cellpose seg not working #1
Description
Trying to run cellpose segmentation in a single core locally in MacOS:
Sample:
HN46
Core:
Core05
List of packages installed:
# packages in environment at /opt/homebrew/Caskroom/mambaforge/base/envs/RCellpose:
#
# Name Version Build Channel
abseil-cpp 20230802.0 h61975a4_2
aiohttp 3.9.3 py39h6c40b1e_0
aiohttp-cors 0.7.0 pyhd3eb1b0_0
aiosignal 1.2.0 pyhd3eb1b0_0
aom 3.6.1 he965462_0 conda-forge
arrow-cpp 14.0.2 h3ade35f_1
asciitree 0.3.3 py_2
async-timeout 4.0.3 py39hecd8cb5_0
attrs 23.1.0 py39hecd8cb5_0
aws-c-auth 0.6.19 h6c40b1e_0
aws-c-cal 0.5.20 h3333b6a_0
aws-c-common 0.8.5 h6c40b1e_0
aws-c-compression 0.2.16 h6c40b1e_0
aws-c-event-stream 0.2.15 hcec6c5f_0
aws-c-http 0.6.25 h6c40b1e_0
aws-c-io 0.13.10 h6c40b1e_0
aws-c-mqtt 0.7.13 h6c40b1e_0
aws-c-s3 0.1.51 h6c40b1e_0
aws-c-sdkutils 0.1.6 h6c40b1e_0
aws-checksums 0.1.13 h6c40b1e_0
aws-crt-cpp 0.18.16 hcec6c5f_0
aws-sdk-cpp 1.10.55 h61975a4_0
blas 1.0 mkl
blessed 1.20.0 py39hecd8cb5_0
blosc 1.21.3 hcec6c5f_0
bokeh 3.4.0 py39h20db666_1
bottleneck 1.3.7 py39h7b7cdfe_0
brotli 1.0.9 hca72f7f_7
brotli-bin 1.0.9 hca72f7f_7
brotli-python 1.0.9 py39he9d5cce_7
brunsli 0.1 h23ab428_0
bzip2 1.0.8 h6c40b1e_5
c-ares 1.19.1 h6c40b1e_0
c-blosc2 2.12.0 hcf5af9b_0
ca-certificates 2024.3.11 hecd8cb5_0
cachetools 4.2.2 pyhd3eb1b0_0
cairo 1.16.0 h3ce6f7e_5
cellpose 3.0.8 pypi_0 pypi
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py39h6c40b1e_0
cfitsio 4.1.0 h2c97ad1_0 conda-forge
charls 2.3.4 he49afe7_0 conda-forge
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.1.7 py39hecd8cb5_0
cloudpickle 2.2.1 py39hecd8cb5_0
colorama 0.4.6 py39hecd8cb5_0
colorful 0.5.4 pyhd3eb1b0_0
contourpy 1.2.0 py39ha357a0b_0
cryptography 42.0.5 py39h30e54ef_0
cycler 0.11.0 pyhd3eb1b0_0
cytoolz 0.12.2 py39h6c40b1e_0
dask 2024.5.1 pypi_0 pypi
dav1d 1.2.1 h6c40b1e_0
distlib 0.3.6 py39hecd8cb5_0
distributed 2023.11.0 py39hecd8cb5_0
expat 2.5.0 hcec6c5f_0
fasteners 0.16.3 pyhd3eb1b0_0
fastremap 1.14.1 pypi_0 pypi
ffmpeg 4.4.2 gpl_h3e15351_113 conda-forge
filelock 3.13.1 py39hecd8cb5_0
font-ttf-dejavu-sans-mono 2.37 hd3eb1b0_0
font-ttf-inconsolata 2.001 hcb22688_0
font-ttf-source-code-pro 2.030 hd3eb1b0_0
font-ttf-ubuntu 0.83 h8b1ccd4_0
fontconfig 2.14.2 h5bb23bf_0 conda-forge
fonts-anaconda 1 h8fa9717_0
fonts-conda-ecosystem 1 hd3eb1b0_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.12.1 hd8bbffd_0
frozenlist 1.4.0 py39h6c40b1e_0
fsspec 2023.10.0 py39hecd8cb5_0
gdk-pixbuf 2.42.8 h3648f77_1 conda-forge
gettext 0.22.5 h5ff76d1_2 conda-forge
gettext-tools 0.22.5 h5ff76d1_2 conda-forge
gflags 2.2.2 hcec6c5f_1
giflib 5.2.1 h6c40b1e_3
glib 2.78.4 hcec6c5f_0
glib-tools 2.78.4 hcec6c5f_0
glog 0.5.0 hcec6c5f_1
gmp 6.2.1 he9d5cce_3
gnutls 3.7.9 h1951705_0 conda-forge
google-api-core 2.10.1 py39hecd8cb5_0
google-auth 2.22.0 py39hecd8cb5_0
