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本家様 https://github.com/rsanchezgarc/micrograph_cleaner_em
Cryo-EM micrograph segmentation through deep learning
各自のホームディレクトリに各種pythonアプリの実行環境を用意するのではなく、rootで一元管理させるために「pyenv-conda」を使ってます.
pyenvでOS提供のpython環境から離れ、そのpyenv上にconda環境を独自に敷いてます
ここでは「/apps/pyenv」を起点としています
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-26.1.0-0
source /apps/pyenv/versions/miniforge3-26.1.0-0/etc/profile.d/conda.sh
conda update -n base -c conda-forge conda既にpyenv/conda 環境があるなら
source /apps/pyenv/versions/<conda>/etc/profile.d/conda.shとして「pyenv-conda」環境を整備します
っで、
conda create -n env_micrograph_cleaner_em python=3.10
conda activate env_micrograph_cleaner_em
pip install git+https://github.com/rsanchezgarc/micrograph_cleaner_em.git
中身を確認
conda list
# packages in environment at /apps/pyenv/versions/miniforge3-26.1.0-0/envs/env_micrograph_cleaner_em:
#
# Name Version Build Channel
_openmp_mutex 4.5 20_gnu conda-forge
absl-py 2.4.0 pypi_0 pypi
astunparse 1.6.3 pypi_0 pypi
bzip2 1.0.8 hda65f42_9 conda-forge
ca-certificates 2026.2.25 hbd8a1cb_0 conda-forge
certifi 2026.2.25 pypi_0 pypi
charset-normalizer 3.4.6 pypi_0 pypi
click 8.3.1 pypi_0 pypi
contourpy 1.3.2 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
exceptiongroup 1.3.1 pypi_0 pypi
flatbuffers 25.12.19 pypi_0 pypi
fonttools 4.62.1 pypi_0 pypi
gast 0.7.0 pypi_0 pypi
google-pasta 0.2.0 pypi_0 pypi
grpcio 1.78.0 pypi_0 pypi
h5py 3.16.0 pypi_0 pypi
icu 78.3 h33c6efd_0 conda-forge
idna 3.11 pypi_0 pypi
imageio 2.37.3 pypi_0 pypi
iniconfig 2.3.0 pypi_0 pypi
joblib 1.5.3 pypi_0 pypi
keras 3.12.1 pypi_0 pypi
kiwisolver 1.5.0 pypi_0 pypi
lazy-loader 0.5 pypi_0 pypi
ld_impl_linux-64 2.45.1 default_hbd61a6d_101 conda-forge
libclang 18.1.1 pypi_0 pypi
libexpat 2.7.4 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libgcc 15.2.0 he0feb66_18 conda-forge
libgcc-ng 15.2.0 h69a702a_18 conda-forge
libgomp 15.2.0 he0feb66_18 conda-forge
liblzma 5.8.2 hb03c661_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libsqlite 3.52.0 hf4e2dac_0 conda-forge
libstdcxx 15.2.0 h934c35e_18 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
markdown 3.10.2 pypi_0 pypi
markdown-it-py 4.0.0 pypi_0 pypi
markupsafe 3.0.3 pypi_0 pypi
matplotlib 3.10.8 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
micrograph-cleaner-em 1.0.2 pypi_0 pypi
ml-dtypes 0.5.4 pypi_0 pypi
mrcfile 1.5.4 pypi_0 pypi
namex 0.1.0 pypi_0 pypi
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.4.2 pypi_0 pypi
numpy 2.2.6 pypi_0 pypi
nvidia-cublas-cu12 12.9.1.4 pypi_0 pypi
nvidia-cuda-cupti-cu12 12.9.79 pypi_0 pypi
nvidia-cuda-nvcc-cu12 12.9.86 pypi_0 pypi
nvidia-cuda-nvrtc-cu12 12.9.86 pypi_0 pypi
nvidia-cuda-runtime-cu12 12.9.79 pypi_0 pypi
nvidia-cudnn-cu12 9.20.0.48 pypi_0 pypi
nvidia-cufft-cu12 11.4.1.4 pypi_0 pypi
nvidia-curand-cu12 10.3.10.19 pypi_0 pypi
nvidia-cusolver-cu12 11.7.5.82 pypi_0 pypi
nvidia-cusparse-cu12 12.5.10.65 pypi_0 pypi
nvidia-nccl-cu12 2.29.7 pypi_0 pypi
nvidia-nvjitlink-cu12 12.9.86 pypi_0 pypi
opencv-python-headless 4.13.0.92 pypi_0 pypi
openssl 3.6.1 h35e630c_1 conda-forge
opt-einsum 3.4.0 pypi_0 pypi
optree 0.19.0 pypi_0 pypi
packaging 26.0 pyhcf101f3_0 conda-forge
pandas 2.3.3 pypi_0 pypi
pillow 12.1.1 pypi_0 pypi
pip 26.0.1 pyh8b19718_0 conda-forge
pluggy 1.6.0 pypi_0 pypi
protobuf 5.29.6 pypi_0 pypi
pygments 2.19.2 pypi_0 pypi
pyparsing 3.3.2 pypi_0 pypi
pytest 9.0.2 pypi_0 pypi
python 3.10.20 h3c07f61_0_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
pytz 2026.1.post1 pypi_0 pypi
readline 8.3 h853b02a_0 conda-forge
requests 2.32.5 pypi_0 pypi
rich 14.3.3 pypi_0 pypi
scikit-image 0.25.2 pypi_0 pypi
scipy 1.15.3 pypi_0 pypi
setuptools 82.0.1 pyh332efcf_0 conda-forge
setuptools-scm 9.2.2 pypi_0 pypi
six 1.17.0 pypi_0 pypi
tensorboard 2.20.0 pypi_0 pypi
tensorboard-data-server 0.7.2 pypi_0 pypi
tensorflow 2.20.0 pypi_0 pypi
termcolor 3.3.0 pypi_0 pypi
tifffile 2025.5.10 pypi_0 pypi
tk 8.6.13 noxft_h366c992_103 conda-forge
tomli 2.4.0 pypi_0 pypi
tqdm 4.67.3 pypi_0 pypi
typing-extensions 4.15.0 pypi_0 pypi
tzdata 2025.3 pypi_0 pypi
urllib3 2.6.3 pypi_0 pypi
werkzeug 3.1.6 pypi_0 pypi
wheel 0.46.3 pyhd8ed1ab_0 conda-forge
wrapt 2.1.2 pypi_0 pypi
zstd 1.5.7 hb78ec9c_6 conda-forge
conda deactivateモデルファイルは
mkdir /apps/MicrographCleaner
cd /apps/MicrographCleaner
wget https://scipion.cnb.csic.es/downloads/scipion/software/em/xmipp_model_deepMicrographCleaner.tgz
tar xf xmipp_model_deepMicrographCleaner.tgz
ls -l /apps/MicrographCleaner/deepMicrographCleaner/
-rw-rw-r-- 1 root root 136M Jun 12 2019 defaultModel.kerasEnvironment-modules
「/apps/modulefiles/MicrographCleaner」
#%Module
set root /apps/pyenv/versions/miniforge3-26.1.0-0/envs/env_micrograph_cleaner_em
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
