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royerlab / ultrack

Cell tracking and segmentation software
https://royerlab.github.io/ultrack
BSD 3-Clause "New" or "Revised" License
95 stars 12 forks source link

error running ultrack plugging inside fiji #160

Open jazberna1 opened 2 weeks ago

jazberna1 commented 2 weeks ago

Hello!

I am trying to run ultrack inisde fiji. I have installed ultrack in a conda environment following your install instructions, and pointed fiji to the ultrack enviroment path. I am able to start the server, but when I want to run it using an image, it gives me the following error: I am on windows 10.

[ERROR] Runtime exception during onWebsocketMessage
com.google.gson.JsonSyntaxException: Expected a com.google.gson.JsonObject but was com.google.gson.JsonPrimitive; at path $
    at com.google.gson.internal.bind.TypeAdapters$34$1.read(TypeAdapters.java:1010)
    at com.google.gson.Gson.fromJson(Gson.java:1227)
    at com.google.gson.Gson.fromJson(Gson.java:1137)
    at com.google.gson.Gson.fromJson(Gson.java:1047)
    at com.google.gson.Gson.fromJson(Gson.java:982)
    at org.czbiohub.royerlab.JavaConnector.onMessageConsumer(JavaConnector.java:169)
    at org.czbiohub.royerlab.UltrackWebsocketClient.onMessage(UltrackWebsocketClient.java:99)
    at org.java_websocket.client.WebSocketClient.onWebsocketMessage(WebSocketClient.java:644)
    at org.java_websocket.drafts.Draft_6455.processFrameText(Draft_6455.java:986)
    at org.java_websocket.drafts.Draft_6455.processFrame(Draft_6455.java:910)
    at org.java_websocket.WebSocketImpl.decodeFrames(WebSocketImpl.java:402)
    at org.java_websocket.WebSocketImpl.decode(WebSocketImpl.java:234)
    at org.java_websocket.client.WebSocketClient.run(WebSocketClient.java:527)
    at java.lang.Thread.run(Thread.java:750)

Any help will be much appreciated.

Thanks Jorge

JoOkuma commented 2 weeks ago

cc @ilan-theodoro could you check this?

ilan-theodoro commented 2 weeks ago

Hi @jazberna1!

Can you send me a screenshot of the logs that are bultin the plugin (the right panel)?

jazberna1 commented 1 week ago

Hi!

screenshot attached.

Many thanks!

Capture
ilan-theodoro commented 1 week ago

We are dealing with some problems in your environment. Can you conda activate it and then conda list it so we can troubleshoot the environment packages?

@JoOkuma, Have you been familiar with this error before? Is it something related to Numpy 2.0?

jazberna1 commented 1 week ago

Hi!

This is the list of packages in our ultrack environment:

Thanks Jorge

# packages in environment at C:\Users\Malieva\.conda\envs\ultrack:
#
# Name                    Version                   Build  Channel
aiobotocore               2.15.2                   pypi_0    pypi
aiohappyeyeballs          2.4.3                    pypi_0    pypi
aiohttp                   3.10.10                  pypi_0    pypi
aioitertools              0.12.0                   pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
alabaster                 1.0.0                    pypi_0    pypi
annotated-types           0.7.0                    pypi_0    pypi
anyio                     4.6.2.post1              pypi_0    pypi
app-model                 0.3.0                    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
blosc2                    2.7.1                    pypi_0    pypi
botocore                  1.35.36                  pypi_0    pypi
build                     1.2.2.post1              pypi_0    pypi
bzip2                     1.0.8                h2466b09_7    conda-forge
ca-certificates           2024.9.24            haa95532_0
cachey                    0.2.1                    pypi_0    pypi
certifi                   2024.8.30                pypi_0    pypi
cffi                      1.17.1                   pypi_0    pypi
charset-normalizer        3.4.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloudpickle               3.1.0                    pypi_0    pypi
colorama                  0.4.6                    pypi_0    pypi
comm                      0.2.2                    pypi_0    pypi
contourpy                 1.3.0                    pypi_0    pypi
cucim                     22.4.0                    dev_0    <develop>
cuda-cccl                 12.6.77                       0    nvidia
cuda-cccl_win-64          12.6.77                       0    nvidia
cuda-cudart               12.4.127                      0    nvidia
cuda-cudart-dev           12.4.127                      0    nvidia
cuda-cudart-dev_win-64    12.6.77              he0c23c2_0    conda-forge
cuda-cudart-static_win-64 12.6.77              he0c23c2_0    conda-forge
cuda-cudart_win-64        12.6.77              he0c23c2_0    conda-forge
cuda-cupti                12.4.127                      0    nvidia
cuda-libraries            12.4.1                        0    nvidia
cuda-libraries-dev        12.4.1                        0    nvidia
cuda-nvrtc                12.4.127                      0    nvidia
cuda-nvrtc-dev            12.4.127                      0    nvidia
cuda-nvtx                 12.4.127                      0    nvidia
cuda-opencl               12.6.77                       0    nvidia
cuda-opencl-dev           12.6.77                       0    nvidia
cuda-profiler-api         12.6.77                       0    nvidia
cuda-runtime              12.4.1                        0    nvidia
cuda-version              12.6                          3    nvidia
cupy                      13.3.0          py311hd45bd00_2    conda-forge
cupy-core                 13.3.0          py311h54f43e2_2    conda-forge
cycler                    0.12.1                   pypi_0    pypi
dask                      2024.10.0                pypi_0    pypi
debugpy                   1.8.7                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
distributed               2024.10.0                pypi_0    pypi
docstring-parser          0.16                     pypi_0    pypi
docutils                  0.21.2                   pypi_0    pypi
edt                       2.4.1                    pypi_0    pypi
executing                 2.1.0                    pypi_0    pypi
fastapi                   0.115.4                  pypi_0    pypi
fasteners                 0.19                     pypi_0    pypi
fastrlock                 0.8.2           py311h12c1d0e_2    conda-forge
filelock                  3.13.1                   pypi_0    pypi
flexcache                 0.3                      pypi_0    pypi
flexparser                0.3.1                    pypi_0    pypi
fonttools                 4.54.1                   pypi_0    pypi
freetype-py               2.5.1                    pypi_0    pypi
frozenlist                1.5.0                    pypi_0    pypi
fsspec                    2024.2.0                 pypi_0    pypi
gevent                    24.10.3                  pypi_0    pypi
git                       2.45.2               haa95532_1    anaconda
glib                      2.82.2               h7025463_0    conda-forge
glib-tools                2.82.2               h4394cf3_0    conda-forge
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
gurobi                    11.0.3                  py311_0    gurobi
h11                       0.14.0                   pypi_0    pypi
heapdict                  1.0.1                    pypi_0    pypi
higra                     0.6.10          py311hcf9f919_0    conda-forge
hsluv                     5.0.4                    pypi_0    pypi
httpcore                  1.0.6                    pypi_0    pypi
httpx                     0.27.2                   pypi_0    pypi
icu                       75.1                 he0c23c2_0    conda-forge
idna                      3.10                     pypi_0    pypi
imagecodecs               2024.9.22                pypi_0    pypi
imageio                   2.36.0                   pypi_0    pypi
