Welcome to TranSPHIRE’s documentation!¶
TranSPHIRE is an automated pre-processing tool designed for on-the-fly processing during data aquisition. It is an open source project published under the GPLv3 license and the code is available on GitHub.
TranSPHIRE coveres the inital steps of the Single Particle Analysis pipeline.
Pre-processing¶
- Motion correction (Outputs can be used to run particle polishing in Relion)
- MotionCor2 - (Not free for commercial use, a license needs to be bought separately)
- Unblur
Processing¶
Feedback loop¶
Additionally, TranSPHIRE implements a new Feedback loop that automatically re-trains and therefore adapts the model used for particle picking to the data set at hand.
- Particle picking
- Particle extraction
- Wait for a number of extracted particles to accumulate
- 2D classification
- 2D class selection
- Class member extraction
- Re-training of the picking model
1.with the re-trained model
Hardware recommendations¶
Hardware recommendations can be found at the Hardware recommendations page.
Installation¶
The installation instructions can be found at the Installation page.
Contribute¶
If you want to contribute to the TranSPHIRE project, please checkout the How to contribute page.
License¶
TranSPHIRE is an open source project published under the GPLv3 license.
Code availability¶
The source code is available on GitHub.
Contents:
- Welcome to TranSPHIRE’s documentation!
- Hardware recommendations
- Changelog
- Installation
- Tutorial
- FAQ
- Frames and jpg/meta files are stored in different locations, is that a problem?
- How can I handle multiple gain references in one session?
- What is the output folder structure of TranSPHIRE?
- How to create a template for faster setup?
- What kind of computer should I use?
- How do I measure my particle radius in pixels?
- What box size should I use?
- How can I see how many particles have been extracted?
- How do I cite TranSPHIRE?
- How to contribute
- transphire package (Developer area)
- Subpackages
- Submodules
- transphire.buttoncontainer module
- transphire.emaildialog module
- transphire.framecontainer module
- transphire.framewidget module
- transphire.inputbox module
- transphire.loadcontent module
- transphire.loadcontentcontainer module
- transphire.loadwindow module
- transphire.logviewer module
- transphire.logviewerdialog module
- transphire.mainwindow module
- transphire.messagebox module
- transphire.mountcalculator module
- transphire.mountcontainer module
- transphire.mountwidget module
- transphire.mountworker module
- transphire.notificationcontainer module
- transphire.notificationwidget module
- transphire.passworddialog module
- transphire.plotcontainer module
- transphire.plotwidget module
- transphire.plotworker module
- transphire.processthread module
- transphire.processworker module
- transphire.separator module
- transphire.settingscontainer module
- transphire.settingswidget module
- transphire.statuscontainer module
- transphire.statuswidget module
- transphire.tabdocker module
- transphire.templatedialog module
- transphire.transphire_class2d module
- transphire.transphire_content module
- transphire.transphire_ctf module
- transphire.transphire_extract module
- transphire.transphire_import module
- transphire.transphire_motion module
- transphire.transphire_picking module
- transphire.transphire_plot module
- transphire.transphire_select2d module
- transphire.transphire_software module
- transphire.transphire_train2d module
- transphire.transphire_utils module
- Module contents
Citation¶
Main paper: Stabrin, M., Schoenfeld, F., Wagner, T. et al. TranSPHIRE: automated and feedback-optimized on-the-fly processing for cryo-EM. Nat Commun 11, 5716 (2020). https://doi.org/10.1038/s41467-020-19513-2
Please also properly cite the individual tools that you used during the TranSPHIRE run.