Cellpose not making full use of GPU
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Hi,
I am having a problem getting the GPU version of cellpose to work.
Install problem
I installed the GPU version of cellpose as described on the main page. However if I use the CellposeModel.eval() function it seems like only a part of this function is actually making use of the GPU. Specifically when the dynamics.resize_and_compute_masks() function is running I find that there is 0% cuda activity on the GPU (checking via task manager).
I am not sure wether this part does not support GPU acceleration anyway or if I made a mistake setting up the environment.
Environment info
I am running cellpose via a jupyter notebook inside Pycharm (Pro). Here is the list of the installed packages in my environment.
# Name Version Build Channel
aiofiles 22.1.0 pypi_0 pypi
aiosqlite 0.20.0 pypi_0 pypi
alabaster 0.7.13 pyhd8ed1ab_0 conda-forge
annotated-types 0.6.0 pyhd8ed1ab_0 conda-forge
anyio 4.3.0 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h63175ca_0 conda-forge
app-model 0.2.7 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
aquirdturtle-collapsible-headings 3.1.0 pypi_0 pypi
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py38h91455d4_4 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asciitree 0.3.3 py_2 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
babel 2.15.0 pypi_0 pypi
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
blas 2.112 mkl conda-forge
blas-devel 3.9.0 12_win64_mkl conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.5 hdccc3a2_0 conda-forge
brotli-python 1.0.9 py38hd3f51b4_9 conda-forge
bzip2 1.0.8 hcfcfb64_5 conda-forge
c-blosc2 2.12.0 h183a6f4_0 conda-forge
c-compiler 1.7.0 hcfcfb64_1 conda-forge
ca-certificates 2024.6.2 h56e8100_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachey 0.2.1 pyh9f0ad1d_0 conda-forge
cellpose 3.0.8 pypi_0 pypi
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py38h91455d4_0 conda-forge
cfitsio 4.2.0 h9ebe7e4_0 conda-forge
charls 2.4.2 h1537add_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 win_pyh7428d3b_0 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
contourpy 1.1.1 pypi_0 pypi
cuda 12.1.0 0 nvidia
cuda-cccl 12.4.127 0 nvidia
cuda-command-line-tools 12.1.1 0 nvidia
cuda-compiler 12.4.1 h63438b5_0 conda-forge
cuda-cudart 12.1.105 0 nvidia
cuda-cudart-dev 12.1.105 0 nvidia
cuda-cuobjdump 12.4.127 0 nvidia
cuda-cupti 12.1.105 0 nvidia
cuda-cuxxfilt 12.4.127 0 nvidia
cuda-demo-suite 12.4.127 0 nvidia
cuda-documentation 12.4.127 0 nvidia
cuda-libraries 12.1.0 0 nvidia
cuda-libraries-dev 12.1.0 0 nvidia
cuda-nsight-compute 12.4.1 0 nvidia
cuda-nvcc 12.4.131 0 nvidia
cuda-nvdisasm 12.5.39 he0c23c2_0 conda-forge
cuda-nvml-dev 12.5.39 he0c23c2_0 conda-forge
cuda-nvprof 12.5.39 he0c23c2_0 conda-forge
cuda-nvprune 12.4.127 0 nvidia
cuda-nvrtc 12.1.105 0 nvidia
cuda-nvrtc-dev 12.1.105 0 nvidia
cuda-nvtx 12.1.105 0 nvidia
cuda-nvvp 12.5.39 he0c23c2_0 conda-forge
cuda-opencl 12.4.127 0 nvidia
cuda-opencl-dev 12.4.127 0 nvidia
cuda-profiler-api 12.4.127 0 nvidia
cuda-runtime 12.1.0 0 nvidia
cuda-sanitizer-api 12.5.39 he0c23c2_0 conda-forge
cuda-toolkit 12.1.0 0 nvidia
cuda-tools 12.1.0 0 nvidia
cuda-version 12.5 hd4f0392_3 conda-forge
cuda-visual-tools 12.1.0 0 nvidia
cxx-compiler 1.7.0 h91493d7_1 conda-forge
cycler 0.12.1 pypi_0 pypi