imagesize                 1.4.1                    pypi_0    pypi
importlib-metadata        8.5.0                    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                   8.29.0                   pypi_0    pypi
jedi                      0.19.1                   pypi_0    pypi
jinja2                    3.1.3                    pypi_0    pypi
jmespath                  1.0.1                    pypi_0    pypi
jsonschema                4.23.0                   pypi_0    pypi
jsonschema-specifications 2024.10.1                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
libblas                   3.9.0              25_win64_mkl    conda-forge
libcblas                  3.9.0              25_win64_mkl    conda-forge
libclang13                19.1.3          default_ha5278ca_0    conda-forge
libcublas                 12.4.5.8                      0    nvidia
libcublas-dev             12.4.5.8                      0    nvidia
libcufft                  11.2.1.3                      0    nvidia
libcufft-dev              11.2.1.3                      0    nvidia
libcurand                 10.3.7.77                     0    nvidia
libcurand-dev             10.3.7.77                     0    nvidia
libcusolver               11.6.1.9                      0    nvidia
libcusolver-dev           11.6.1.9                      0    nvidia
libcusparse               12.3.1.170                    0    nvidia
libcusparse-dev           12.3.1.170                    0    nvidia
libexpat                  2.6.3                he0c23c2_0    conda-forge
libffi                    3.4.2                h8ffe710_5    conda-forge
libglib                   2.82.2               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              25_win64_mkl    conda-forge
libnpp                    12.2.5.30                     0    nvidia
libnpp-dev                12.2.5.30                     0    nvidia
libnvfatbin               12.6.77                       0    nvidia
libnvfatbin-dev           12.6.77                       0    nvidia
libnvjitlink              12.4.127                      0    nvidia
libnvjitlink-dev          12.4.127                      0    nvidia
libnvjpeg                 12.3.1.117                    0    nvidia
libnvjpeg-dev             12.3.1.117                    0    nvidia
libogg                    1.3.5                h2466b09_0    conda-forge
libpng                    1.6.44               h3ca93ac_0    conda-forge
libsqlite                 3.47.0               h2466b09_1    conda-forge
libvorbis                 1.3.7                h0e60522_0    conda-forge
libxml2                   2.13.4               h442d1da_2    conda-forge
libzlib                   1.3.1                h2466b09_2    conda-forge
llvmlite                  0.43.0                   pypi_0    pypi
locket                    1.0.0                    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
matplotlib                3.9.2                    pypi_0    pypi
matplotlib-inline         0.1.7                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
mip                       1.16rc0                  pypi_0    pypi
mkl                       2024.2.2            h66d3029_14    conda-forge
mpmath                    1.3.0                    pypi_0    pypi
msgpack                   1.1.0                    pypi_0    pypi
multidict                 6.1.0                    pypi_0    pypi
napari                    0.5.4                    pypi_0    pypi
napari-console            0.1.0                    pypi_0    pypi
napari-plugin-engine      0.2.0                    pypi_0    pypi
napari-svg                0.2.0                    pypi_0    pypi
ndindex                   1.9.2                    pypi_0    pypi
nest-asyncio              1.6.0                    pypi_0    pypi
networkx                  3.2.1                    pypi_0    pypi
npe2                      0.7.7                    pypi_0    pypi
numba                     0.60.0                   pypi_0    pypi
numcodecs                 0.13.1                   pypi_0    pypi
numexpr                   2.10.1                   pypi_0    pypi
numpy                     2.0.2                    pypi_0    pypi
numpydoc                  1.8.0                    pypi_0    pypi
ome-zarr                  0.9.0                    pypi_0    pypi
openssl                   3.3.2                h2466b09_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandas                    2.2.3                    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                    10.2.0                   pypi_0    pypi
pint                      0.24.3                   pypi_0    pypi
pip                       24.3.1             pyh8b19718_0    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
propcache                 0.2.0                    pypi_0    pypi
psutil                    6.1.0                    pypi_0    pypi
psycopg2-binary           2.9.10                   pypi_0    pypi
psygnal                   0.11.1                   pypi_0    pypi
pthreads-win32            2.9.1                h2466b09_4    conda-forge
pure-eval                 0.2.3                    pypi_0    pypi
py-cpuinfo                9.0.0                    pypi_0    pypi
pyconify                  0.1.6                    pypi_0    pypi
