search

MouseLand / cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
https://www.cellpose.org/
BSD 3-Clause "New" or "Revised" License
1.24k stars 359 forks source link

Cellpose not making full use of GPU #957

Open KandlerJ opened 2 weeks ago

KandlerJ commented 2 weeks ago

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