cytoolz 0.12.3 py38h91455d4_0 conda-forge
dask-core 2023.5.0 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 hcfcfb64_0 conda-forge
debugpy 1.8.1 py38hd3f51b4_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
docstring_parser 0.16 pyhd8ed1ab_0 conda-forge
docutils 0.20.1 py38haa244fe_3 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.1 pypi_0 pypi
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.6.2 h63175ca_0 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
fastremap 1.14.1 pypi_0 pypi
filelock 3.14.0 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_2 conda-forge
fontconfig 2.14.2 hbde0cde_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.51.0 pypi_0 pypi
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 hdaf720e_2 conda-forge
freetype-py 2.4.0 pyhd8ed1ab_0 conda-forge
fsspec 2024.5.0 pyhff2d567_0 conda-forge
gettext 0.22.5 h5728263_2 conda-forge
gettext-tools 0.22.5 h7d00a51_2 conda-forge
giflib 5.2.2 h64bf75a_0 conda-forge
glib 2.80.2 h0df6a38_0 conda-forge
glib-tools 2.80.2 h2f9d560_0 conda-forge
gst-plugins-base 1.22.9 h001b923_1 conda-forge
gstreamer 1.22.9 hb4038d2_1 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
heapdict 1.0.1 py_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
hsluv 5.0.4 pyhd8ed1ab_0 conda-forge
httpcore 1.0.5 pyhd8ed1ab_0 conda-forge
httpx 0.27.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 73.2 h63175ca_0 conda-forge
idna 3.7 pyhd8ed1ab_0 conda-forge
imagecodecs 2023.3.16 pypi_0 pypi
imageio 2.34.1 pyh4b66e23_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.1.0 pyha770c72_0 conda-forge
importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
in-n-out 0.2.0 pyhd8ed1ab_0 conda-forge
intel-openmp 2021.4.0 pypi_0 pypi
ipykernel 6.29.4 pypi_0 pypi
ipython 8.12.3 pypi_0 pypi
ipython-genutils 0.2.0 pypi_0 pypi
ipywidgets 8.1.2 pyhd8ed1ab_1 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
json5 0.9.25 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py38haa244fe_3 conda-forge
jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.22.0 pyhd8ed1ab_0 conda-forge
jupyter 1.0.0 pyhd8ed1ab_10 conda-forge
jupyter-client 7.4.9 pypi_0 pypi
jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge
jupyter-server-fileid 0.9.2 pypi_0 pypi
jupyter-server-ydoc 0.8.0 pypi_0 pypi
jupyter-ydoc 0.2.5 pypi_0 pypi
jupyter_console 6.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py38haa244fe_0 conda-forge
jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.14.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge
jupyterlab 3.6.7 pypi_0 pypi
jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge
jupyterlab_server 2.27.1 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.10 pyhd8ed1ab_0 conda-forge
jxrlib 1.1 hcfcfb64_3 conda-forge
kiwisolver 1.4.5 py38hb1fd069_1 conda-forge
krb5 1.21.2 heb0366b_0 conda-forge
lazy_loader 0.4 pyhd8ed1ab_0 conda-forge
lcms2 2.15 h3e3b177_1 conda-forge
lerc 4.0.0 h63175ca_0 conda-forge
libaec 1.1.3 h63175ca_0 conda-forge
libasprintf 0.22.5 h5728263_2 conda-forge
libasprintf-devel 0.22.5 h5728263_2 conda-forge
libavif 0.11.1 ha7b97ba_2 conda-forge
libblas 3.9.0 12_win64_mkl conda-forge
libbrotlicommon 1.0.9 hcfcfb64_9 conda-forge
libbrotlidec 1.0.9 hcfcfb64_9 conda-forge
libbrotlienc 1.0.9 hcfcfb64_9 conda-forge
libcblas 3.9.0 12_win64_mkl conda-forge
libclang 15.0.7 default_h3a3e6c3_5 conda-forge