pycparser                 2.22                     pypi_0    pypi
pydantic                  2.9.2                    pypi_0    pypi
pydantic-compat           0.1.2                    pypi_0    pypi
pydantic-core             2.23.4                   pypi_0    pypi
pydot                     3.0.2                    pypi_0    pypi
pygments                  2.18.0                   pypi_0    pypi
pyopengl                  3.1.7                    pypi_0    pypi
pyparsing                 3.2.0                    pypi_0    pypi
pyproject-hooks           1.2.0                    pypi_0    pypi
pyqt                      5.15.9          py311h125bc19_5    conda-forge
pyqt5-sip                 12.12.2         py311h12c1d0e_5    conda-forge
python                    3.11.10         hce54a09_3_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
python_abi                3.11                    5_cp311    conda-forge
pytorch-cuda              12.4                 h3fd98bf_7    pytorch
pytz                      2024.2                   pypi_0    pypi
pywin32                   308                      pypi_0    pypi
pyyaml                    6.0.2                    pypi_0    pypi
pyzmq                     26.2.0                   pypi_0    pypi
qt-main                   5.15.15              h264fbc2_0    conda-forge
qtawesome                 1.3.1                    pypi_0    pypi
qtconsole                 5.6.1                    pypi_0    pypi
qtpy                      2.4.2                    pypi_0    pypi
referencing               0.35.1                   pypi_0    pypi
requests                  2.32.3                   pypi_0    pypi
rich                      13.9.4                   pypi_0    pypi
rpds-py                   0.20.1                   pypi_0    pypi
s3fs                      2024.2.0                 pypi_0    pypi
scikit-image              0.24.0                   pypi_0    pypi
scipy                     1.14.1                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
setuptools                75.3.0             pyhd8ed1ab_0    conda-forge
shellingham               1.5.4                    pypi_0    pypi
sip                       6.7.12          py311h12c1d0e_0    conda-forge
six                       1.16.0                   pypi_0    pypi
sniffio                   1.3.1                    pypi_0    pypi
snowballstemmer           2.2.0                    pypi_0    pypi
sortedcontainers          2.4.0                    pypi_0    pypi
sphinx                    8.1.3                    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                2.0.36                   pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
starlette                 0.41.2                   pypi_0    pypi
superqt                   0.6.7                    pypi_0    pypi
sympy                     1.13.1                   pypi_0    pypi
tabulate                  0.9.0                    pypi_0    pypi
tbb                       2021.13.0            hc790b64_0    conda-forge
tblib                     3.0.0                    pypi_0    pypi
tifffile                  2024.9.20                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                   1.1.0                    pypi_0    pypi
toolz                     1.0.0                    pypi_0    pypi
torch                     2.5.1+cu118              pypi_0    pypi
torchaudio                2.5.1+cu118              pypi_0    pypi
torchvision               0.20.1+cu118             pypi_0    pypi
tornado                   6.4.1                    pypi_0    pypi
tqdm                      4.66.6                   pypi_0    pypi
traitlets                 5.14.3                   pypi_0    pypi
typer                     0.12.5                   pypi_0    pypi
typing-extensions         4.9.0                    pypi_0    pypi
tzdata                    2024.2                   pypi_0    pypi
ucrt                      10.0.22621.0         h57928b3_1    conda-forge
ultrack                   0.6.1                    pypi_0    pypi
urllib3                   2.2.3                    pypi_0    pypi
uvicorn                   0.32.0                   pypi_0    pypi
vc                        14.3                h8a93ad2_22    conda-forge
vc14_runtime              14.40.33810         hcc2c482_22    conda-forge
vispy                     0.14.3                   pypi_0    pypi
vs2015_runtime            14.40.33810         h3bf8584_22    conda-forge
wcwidth                   0.2.13                   pypi_0    pypi
websocket                 0.2.1                    pypi_0    pypi
websockets                13.1                     pypi_0    pypi
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0                   pypi_0    pypi
xz                        5.2.6                h8d14728_0    conda-forge
yarl                      1.17.1                   pypi_0    pypi
zarr                      2.18.3                   pypi_0    pypi
zict                      3.0.0                    pypi_0    pypi
zipp                      3.20.2                   pypi_0    pypi
zope-event                5.0                      pypi_0    pypi
zope-interface            7.1.1                    pypi_0    pypi
zstd                      1.5.6                h0ea2cb4_0    conda-forge
JoOkuma commented 1 week ago