googleapis-common-protos 1.56.4 py39hecd8cb5_0
gpustat 1.1.1 py39hecd8cb5_0
graphite2 1.3.14 he9d5cce_1
grpc-cpp 1.48.2 hbe2b35a_4
grpcio 1.48.2 py39h38f05b6_4
gtest 1.14.0 ha357a0b_0
harfbuzz 4.3.0 hffc734d_2
hdf5 1.12.1 ha01d115_3
heapdict 1.0.1 pyhd3eb1b0_0
icu 73.2 hf5e326d_0 conda-forge
idna 3.4 py39hecd8cb5_0
imagecodecs 2022.9.26 py39h1e0cc1c_3 conda-forge
imageio 2.33.1 py39hecd8cb5_0
importlib-metadata 7.0.1 py39hecd8cb5_0
importlib_resources 6.1.1 py39hecd8cb5_1
intel-openmp 2023.1.0 ha357a0b_43548
jasper 2.0.33 h7c6fec8_1 conda-forge
jinja2 3.1.3 py39hecd8cb5_0
joblib 1.4.2 pypi_0 pypi
jpeg 9e h6c40b1e_1
jsonschema 4.19.2 py39hecd8cb5_0
jsonschema-specifications 2023.7.1 py39hecd8cb5_0
jxrlib 1.1 haf1e3a3_2
kiwisolver 1.4.4 py39hcec6c5f_0
krb5 1.20.1 h428f121_1
lame 3.100 h1de35cc_0
lazy_loader 0.3 py39hecd8cb5_0
lcms2 2.14 h90f4b2a_0 conda-forge
lerc 4.0.0 hb486fe8_0 conda-forge
libaec 1.1.3 h73e2aa4_0 conda-forge
libasprintf 0.22.5 h5ff76d1_2 conda-forge
libasprintf-devel 0.22.5 h5ff76d1_2 conda-forge
libavif 0.11.1 h6c40b1e_0
libblas 3.9.0 1_h508aa58_netlib conda-forge
libbrotlicommon 1.0.9 hca72f7f_7
libbrotlidec 1.0.9 hca72f7f_7
libbrotlienc 1.0.9 hca72f7f_7
libcblas 3.9.0 5_h0661a58_netlib conda-forge
libcurl 8.5.0 hf20ceda_0
libcxx 16.0.6 hd57cbcb_0 conda-forge
libdeflate 1.14 hb7f2c08_0 conda-forge
libedit 3.1.20230828 h6c40b1e_0
libev 4.33 h9ed2024_1
libevent 2.1.12 h04015c4_1
libffi 3.4.4 hecd8cb5_0
libgettextpo 0.22.5 h5ff76d1_2 conda-forge
libgettextpo-devel 0.22.5 h5ff76d1_2 conda-forge
libgfortran 5.0.0 11_3_0_hecd8cb5_28
libgfortran5 11.3.0 h9dfd629_28
libglib 2.78.4 h19e1a8f_0
libiconv 1.17 hd75f5a5_2 conda-forge
libidn2 2.3.4 h6c40b1e_0
libintl 0.22.5 h5ff76d1_2 conda-forge
libintl-devel 0.22.5 h5ff76d1_2 conda-forge
liblapack 3.9.0 5_h0661a58_netlib conda-forge
liblapacke 3.9.0 5_h0661a58_netlib conda-forge
libnghttp2 1.57.0 h9beae6a_0
libopencv 4.5.5 py39h6ed1040_12 conda-forge
libpng 1.6.39 h6c40b1e_0
libprotobuf 3.20.3 hfff2838_0
libsqlite 3.45.2 h92b6c6a_0 conda-forge
libssh2 1.10.0 h04015c4_2
libtasn1 4.19.0 h6c40b1e_0
libthrift 0.15.0 h70b4b81_2
libtiff 4.4.0 h6268bbc_5 conda-forge
libunistring 0.9.10 h9ed2024_0
libuv 1.48.0 h67532ce_0 conda-forge
libvpx 1.13.1 hcec6c5f_0
libwebp 1.2.4 hf6ce154_1
libwebp-base 1.2.4 h6c40b1e_1
libxml2 2.12.6 hc0ae0f7_1 conda-forge
libzlib 1.2.13 h8a1eda9_5 conda-forge
libzopfli 1.0.3 hb1e8313_0
llvm-openmp 14.0.6 h0dcd299_0
llvmlite 0.42.0 pypi_0 pypi
locket 1.0.0 py39hecd8cb5_0
loguru 0.5.3 py39hecd8cb5_4
lz4 4.3.2 py39h6c40b1e_0
lz4-c 1.9.4 hcec6c5f_0
markupsafe 2.1.3 py39h6c40b1e_0
matplotlib 3.8.0 py39hecd8cb5_0
matplotlib-base 3.8.0 py39hb47e01b_0
mkl 2023.1.0 h8e150cf_43560
mkl-service 2.4.0 py39h6c40b1e_1
mkl_fft 1.3.8 py39h6c40b1e_0
mkl_random 1.2.4 py39ha357a0b_0
mpmath 1.3.0 pypi_0 pypi