libclang13 15.0.7 default_hf64faad_5 conda-forge
libcublas 12.1.0.26 0 nvidia
libcublas-dev 12.1.0.26 0 nvidia
libcufft 11.0.2.4 0 nvidia
libcufft-dev 11.0.2.4 0 nvidia
libcurand 10.3.5.147 0 nvidia
libcurand-dev 10.3.5.147 0 nvidia
libcurl 8.7.1 hd5e4a3a_0 conda-forge
libcusolver 11.4.4.55 0 nvidia
libcusolver-dev 11.4.4.55 0 nvidia
libcusparse 12.0.2.55 0 nvidia
libcusparse-dev 12.0.2.55 0 nvidia
libdeflate 1.18 hcfcfb64_0 conda-forge
libexpat 2.6.2 h63175ca_0 conda-forge
libffi 3.4.2 h8ffe710_5 conda-forge
libgettextpo 0.22.5 h5728263_2 conda-forge
libgettextpo-devel 0.22.5 h5728263_2 conda-forge
libglib 2.80.2 h0df6a38_0 conda-forge
libhwloc 2.10.0 default_h2fffb23_1000 conda-forge
libiconv 1.17 hcfcfb64_2 conda-forge
libintl 0.22.5 h5728263_2 conda-forge
libintl-devel 0.22.5 h5728263_2 conda-forge
libjpeg-turbo 2.1.5.1 hcfcfb64_1 conda-forge
liblapack 3.9.0 12_win64_mkl conda-forge
liblapacke 3.9.0 12_win64_mkl conda-forge
libnpp 12.0.2.50 0 nvidia
libnpp-dev 12.0.2.50 0 nvidia
libnvjitlink 12.1.105 0 nvidia
libnvjitlink-dev 12.1.105 0 nvidia
libnvjpeg 12.1.1.14 0 nvidia
libnvjpeg-dev 12.1.1.14 0 nvidia
libnvvm-samples 12.1.105 0 nvidia
libogg 1.3.4 h8ffe710_1 conda-forge
libpng 1.6.43 h19919ed_0 conda-forge
libsodium 1.0.18 h8d14728_1 conda-forge
libsqlite 3.45.3 hcfcfb64_0 conda-forge
libssh2 1.11.0 h7dfc565_0 conda-forge
libtiff 4.5.1 h6c8260b_1 conda-forge
libuv 1.48.0 hcfcfb64_0 conda-forge
libvorbis 1.3.7 h0e60522_0 conda-forge
libwebp-base 1.4.0 hcfcfb64_0 conda-forge
libxcb 1.15 hcd874cb_0 conda-forge
libxml2 2.12.7 h283a6d9_0 conda-forge
libzlib 1.2.13 hcfcfb64_5 conda-forge
libzopfli 1.0.3 h0e60522_0 conda-forge
llvmlite 0.41.1 pypi_0 pypi
locket 1.0.0 pyhd8ed1ab_0 conda-forge
lz4-c 1.9.4 hcfcfb64_0 conda-forge
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 0.8.2 pyhd8ed1ab_1 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py38h91455d4_0 conda-forge
matplotlib 3.7.5 pypi_0 pypi
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
mkl 2021.4.0 pypi_0 pypi
mkl-devel 2021.4.0 h57928b3_730 conda-forge
mkl-include 2021.4.0 h0e2418a_729 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.8 py38h7b008d5_0 conda-forge
msys2-conda-epoch 20160418 1 conda-forge
napari 0.4.19.post1 pyh9208f05_0 conda-forge
napari-console 0.0.9 pyh9208f05_0 conda-forge
napari-plugin-engine 0.2.0 pyhd8ed1ab_2 conda-forge
napari-svg 0.1.10 pyhd8ed1ab_0 conda-forge
natsort 8.4.0 pypi_0 pypi
nbclassic 1.0.0 pypi_0 pypi
nbclient 0.10.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.16.4 hd8ed1ab_0 conda-forge
nbconvert-core 7.16.4 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.16.4 hd8ed1ab_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
networkx 3.1 pyhd8ed1ab_0 conda-forge
notebook 7.2.0 pypi_0 pypi
notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge
npe2 0.7.5 pyhd8ed1ab_0 conda-forge
nsight-compute 2024.2.0.16 h96209f7_0 conda-forge
numba 0.58.1 pypi_0 pypi
numcodecs 0.12.1 py38h2698bfa_1 conda-forge
numpy 1.24.4 py38h1d91fd2_0 conda-forge
numpydoc 1.7.0 pyhd8ed1ab_0 conda-forge
opencv-python-headless 4.9.0.80 pypi_0 pypi
openjpeg 2.5.0 ha2aaf27_2 conda-forge
openssl 3.3.1 h2466b09_0 conda-forge
overrides 7.7.0 pyhd8ed1ab_0 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
pandas 2.0.3 py38hf08cf0d_1 conda-forge
pandoc 3.2 h57928b3_0 conda-forge
pandocfilters 1.5.1 pypi_0 pypi