Hi @jazberna1, it's the same problem you had in #153

You can use your other existing environment or install numpy==1.23.5

ilan-theodoro commented 1 week ago

@jazberna1

@JoOkuma answered faster, so I am complementing his answer.

so, the problem is actually on your cucim version.

You're using cucim version 22.04, which references np.bool8, deprecated since numpy version 1.24 and removed from version 2.0. In cucim==22.04 they have the following code:

https://github.com/rapidsai/cucim/blob/73801e68cedc3b1c5e0ffd795620cf2f73c3730e/python/cucim/src/cucim/skimage/util/dtype.py#L28C1-L29C1

but since cucim==22.12 they replaced by

https://github.com/rapidsai/cucim/blob/0f1f029dc2d7826f8ab8df8e5b894657931dd90c/python/cucim/src/cucim/skimage/util/dtype.py#L42.

I think there are two solutions for your problem. Either update cucim or pin numpy to numpy<2.0. The latter option should be faster.

jazberna1 commented 1 week ago

Hello,

I have upgraded cucim to 22.12.0 and kept numpy to 2.0.2.

However I still get this error:

Capture

This is again conda list:

# packages in environment at C:\Users\Malieva\.conda\envs\ultrack:
#
# Name                    Version                   Build  Channel
aiobotocore               2.15.2                   pypi_0    pypi
aiohappyeyeballs          2.4.3                    pypi_0    pypi
aiohttp                   3.10.10                  pypi_0    pypi
aioitertools              0.12.0                   pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
alabaster                 1.0.0                    pypi_0    pypi
annotated-types           0.7.0                    pypi_0    pypi
anyio                     4.6.2.post1              pypi_0    pypi
app-model                 0.3.0                    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
blosc2                    2.7.1                    pypi_0    pypi
botocore                  1.35.36                  pypi_0    pypi
build                     1.2.2.post1              pypi_0    pypi
bzip2                     1.0.8                h2466b09_7    conda-forge
ca-certificates           2024.9.24            haa95532_0
cachey                    0.2.1                    pypi_0    pypi
certifi                   2024.8.30                pypi_0    pypi
cffi                      1.17.1                   pypi_0    pypi
charset-normalizer        3.4.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloudpickle               3.1.0                    pypi_0    pypi
colorama                  0.4.6                    pypi_0    pypi
comm                      0.2.2                    pypi_0    pypi
contourpy                 1.3.0                    pypi_0    pypi
cucim                     22.12.0                   dev_0    <develop>
cuda-cccl                 12.6.77                       0    nvidia
cuda-cccl_win-64          12.6.77                       0    nvidia
cuda-cudart               12.4.127                      0    nvidia
cuda-cudart-dev           12.4.127                      0    nvidia
cuda-cudart-dev_win-64    12.6.77              he0c23c2_0    conda-forge
cuda-cudart-static_win-64 12.6.77              he0c23c2_0    conda-forge
cuda-cudart_win-64        12.6.77              he0c23c2_0    conda-forge
cuda-cupti                12.4.127                      0    nvidia
cuda-libraries            12.4.1                        0    nvidia
cuda-libraries-dev        12.4.1                        0    nvidia
cuda-nvrtc                12.4.127                      0    nvidia
cuda-nvrtc-dev            12.4.127                      0    nvidia
cuda-nvtx                 12.4.127                      0    nvidia
cuda-opencl               12.6.77                       0    nvidia
cuda-opencl-dev           12.6.77                       0    nvidia
cuda-profiler-api         12.6.77                       0    nvidia
cuda-runtime              12.4.1                        0    nvidia
cuda-version              12.6                          3    nvidia
cupy                      13.3.0          py311hd45bd00_2    conda-forge
cupy-core                 13.3.0          py311h54f43e2_2    conda-forge
cycler                    0.12.1                   pypi_0    pypi
dask                      2024.10.0                pypi_0    pypi
debugpy                   1.8.7                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
distributed               2024.10.0                pypi_0    pypi