msgpack-python 1.0.3 py39haf03e11_0
multidict 6.0.4 py39h6c40b1e_0
munkres 1.1.4 py_0
napari-lazy-openslide 0.3.0 pypi_0 pypi
napari-plugin-engine 0.2.0 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
ncurses 6.4 hcec6c5f_0
nettle 3.9.1 h8e11ae5_0 conda-forge
networkx 3.1 py39hecd8cb5_0
nodejs 20.9.0 hfc0f20e_1 conda-forge
numba 0.59.1 pypi_0 pypi
numcodecs 0.12.1 py39h2d76c9a_0
numexpr 2.8.7 py39h827a554_0
numpy 1.26.4 py39h827a554_0
numpy-base 1.26.4 py39ha186be2_0
nvidia-ml-py 12.535.133 py39hecd8cb5_0
ome-types 0.5.1.post1 pypi_0 pypi
opencensus 0.11.3 py39hecd8cb5_0
opencensus-context 0.1.3 py39hecd8cb5_0
opencv 4.5.5 py39h6e9494a_12 conda-forge
opencv-python-headless 4.9.0.80 pypi_0 pypi
openh264 2.3.1 hf0c8a7f_2 conda-forge
openjdk 22.0.1 hbeb2e11_0 conda-forge
openjpeg 2.5.0 h5d0d7b0_1 conda-forge
openslide 3.4.1 ha6c4cbf_5 conda-forge
openslide-python 1.3.1 pypi_0 pypi
openssl 3.3.0 hfb2fe0b_3 conda-forge
orc 1.7.4 h995b336_1
p11-kit 0.24.1 h65f8906_0 conda-forge
packaging 23.2 py39hecd8cb5_0
palom 2024.4.1 pypi_0 pypi
pandas 2.2.1 py39hcec6c5f_0
partd 1.4.1 py39hecd8cb5_0
pcre2 10.42 h9b97e30_0
pillow 9.4.0 py39hcec6c5f_0
pint 0.23 pypi_0 pypi
pip 23.3.1 py39hecd8cb5_0
pixman 0.40.0 h9ed2024_1
platformdirs 2.5.2 py39hecd8cb5_0
prometheus_client 0.13.1 pyhd3eb1b0_0
protobuf 3.20.3 py39hcec6c5f_0
psutil 5.9.0 py39hca72f7f_0
py-opencv 4.5.5 py39h71a6800_12 conda-forge
py-spy 0.3.14 h7242b5c_0
pyarrow 14.0.2 py39h323519f_0
pyasn1 0.4.8 pyhd3eb1b0_0
pyasn1-modules 0.2.8 py_0
pycparser 2.21 pyhd3eb1b0_0
pydantic 1.10.12 py39h6c40b1e_1
pydantic-compat 0.1.2 pypi_0 pypi
pyopenssl 24.0.0 py39hecd8cb5_0
pyparsing 3.0.9 py39hecd8cb5_0
pysocks 1.7.1 py39hecd8cb5_0
python 3.9.19 h5ee71fb_0
python-dateutil 2.8.2 pyhd3eb1b0_0
python-lmdb 1.4.1 py39hcec6c5f_0
python-tzdata 2023.3 pyhd3eb1b0_0
python_abi 3.9 2_cp39 conda-forge
pytz 2023.3.post1 py39hecd8cb5_0
pywavelets 1.6.0 pypi_0 pypi
pyyaml 6.0.1 py39h6c40b1e_0
ray-core 2.9.0 py39h51e73cb_1 conda-forge
ray-default 2.9.0 py39h98b42ae_1 conda-forge
re2 2022.04.01 he9d5cce_0
readline 8.2 hca72f7f_0
referencing 0.30.2 py39hecd8cb5_0
requests 2.31.0 py39hecd8cb5_1
roifile 2024.3.20 pypi_0 pypi
rpds-py 0.10.6 py39hf2ad997_0
rsa 4.7.2 pyhd3eb1b0_1
scikit-image 0.19.3 pypi_0 pypi
scikit-learn 1.5.0 pypi_0 pypi
scipy 1.12.0 py39hdb2ea58_0
setproctitle 1.2.2 py39h9ed2024_1004
setuptools 68.2.2 py39hecd8cb5_0
six 1.16.0 pyhd3eb1b0_1
smart_open 5.2.1 py39hecd8cb5_0
snappy 1.1.10 hcec6c5f_1
sortedcontainers 2.4.0 pyhd3eb1b0_0
sqlite 3.41.2 h6c40b1e_0
svt-av1 1.4.1 hf0c8a7f_0 conda-forge
sympy 1.12 pypi_0 pypi
tbb 2021.8.0 ha357a0b_0
tblib 1.7.0 pyhd3eb1b0_0
threadpoolctl 3.5.0 pypi_0 pypi
tifffile 2022.10.10 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h5d9f67b_0
toolz 0.12.0 py39hecd8cb5_0
torch 2.2.2 pypi_0 pypi