parso 0.8.4 pyhd8ed1ab_0 conda-forge
partd 1.4.1 pyhd8ed1ab_0 conda-forge
pcre2 10.43 h17e33f8_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.3.0 pypi_0 pypi
pint 0.21 pyhd8ed1ab_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge
ply 3.11 pyhd8ed1ab_2 conda-forge
pooch 1.8.1 pyhd8ed1ab_0 conda-forge
prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.43 pypi_0 pypi
prompt_toolkit 3.0.42 hd8ed1ab_0 conda-forge
psutil 5.9.8 py38h91455d4_0 conda-forge
psygnal 0.11.1 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 hcd874cb_1001 conda-forge
pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pyconify 0.1.6 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pydantic 2.7.1 pyhd8ed1ab_0 conda-forge
pydantic-compat 0.1.2 pyhd8ed1ab_0 conda-forge
pydantic-core 2.18.2 py38h2e0ef18_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.2 pypi_0 pypi
pyproject_hooks 1.1.0 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py38hd6c051e_5 conda-forge
pyqt5-sip 12.12.2 py38hd3f51b4_5 conda-forge
pyqt6 6.7.0 pypi_0 pypi
pyqt6-qt6 6.7.0 pypi_0 pypi
pyqt6-sip 13.6.0 pypi_0 pypi
pyqtgraph 0.13.3 pypi_0 pypi
pysocks 1.7.1 pyh0701188_6 conda-forge
python 3.8.19 h4de0772_0_cpython conda-forge
python-build 1.2.1 pyhd8ed1ab_0 conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
python-fastjsonschema 2.19.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.8 4_cp38 conda-forge
pytorch 2.3.1 py3.8_cuda12.1_cudnn8_0 pytorch
pytorch-cuda 12.1 hde6ce7c_5 pytorch
pytorch-mutex 1.0 cuda pytorch
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 py38he7056a7_1 conda-forge
pywin32 306 pypi_0 pypi
pywinpty 2.0.13 py38hd3f51b4_0 conda-forge
pyyaml 6.0.1 py38h91455d4_1 conda-forge
pyzmq 26.0.3 py38h3c56b06_0 conda-forge
qt-main 5.15.8 he5a7383_16 conda-forge
qtconsole-base 5.5.2 pyha770c72_0 conda-forge
qtpy 2.4.1 pyhd8ed1ab_0 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rich 13.7.1 pyhd8ed1ab_0 conda-forge
roifile 2023.5.12 pypi_0 pypi
rpds-py 0.18.1 py38h2e0ef18_0 conda-forge
scikit-image 0.21.0 py38hd3f51b4_0 conda-forge
scipy 1.10.1 pypi_0 pypi
send2trash 1.8.3 pyh5737063_0 conda-forge
setuptools 69.5.1 pyhd8ed1ab_0 conda-forge
shellingham 1.5.4 pyhd8ed1ab_0 conda-forge
sip 6.7.12 py38hd3f51b4_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.10 hfb803bf_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sphinx 7.1.2 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.4 pyhd8ed1ab_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
stack-data 0.6.3 pypi_0 pypi
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
superqt 0.6.6 pypi_0 pypi
sympy 1.12 pyh04b8f61_3 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
tbb 2021.12.0 pypi_0 pypi
terminado 0.18.1 pyh5737063_0 conda-forge
tifffile 2023.7.10 pyhd8ed1ab_0 conda-forge
tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h5226925_1 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomli-w 1.0.0 pyhd8ed1ab_0 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tornado 6.4 py38h91455d4_0 conda-forge
tqdm 4.66.4 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
typer 0.12.3 pyhd8ed1ab_0 conda-forge
typer-slim 0.12.3 pyhd8ed1ab_0 conda-forge
typer-slim-standard 0.12.3 hd8ed1ab_0 conda-forge
types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge
typing-extensions 4.11.0 hd8ed1ab_0 conda-forge
typing_extensions 4.11.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
