===============
TomoTwin plugin
===============
This plugin provides a wrapper for `TomoTwin <https://github.com/MPI-Dortmund/tomotwin-cryoet>`_ software: Particle picking in Tomograms using triplet networks and metric learning
.. image:: https://img.shields.io/pypi/v/scipion-em-tomotwin.svg
:target: https://pypi.python.org/pypi/scipion-em-tomotwin
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-tomotwin.svg
:target: https://pypi.python.org/pypi/scipion-em-tomotwin
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-tomotwin.svg
:target: https://pypi.python.org/pypi/scipion-em-tomotwin
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-tomotwin?server=https%3A%2F%2Fsonarcloud.io
:target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-tomotwin
:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/dm/scipion-em-tomotwin
:target: https://pypi.python.org/pypi/scipion-em-tomotwin
:alt: Downloads
Installation
-------------
You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
a) Stable version
.. code-block::
scipion installp -p scipion-em-tomotwin
b) Developer's version
* download repository
.. code-block::
git clone -b devel https://github.com/scipion-em/scipion-em-tomotwin.git
* install
.. code-block::
scipion installp -p /path/to/scipion-em-tomotwin --devel
TomoTwin software will be installed automatically with the plugin but you can also use an existing installation by providing *TOMOTWIN_ENV_ACTIVATION* (see below).
**Important:** you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.
Configuration variables
-----------------------
*CONDA_ACTIVATION_CMD*: If undefined, it will rely on conda command being in the
PATH (not recommended), which can lead to execution problems mixing scipion
python with conda ones. One example of this could can be seen below but
depending on your conda version and shell you will need something different:
CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)"
*TOMOTWIN_ENV_ACTIVATION* (default = conda activate tomotwin-0.9.1):
Command to activate the TomoTwin environment. Tomotwin uses cuda-11.8, so you might want to activate specific CUDA libs via e.g. `TOMOTWIN_ENV_ACTIVATION = . /etc/profile.d/lmod.sh && module load cuda/11.8 && conda activate tomotwin-0.9.1`
*TOMOTWIN_MODEL* (default = software/em/tomotwin_model-092023/tomotwin_model_p120_092023_loss.pth):
Path to the pre-trained model.
*NAPARI_ENV_ACTIVATION* (default = conda activate napari-0.4.19):
Command to activate the Napari viewer environment.
Verifying
---------
To check the installation, simply run the following Scipion tests:
* ``scipion tests tomotwin.tests.test_protocols_tomotwin.TestTomoTwinRefBased``
* ``scipion tests tomotwin.tests.test_protocols_tomotwin.TestTomoTwinClusterBased``
Supported versions
------------------
0.8.0, 0.9.0b1, 0.9.1
Protocols
----------
* clustering-based picking (step 1)
* clustering-based picking (step 2)
* create tomo masks
* reference-based picking
References
-----------
1. TomoTwin: Generalized 3D Localization of Macromolecules in Cryo-electron Tomograms with Structural Data Mining. Gavin Rice, Thorsten Wagner, Markus Stabrin, Stefan Raunser. https://www.biorxiv.org/content/10.1101/2022.06.24.497279v1
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"description": "===============\nTomoTwin plugin\n===============\n\nThis plugin provides a wrapper for `TomoTwin <https://github.com/MPI-Dortmund/tomotwin-cryoet>`_ software: Particle picking in Tomograms using triplet networks and metric learning\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-tomotwin.svg\n :target: https://pypi.python.org/pypi/scipion-em-tomotwin\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-tomotwin.svg\n :target: https://pypi.python.org/pypi/scipion-em-tomotwin\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-tomotwin.svg\n :target: https://pypi.python.org/pypi/scipion-em-tomotwin\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-tomotwin?server=https%3A%2F%2Fsonarcloud.io\n :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-tomotwin\n :alt: SonarCloud quality gate\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-tomotwin\n :target: https://pypi.python.org/pypi/scipion-em-tomotwin\n :alt: Downloads\n\nInstallation\n-------------\n\nYou will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:\n\na) Stable version\n\n.. code-block::\n\n scipion installp -p scipion-em-tomotwin\n\nb) Developer's version\n\n * download repository\n\n .. code-block::\n\n git clone -b devel https://github.com/scipion-em/scipion-em-tomotwin.git\n\n * install\n\n .. code-block::\n\n scipion installp -p /path/to/scipion-em-tomotwin --devel\n\nTomoTwin software will be installed automatically with the plugin but you can also use an existing installation by providing *TOMOTWIN_ENV_ACTIVATION* (see below).\n\n**Important:** you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.\n\nConfiguration variables\n-----------------------\n*CONDA_ACTIVATION_CMD*: If undefined, it will rely on conda command being in the\nPATH (not recommended), which can lead to execution problems mixing scipion\npython with conda ones. One example of this could can be seen below but\ndepending on your conda version and shell you will need something different:\nCONDA_ACTIVATION_CMD = eval \"$(/extra/miniconda3/bin/conda shell.bash hook)\"\n\n*TOMOTWIN_ENV_ACTIVATION* (default = conda activate tomotwin-0.9.1):\nCommand to activate the TomoTwin environment. Tomotwin uses cuda-11.8, so you might want to activate specific CUDA libs via e.g. `TOMOTWIN_ENV_ACTIVATION = . /etc/profile.d/lmod.sh && module load cuda/11.8 && conda activate tomotwin-0.9.1`\n\n*TOMOTWIN_MODEL* (default = software/em/tomotwin_model-092023/tomotwin_model_p120_092023_loss.pth):\nPath to the pre-trained model.\n\n*NAPARI_ENV_ACTIVATION* (default = conda activate napari-0.4.19):\nCommand to activate the Napari viewer environment.\n\nVerifying\n---------\nTo check the installation, simply run the following Scipion tests:\n\n* ``scipion tests tomotwin.tests.test_protocols_tomotwin.TestTomoTwinRefBased``\n* ``scipion tests tomotwin.tests.test_protocols_tomotwin.TestTomoTwinClusterBased``\n\nSupported versions\n------------------\n\n0.8.0, 0.9.0b1, 0.9.1\n\nProtocols\n----------\n\n* clustering-based picking (step 1)\n* clustering-based picking (step 2)\n* create tomo masks\n* reference-based picking\n\nReferences\n-----------\n\n1. TomoTwin: Generalized 3D Localization of Macromolecules in Cryo-electron Tomograms with Structural Data Mining. Gavin Rice, Thorsten Wagner, Markus Stabrin, Stefan Raunser. https://www.biorxiv.org/content/10.1101/2022.06.24.497279v1\n\n\n",
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