docstring-parser          0.16                     pypi_0    pypi
docutils                  0.21.2                   pypi_0    pypi
edt                       2.4.1                    pypi_0    pypi
executing                 2.1.0                    pypi_0    pypi
fastapi                   0.115.4                  pypi_0    pypi
fasteners                 0.19                     pypi_0    pypi
fastrlock                 0.8.2           py311h12c1d0e_2    conda-forge
filelock                  3.13.1                   pypi_0    pypi
flexcache                 0.3                      pypi_0    pypi
flexparser                0.3.1                    pypi_0    pypi
fonttools                 4.54.1                   pypi_0    pypi
freetype-py               2.5.1                    pypi_0    pypi
frozenlist                1.5.0                    pypi_0    pypi
fsspec                    2024.2.0                 pypi_0    pypi
gevent                    24.10.3                  pypi_0    pypi
git                       2.45.2               haa95532_1    anaconda
glib                      2.82.2               h7025463_0    conda-forge
glib-tools                2.82.2               h4394cf3_0    conda-forge
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
gurobi                    11.0.3                  py311_0    gurobi
h11                       0.14.0                   pypi_0    pypi
heapdict                  1.0.1                    pypi_0    pypi
higra                     0.6.10          py311hcf9f919_0    conda-forge
hsluv                     5.0.4                    pypi_0    pypi
httpcore                  1.0.6                    pypi_0    pypi
httpx                     0.27.2                   pypi_0    pypi
icu                       75.1                 he0c23c2_0    conda-forge
idna                      3.10                     pypi_0    pypi
imagecodecs               2024.9.22                pypi_0    pypi
imageio                   2.36.0                   pypi_0    pypi
imagesize                 1.4.1                    pypi_0    pypi
importlib-metadata        8.5.0                    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                   8.29.0                   pypi_0    pypi
jedi                      0.19.1                   pypi_0    pypi
jinja2                    3.1.3                    pypi_0    pypi
jmespath                  1.0.1                    pypi_0    pypi
jsonschema                4.23.0                   pypi_0    pypi
jsonschema-specifications 2024.10.1                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
libblas                   3.9.0              25_win64_mkl    conda-forge
libcblas                  3.9.0              25_win64_mkl    conda-forge
libclang13                19.1.3          default_ha5278ca_0    conda-forge
libcublas                 12.4.5.8                      0    nvidia
libcublas-dev             12.4.5.8                      0    nvidia
libcufft                  11.2.1.3                      0    nvidia
libcufft-dev              11.2.1.3                      0    nvidia
libcurand                 10.3.7.77                     0    nvidia
libcurand-dev             10.3.7.77                     0    nvidia
libcusolver               11.6.1.9                      0    nvidia
libcusolver-dev           11.6.1.9                      0    nvidia
libcusparse               12.3.1.170                    0    nvidia
libcusparse-dev           12.3.1.170                    0    nvidia
libexpat                  2.6.3                he0c23c2_0    conda-forge
libffi                    3.4.2                h8ffe710_5    conda-forge
libglib                   2.82.2               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              25_win64_mkl    conda-forge
libnpp                    12.2.5.30                     0    nvidia
libnpp-dev                12.2.5.30                     0    nvidia
libnvfatbin               12.6.77                       0    nvidia
libnvfatbin-dev           12.6.77                       0    nvidia
libnvjitlink              12.4.127                      0    nvidia
libnvjitlink-dev          12.4.127                      0    nvidia
libnvjpeg                 12.3.1.117                    0    nvidia
libnvjpeg-dev             12.3.1.117                    0    nvidia
libogg                    1.3.5                h2466b09_0    conda-forge
