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        "author": "Markus Stabrin",
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        "description": "[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2553388.svg)](https://doi.org/10.5281/zenodo.2553388)\n\n\nA tutorial is available in the wiki.\n\n[Wiki](https://github.com/MPI-Dortmund/transphire/wiki)\n\n\n# Transphire\n\nCryo-EM on the fly processing pipeline.\n\nIf you have any questions contact:  \nmarkus.stabrin@mpi-dortmund.mpg.de\n\n## External programs\n\nTo enjoy the full functionaly of TranSPHIRE, install the following programs:\n\nIMOD 4.9: http://bio3d.colorado.edu/imod  \nMotionCor2 1.0.0/1.0.5/1.1.0: http://msg.ucsf.edu/em/software/motioncor2.html  \nSumMovie 1.0.2: http://grigoriefflab.janelia.org/unblur  \nCTER 1.0: http://sphire.mpg.de  \nCTFFIND 4.1.8/4.1.10: http://grigoriefflab.janelia.org/ctf  \nGctf 1.06,1.18: https://www.mrc-lmb.cam.ac.uk/kzhang  \ncrYOLO 1.0.4/1.0.5/1.1.0: http://sphire.mpg.de  \n\n## Installation\n\nTranSPHIRE needs an environment that includes Python version 3.6, QT version 5 and PyQt version 5.\n\n### Installation using Anaconda\n\nhttps://www.anaconda.com/download/#linux\n\nCreate a new virtual environment\n\n> conda create -n transphire python=3.6 pyqt=5\n\nActivate the environment\n\n> source activate transphire\n\nor\n\n> conda activate transphire\n\nDepending on your installation of anaconda.\n\nInstall transphire\n\n> pip install transphire\n\n\n### Installation inside your own environment that matches the requirements\n\nInstall transphire\n\n> pip install transphire\n\n\n## Run TranSPHIRE\n\nMake sure, that you have your transphire environment active.\nIf you start TranSPHIRE for the first time:\n\n> transphire --edit\\_settings\n\nIn case the appearing window is too large for your screen, adjust the font size (default 20).  \nFor example:\n\n> transphire --edit\\_settings --font 8\n\nFirst got to the **TranSPHIRE settings** tab and after that the **Font** tab.\nAdjust the *Font* value.\nIf necessary, the other options can be adjusted at a later point, after the GUI is opened.\n\nOpen the other tabs and adjust the settings according to your system.\n\nClose the dialog and the GUI will open.\n\nIn the future, you only need to run:\n\n> transphire\n\nIf you want to run TranSPHIRE, fill in the tabs from left to right (General to CTF) and press the Start button.\n\nA more detailed tutorial will be available soon.\n\n## FAQ\n\nPlease refere to this link: [https://github.com/MPI-Dortmund/transphire/wiki/FAQ](https://github.com/MPI-Dortmund/transphire/wiki/FAQ)\n\n\n",
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