membrain-seg

Membrain-Seg is a Python project developed by teamtomo for membrane segmentation in 3D for cryo-electron tomography (cryo-ET).
This tool aims to provide researchers with an efficient and reliable method for segmenting membranes in 3D microscopic images.
Membrain-Seg is currently under early development, so we may make breaking changes between releases.
 
Membrain-Segはteamtomoによって開発されたPythonプロジェクトで、低温電子トモグラフィー（cryo-ET）のための3Dでの膜セグメンテーションのためのものです。
このツールは、3D顕微鏡画像の膜をセグメンテーションするための効率的で信頼性の高い方法を研究者に提供することを目的としています。
Membrain-Segは現在開発初期段階にあり、リリースとリリースの間に変更を加える可能性があります。

[root@rockylinux8 ~]# cat /etc/redhat-release
Rocky Linux release 8.10 (Green Obsidian)
 
[root@rockylinux8 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module  550.107.02  Wed Jul 24 23:53:00 UTC 2024
GCC version:  gcc version 8.5.0 20210514 (Red Hat 8.5.0-22) (GCC)
 
[root@rockylinux8 ~]# nvidia-smi -L
GPU 0: NVIDIA GeForce GTX 1070 (UUID: GPU-a49de51b-de1e-52f3-1e3f-ce704e159713)
 
[root@rockylinux8 ~]#

git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2024.10-1

[root@rockylinux8 ~]# source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profile.d/conda.sh
 
[root@rockylinux8 ~]# conda create --name membrain-seg python=3.9 -y
 
[root@rockylinux8 ~]# conda activate membrain-seg
 
(membrain-seg) [root@rockylinux8 ~]#
 
(membrain-seg) [root@rockylinux8 ~]# pip install membrain-seg

(membrain-seg) [root@rockylinux8 ~]# conda list
 :
membrain-seg              0.0.5                    pypi_0    pypi
monai                     1.4.0                    pypi_0    pypi
 :
mrcfile                   1.5.3                    pypi_0    pypi
 :
numpy                     1.26.4                   pypi_0    pypi
nvidia-cublas-cu12        12.4.5.8                 pypi_0    pypi
nvidia-cuda-cupti-cu12    12.4.127                 pypi_0    pypi
nvidia-cuda-nvrtc-cu12    12.4.127                 pypi_0    pypi
nvidia-cuda-runtime-cu12  12.4.127                 pypi_0    pypi
nvidia-cudnn-cu12         9.1.0.70                 pypi_0    pypi
nvidia-cufft-cu12         11.2.1.3                 pypi_0    pypi
nvidia-curand-cu12        10.3.5.147               pypi_0    pypi
nvidia-cusolver-cu12      11.6.1.9                 pypi_0    pypi
nvidia-cusparse-cu12      12.3.1.170               pypi_0    pypi
nvidia-nccl-cu12          2.21.5                   pypi_0    pypi
nvidia-nvjitlink-cu12     12.4.127                 pypi_0    pypi
nvidia-nvtx-cu12          12.4.127                 pypi_0    pypi
 :
python                    3.9.20               he870216_1
 :
torch                     2.5.1                    pypi_0    pypi
 :
(membrain-seg) [root@rockylinux8 ~]#

(membrain-seg) [root@rockylinux8 ~]# which python
/apps/pyenv/versions/anaconda3-2024.10-1/envs/membrain-seg/bin/python
(membrain-seg) [root@rockylinux8 ~]# python
Python 3.9.20 (main, Oct  3 2024, 07:27:41)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torch
>>> print(torch.cuda.is_available())
True
>>> print(torch.cuda.get_device_name())
NVIDIA GeForce GTX 1070
>>> quit();
(membrain-seg) [root@rockylinux8 ~]#

(membrain-seg) [root@rockylinux8 ~]# which membrain
/apps/pyenv/versions/anaconda3-2024.10-1/envs/membrain-seg/bin/membrain
 
(membrain-seg) [root@rockylinux8 ~]# membrain
 
 Usage: membrain [OPTIONS] COMMAND [ARGS]...
 
 MemBrain-seg's training / prediction module.
 You can choose between the different options listed below.
 To see the help for a specific command, run:
 
 membrain <command> --help
 
 -------
 
 Example:
 -------
 membrain segment --tomogram-path <path-to-your-tomo>
 --ckpt-path <path-to-your-model>
 
 -------
 
lq Options qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqk
x --help          Show this message and exit.                                                              x
mqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqj
lq Commands qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqk
x segment               Segment tomograms using a trained model.                                           x
x components            Compute connected components of your segmented tomogram.                           x
x thresholds            Process the provided scoremap using given thresholds.                              x
x skeletonize           Perform skeletonization on labeled tomograms using nonmax-suppression technique.   x
x train                 Initiates the MemBrain training routine.                                           x
x train_advanced        Initiates the MemBrain training routine with more advanced options.                x
x data_structure_help   Display information about the training data directory structure.                   x
mqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqj
 
(membrain-seg) [root@rockylinux8 ~]#

#%Module1.0
set          root /apps/pyenv/versions/anaconda3-2024.10-1/envs/membrain-seg
prepend-path PATH $root/bin