libpng                    1.6.44               h3ca93ac_0    conda-forge
libsqlite                 3.47.0               h2466b09_1    conda-forge
libvorbis                 1.3.7                h0e60522_0    conda-forge
libxml2                   2.13.4               h442d1da_2    conda-forge
libzlib                   1.3.1                h2466b09_2    conda-forge
llvmlite                  0.43.0                   pypi_0    pypi
locket                    1.0.0                    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
matplotlib                3.9.2                    pypi_0    pypi
matplotlib-inline         0.1.7                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
mip                       1.16rc0                  pypi_0    pypi
mkl                       2024.2.2            h66d3029_14    conda-forge
mpmath                    1.3.0                    pypi_0    pypi
msgpack                   1.1.0                    pypi_0    pypi
multidict                 6.1.0                    pypi_0    pypi
napari                    0.5.4                    pypi_0    pypi
napari-console            0.1.0                    pypi_0    pypi
napari-plugin-engine      0.2.0                    pypi_0    pypi
napari-svg                0.2.0                    pypi_0    pypi
ndindex                   1.9.2                    pypi_0    pypi
nest-asyncio              1.6.0                    pypi_0    pypi
networkx                  3.2.1                    pypi_0    pypi
npe2                      0.7.7                    pypi_0    pypi
numba                     0.60.0                   pypi_0    pypi
numcodecs                 0.13.1                   pypi_0    pypi
numexpr                   2.10.1                   pypi_0    pypi
numpy                     2.0.2                    pypi_0    pypi
numpydoc                  1.8.0                    pypi_0    pypi
ome-zarr                  0.9.0                    pypi_0    pypi
openssl                   3.3.2                h2466b09_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandas                    2.2.3                    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                    10.2.0                   pypi_0    pypi
pint                      0.24.3                   pypi_0    pypi
pip                       24.3.1             pyh8b19718_0    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
propcache                 0.2.0                    pypi_0    pypi
psutil                    6.1.0                    pypi_0    pypi
psycopg2-binary           2.9.10                   pypi_0    pypi
psygnal                   0.11.1                   pypi_0    pypi
pthreads-win32            2.9.1                h2466b09_4    conda-forge
pure-eval                 0.2.3                    pypi_0    pypi
py-cpuinfo                9.0.0                    pypi_0    pypi
pyconify                  0.1.6                    pypi_0    pypi
pycparser                 2.22                     pypi_0    pypi
pydantic                  2.9.2                    pypi_0    pypi
pydantic-compat           0.1.2                    pypi_0    pypi
pydantic-core             2.23.4                   pypi_0    pypi
pydot                     3.0.2                    pypi_0    pypi
pygments                  2.18.0                   pypi_0    pypi
pyopengl                  3.1.7                    pypi_0    pypi
pyparsing                 3.2.0                    pypi_0    pypi
pyproject-hooks           1.2.0                    pypi_0    pypi
pyqt                      5.15.9          py311h125bc19_5    conda-forge
pyqt5-sip                 12.12.2         py311h12c1d0e_5    conda-forge
python                    3.11.10         hce54a09_3_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
python_abi                3.11                    5_cp311    conda-forge
pytorch-cuda              12.4                 h3fd98bf_7    pytorch
pytz                      2024.2                   pypi_0    pypi
pywin32                   308                      pypi_0    pypi
pyyaml                    6.0.2                    pypi_0    pypi
pyzmq                     26.2.0                   pypi_0    pypi
qt-main                   5.15.15              h264fbc2_0    conda-forge
qtawesome                 1.3.1                    pypi_0    pypi
qtconsole                 5.6.1                    pypi_0    pypi