tornado 6.3.3 py39h6c40b1e_0
tqdm 4.66.4 pypi_0 pypi
typing-extensions 4.9.0 py39hecd8cb5_1
typing_extensions 4.9.0 py39hecd8cb5_1
tzdata 2024a h04d1e81_0
urllib3 1.26.18 py39hecd8cb5_0
utf8proc 2.6.1 h6c40b1e_1
virtualenv 20.17.1 py39hecd8cb5_0
wcwidth 0.2.5 pyhd3eb1b0_0
wheel 0.41.2 py39hecd8cb5_0
x264 1!164.3095 h775f41a_2 conda-forge
x265 3.5 hbb4e6a2_3 conda-forge
xsdata 24.3.1 pypi_0 pypi
xyzservices 2022.9.0 py39hecd8cb5_1
xz 5.4.6 h6c40b1e_0
yamale 4.0.4 pypi_0 pypi
yaml 0.2.5 haf1e3a3_0
yarl 1.9.3 py39h6c40b1e_0
zarr 2.13.3 py39hecd8cb5_0
zfp 1.0.0 hcec6c5f_0
zict 3.0.0 py39hecd8cb5_0
zipp 3.17.0 py39hecd8cb5_0
zlib 1.2.13 h8a1eda9_5 conda-forge
zlib-ng 2.0.7 h6c40b1e_0
zstd 1.5.5 hc035e20_0
Current outputs
❯ tree
.
├── dearray
│ └── 5.ome.tif
├── markers.csv
├── median_subtracted
├── quantification
└── segmentation
└── mesmer-5
├── cytosol.tif
└── nucleus.tif
Command used:
python main.py /Users/jnimoca/Jose_BI/P12E22_Rafaels_Cellpose/HN46_Core05 5
Traceback:
Job begins: /Users/jnimoca/Jose_BI/P12E22_Rafaels_Cellpose/HN46_Core05
Importing parameters
Intel MKL WARNING: Support of Intel(R) Streaming SIMD Extensions 4.2 (Intel(R) SSE4.2) enabled only processors has been deprecated. Intel oneAPI Math Kernel Library 2025.0 will require Intel(R) Advanced Vector Extensions (Intel(R) AVX) instructions.
Intel MKL WARNING: Support of Intel(R) Streaming SIMD Extensions 4.2 (Intel(R) SSE4.2) enabled only processors has been deprecated. Intel oneAPI Math Kernel Library 2025.0 will require Intel(R) Advanced Vector Extensions (Intel(R) AVX) instructions.
Images: 1
Fatal Python error: config_get_locale_encoding: failed to get the locale encoding: nl_langinfo(CODESET) failed
Python runtime state: preinitialized
/opt/homebrew/Caskroom/mambaforge/base/envs/RCellpose/lib/python3.9/site-packages/threadpoolctl.py:1214: RuntimeWarning:
Found Intel OpenMP ('libiomp') and LLVM OpenMP ('libomp') loaded at
the same time. Both libraries are known to be incompatible and this
can cause random crashes or deadlocks on Linux when loaded in the
same Python program.
Using threadpoolctl may cause crashes or deadlocks. For more
information and possible workarounds, please see
https://github.com/joblib/threadpoolctl/blob/master/multiple_openmp.md
warnings.warn(msg, RuntimeWarning)
Subtracting median
5.ome.tif
2024-05-24 14:49:38,987 [INFO] WRITING LOG OUTPUT TO /Users/jnimoca/.cellpose/run.log
2024-05-24 14:49:38,993 [INFO]
cellpose version: 3.0.8
platform: darwin
python version: 3.9.19
torch version: 2.2.2
2024-05-24 14:49:39,000 [INFO] >>>> using CPU
2024-05-24 14:49:39,004 [INFO] >> cyto3 << model set to be used
2024-05-24 14:49:39,244 [INFO] >>>> loading model /Users/jnimoca/.cellpose/models/cyto3
[1] 74812 segmentation fault python main.py /Users/jnimoca/Jose_BI/P12E22_Rafaels_Cellpose/HN46_Core05 5