ucrt 10.0.22621.0 h57928b3_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
vc 14.3 hcf57466_18 conda-forge
vc14_runtime 14.38.33130 h82b7239_18 conda-forge
vispy 0.14.2 py38haf47d59_1 conda-forge
vs2015_runtime 14.38.33130 hcb4865c_18 conda-forge
vs2019_win-64 19.29.30139 he1865b1_20 conda-forge
vswhere 3.1.4 h57928b3_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.10 pyhd8ed1ab_0 conda-forge
win_inet_pton 1.1.0 pyhd8ed1ab_6 conda-forge
winpty 0.4.3 4 conda-forge
wrapt 1.16.0 py38h91455d4_0 conda-forge
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
y-py 0.6.2 pypi_0 pypi
yaml 0.2.5 h8ffe710_2 conda-forge
ypy-websocket 0.8.4 pypi_0 pypi
zarr 2.17.1 pyhd8ed1ab_0 conda-forge
zeromq 4.3.5 he1f189c_4 conda-forge
zfp 1.0.1 h63175ca_0 conda-forge
zipp 3.18.2 pypi_0 pypi
zlib-ng 2.0.7 hcfcfb64_0 conda-forge
zstd 1.5.6 h0ea2cb4_0 conda-forge
Run log
2024-06-10 11:52:34,981 [INFO] WRITING LOG OUTPUT TO C:\Users\analysator\.cellpose\run.log
2024-06-10 11:52:34,981 [INFO]
cellpose version: 3.0.8
platform: win32
python version: 3.8.19
torch version: 2.3.1
2024-06-10 11:52:35,106 [INFO] ** TORCH CUDA version installed and working. **
2024-06-10 11:52:35,106 [INFO] >>>> using GPU
2024-06-10 11:52:35,168 [INFO] >>>> loading model D:/Jakob/models/cyto3-3560endos
2024-06-10 11:52:35,434 [INFO] >>>> model diam_mean = 30.000 (ROIs rescaled to this size during training)
2024-06-10 11:52:35,434 [INFO] >>>> model diam_labels = 81.307 (mean diameter of training ROIs)
2024-06-10 11:52:35,434 [INFO] multi-stack tiff read in as having 86 planes 1 channels
2024-06-10 11:52:38,013 [INFO] running YX: 86 planes of size (900, 1490)
2024-06-10 11:52:38,013 [INFO] 0%| | 0/3 [00:00<?, ?it/s]
2024-06-10 11:52:38,356 [INFO] 33%|###3 | 1/3 [00:00<00:00, 2.91it/s]
2024-06-10 11:52:38,418 [INFO] 100%|##########| 3/3 [00:00<00:00, 7.39it/s]
2024-06-10 11:52:39,440 [INFO] running ZY: 900 planes of size (86, 1490)
2024-06-10 11:52:39,455 [INFO] 0%| | 0/29 [00:00<?, ?it/s]
2024-06-10 11:52:39,555 [INFO] 10%|# | 3/29 [00:00<00:00, 29.98it/s]
2024-06-10 11:52:39,669 [INFO] 34%|###4 | 10/29 [00:00<00:00, 49.61it/s]
2024-06-10 11:52:39,778 [INFO] 59%|#####8 | 17/29 [00:00<00:00, 56.30it/s]
2024-06-10 11:52:39,887 [INFO] 79%|#######9 | 23/29 [00:00<00:00, 55.77it/s]
2024-06-10 11:52:39,981 [INFO] 100%|##########| 29/29 [00:00<00:00, 55.16it/s]
2024-06-10 11:52:42,731 [INFO] running ZX: 1490 planes of size (86, 900)
2024-06-10 11:52:42,731 [INFO] 0%| | 0/43 [00:00<?, ?it/s]
2024-06-10 11:52:42,872 [INFO] 7%|6 | 3/43 [00:00<00:01, 24.68it/s]
2024-06-10 11:52:42,989 [INFO] 16%|#6 | 7/43 [00:00<00:01, 29.53it/s]
2024-06-10 11:52:43,091 [INFO] 26%|##5 | 11/43 [00:00<00:00, 33.64it/s]
2024-06-10 11:52:43,200 [INFO] 42%|####1 | 18/43 [00:00<00:00, 45.49it/s]
2024-06-10 11:52:43,300 [INFO] 58%|#####8 | 25/43 [00:00<00:00, 53.73it/s]
2024-06-10 11:52:43,403 [INFO] 74%|#######4 | 32/43 [00:00<00:00, 58.41it/s]
2024-06-10 11:52:43,516 [INFO] 91%|######### | 39/43 [00:00<00:00, 59.64it/s]
2024-06-10 11:52:43,575 [INFO] 100%|##########| 43/43 [00:00<00:00, 51.91it/s]
2024-06-10 11:52:46,546 [INFO] network run in 10.91s
2024-06-10 11:58:49,920 [INFO] masks created in 363.37s
As you can see from the log it takes 6 minutes to create the masks and I am wondering whether there is a way to speed this up or not.
Best regards