qtpy                      2.4.2                    pypi_0    pypi
referencing               0.35.1                   pypi_0    pypi
requests                  2.32.3                   pypi_0    pypi
rich                      13.9.4                   pypi_0    pypi
rpds-py                   0.20.1                   pypi_0    pypi
s3fs                      2024.2.0                 pypi_0    pypi
scikit-image              0.24.0                   pypi_0    pypi
scipy                     1.14.1                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
setuptools                75.3.0             pyhd8ed1ab_0    conda-forge
shellingham               1.5.4                    pypi_0    pypi
sip                       6.7.12          py311h12c1d0e_0    conda-forge
six                       1.16.0                   pypi_0    pypi
sniffio                   1.3.1                    pypi_0    pypi
snowballstemmer           2.2.0                    pypi_0    pypi
sortedcontainers          2.4.0                    pypi_0    pypi
sphinx                    8.1.3                    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                2.0.36                   pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
starlette                 0.41.2                   pypi_0    pypi
superqt                   0.6.7                    pypi_0    pypi
sympy                     1.13.1                   pypi_0    pypi
tabulate                  0.9.0                    pypi_0    pypi
tbb                       2021.13.0            hc790b64_0    conda-forge
tblib                     3.0.0                    pypi_0    pypi
tifffile                  2024.9.20                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                   1.1.0                    pypi_0    pypi
toolz                     1.0.0                    pypi_0    pypi
torch                     2.5.1+cu118              pypi_0    pypi
torchaudio                2.5.1+cu118              pypi_0    pypi
torchvision               0.20.1+cu118             pypi_0    pypi
tornado                   6.4.1                    pypi_0    pypi
tqdm                      4.66.6                   pypi_0    pypi
traitlets                 5.14.3                   pypi_0    pypi
typer                     0.12.5                   pypi_0    pypi
typing-extensions         4.9.0                    pypi_0    pypi
tzdata                    2024.2                   pypi_0    pypi
ucrt                      10.0.22621.0         h57928b3_1    conda-forge
ultrack                   0.6.1                    pypi_0    pypi
urllib3                   2.2.3                    pypi_0    pypi
uvicorn                   0.32.0                   pypi_0    pypi
vc                        14.3                h8a93ad2_22    conda-forge
vc14_runtime              14.40.33810         hcc2c482_22    conda-forge
vispy                     0.14.3                   pypi_0    pypi
vs2015_runtime            14.40.33810         h3bf8584_22    conda-forge
wcwidth                   0.2.13                   pypi_0    pypi
websocket                 0.2.1                    pypi_0    pypi
websockets                13.1                     pypi_0    pypi
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0                   pypi_0    pypi
xz                        5.2.6                h8d14728_0    conda-forge
yarl                      1.17.1                   pypi_0    pypi
zarr                      2.18.3                   pypi_0    pypi
zict                      3.0.0                    pypi_0    pypi
zipp                      3.20.2                   pypi_0    pypi
zope-event                5.0                      pypi_0    pypi
zope-interface            7.1.1                    pypi_0    pypi
zstd                      1.5.6                h0ea2cb4_0    conda-forge

Thanks Jorge

JoOkuma commented 1 week ago

Hi @jazberna1, unfortunately, it seems Cucim doesn't play well with Windows.

I would recommend downgrading numpy in this case or uninstalling cucim, it should fallback into CPU processing which will be a bit slower.

jazberna1 commented 1 week ago

Hi @JoOkuma

I couldn't make it to work either uninstalling cucim or downgrading numpy.

Should I close the ticket till more testing is done Windows?

Jorge

JoOkuma commented 1 week ago

@jazberna1 thanks for asking; we can leave it open while we sort this out; this way, we can keep track of this.