulate 0.9.0 pypi_0 pypi
tbb 2021.13.0 hc790b64_0 conda-forge
threadpoolctl 3.5.0 pypi_0 pypi
tifffile 2024.8.30 pypi_0 pypi
tk 8.6.13 h5226925_1 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.2 pyhd8ed1ab_0 conda-forge
tomli-w 1.0.0 pypi_0 pypi
toolz 1.0.0 pypi_0 pypi
torchaudio 2.4.1 pypi_0 pypi
torchvision 0.19.1 pypi_0 pypi
tornado 6.4.1 pypi_0 pypi
tqdm 4.66.5 pypi_0 pypi
traitlets 5.14.3 pypi_0 pypi
triangle 20230923 pypi_0 pypi
typer 0.12.5 pypi_0 pypi
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2024.2 pypi_0 pypi
ucrt 10.0.22621.0 h57928b3_0 conda-forge
urllib3 2.2.3 pyhd8ed1ab_0 conda-forge
vc 14.3 h8a93ad2_21 conda-forge
vc14_runtime 14.40.33810 ha82c5b3_21 conda-forge
vispy 0.12.2 pypi_0 pypi
vs2015_runtime 14.40.33810 h3bf8584_21 conda-forge
waitress 3.0.0 pypi_0 pypi
wcwidth 0.2.13 pypi_0 pypi
werkzeug 3.0.4 pypi_0 pypi
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
win_inet_pton 1.1.0 pyh7428d3b_7 conda-forge
wrapt 1.16.0 pypi_0 pypi
xorg-libxau 1.0.11 hcd874cb_0 conda-forge
xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge
xz 5.2.6 h8d14728_0 conda-forge
yaml 0.2.5 h8ffe710_2 conda-forge
zarr 2.17.1 pypi_0 pypi
zipp 3.20.2 pypi_0 pypi
zstandard 0.23.0 py39h9bf74da_1 conda-forge
zstd 1.5.6 h0ea2cb4_0 conda-forgepip list
pip list
Package Version
---------------------------------- -----------
alabaster 0.7.16
albumentations 1.3.1
alembic 1.13.3
aniso8601 9.0.1
annotated-types 0.7.0
app-model 0.2.8
appdirs 1.4.4
asciitree 0.3.3
asttokens 2.4.1
attrs 24.2.0
babel 2.16.0
blinker 1.8.2
Brotli 1.1.0
build 1.2.2
cachetools 5.5.0
cachey 0.2.1
certifi 2024.8.30
cffi 1.17.1
charset-normalizer 3.3.2
click 8.1.7
cloudpickle 3.0.0
colorama 0.4.6
comm 0.2.2
connected-components-3d 3.18.0
contourpy 1.2.1
cycler 0.12.1
cztile 0.1.2
dask 2024.8.0
databricks-sdk 0.33.0
debugpy 1.8.6
decorator 5.1.1
Deprecated 1.2.14
docker 7.1.0
docstring_parser 0.16
docutils 0.17.1
empanada-dl 0.1.7
empanada-napari 1.1.1
et-xmlfile 1.1.0
exceptiongroup 1.2.2
executing 2.1.0
fasteners 0.19
filelock 3.16.1
Flask 3.0.3
flexcache 0.3
flexparser 0.3.1
fonttools 4.54.1
freetype-py 2.5.1
fsspec 2024.9.0
gitdb 4.0.11
GitPython 3.1.43
google-auth 2.35.0
graphene 3.3
graphql-core 3.2.4
graphql-relay 3.2.0
greenlet 3.1.1
h2 4.1.0
HeapDict 1.0.1
hpack 4.0.0
hsluv 5.0.4
hyperframe 6.0.1
idna 3.10
imagecodecs 2024.9.22
ImageHash 4.3.1
imageio 2.35.1
imagesize 1.4.1
importlib_metadata 8.4.0
importlib_resources 6.4.5
in-n-out 0.2.1
ipykernel 6.29.5
ipython 8.18.1
itsdangerous 2.2.0
jedi 0.19.1
Jinja2 3.1.4
joblib 1.4.2
jsonschema 4.23.0
jsonschema-specifications 2023.12.1
jupyter_client 8.6.3
jupyter_core 5.7.2
kiwisolver 1.4.7
lazy_loader 0.4
llvmlite 0.42.0
locket 1.0.0
magicgui 0.9.1
Mako 1.3.5
Markdown 3.7
markdown-it-py 3.0.0
MarkupSafe 2.1.5
matplotlib 3.8.4
matplotlib-inline 0.1.7
mdurl 0.1.2
mlflow 2.16.2
mlflow-skinny 2.16.2
mpmath 1.3.0
napari 0.4.18
napari-console 0.1.0
napari-plugin-engine 0.2.0
napari-plugin-manager 0.1.3
napari-svg 0.2.0
nest-asyncio 1.6.0
networkx 3.2.1
npe2 0.7.7
numba 0.59.0
numcodecs 0.12.1
numpy 1.22.0
numpydoc 1.5.0
opencv-python 4.9.0.80
opencv-python-headless 4.9.0.80
openpyxl 3.1.5
opentelemetry-api 1.27.0
opentelemetry-sdk 1.27.0
opentelemetry-semantic-conventions 0.48b0
packaging 24.1
pandas 2.0.3
parso 0.8.4
partd 1.4.2
pillow 10.4.0
Pint 0.24.3
pip 24.2
platformdirs 4.3.6
ply 3.11
pooch 1.8.2
prompt_toolkit 3.0.48
protobuf 5.28.2
psutil 6.0.0
psygnal 0.11.1
pure_eval 0.2.3
pyarrow 17.0.0
pyasn1 0.6.1
pyasn1_modules 0.4.1
pyconify 0.1.6
pycparser 2.22
pydantic 1.10.18
pydantic-compat 0.1.2
pydantic_core 2.23.4
Pygments 2.18.0
PyOpenGL 3.1.7
pyparsing 3.1.4
pyproject_hooks 1.2.0
PyQt5 5.15.9
PyQt5-sip 12.12.2
PySocks 1.7.1
python-dateutil 2.9.0.post0
pytz 2024.2
PyWavelets 1.4.1
pywin32 307
PyYAML 6.0.2
pyzmq 26.2.0
qtconsole 5.6.0
QtPy 2.4.1
qudida 0.0.4
referencing 0.35.1
requests 2.32.3
rich 13.9.2
rpds-py 0.20.0
rsa 4.9
scikit-image 0.22.0
scikit-learn 1.5.2
scipy 1.11.4
setuptools 75.1.0
shellingham 1.5.4
SimpleITK 2.4.0
sip 6.7.12
six 1.16.0
smmap 5.0.1
snowballstemmer 2.2.0
Sphinx 4.5.0
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 2.0.35
sqlparse 0.5.1
stack-data 0.6.3
superqt 0.6.7
sympy 1.13.3
tabulate 0.9.0
threadpoolctl 3.5.0
tifffile 2024.8.30
toml 0.10.2
tomli 2.0.2
tomli_w 1.0.0
toolz 1.0.0
torch 2.4.1
torchaudio 2.4.1
torchvision 0.19.1
tornado 6.4.1
tqdm 4.66.5
traitlets 5.14.3
triangle 20230923
typer 0.12.5
typing_extensions 4.12.2
tzdata 2024.2
urllib3 2.2.3
vispy 0.12.2
waitress 3.0.0
wcwidth 0.2.13
Werkzeug 3.0.4
wheel 0.44.0
win_inet_pton 1.1.0
wrapt 1.16.0
zarr 2.17.1
zipp 3.20.2
zstandard 0.23.0