Ot2Rec Report

Automatic report generation for processing of cryo-electron tomography datasets

Ot2Rec report is a tool to automatically generate reports of tomography reconstructions run in Ot2Rec.

The reports currently cover the following Ot2Rec plugins:

• Motioncor2
• IMOD alignment
• IMOD reconstruction
• AreTomo alignment
• AreTomo reconstruction
• Savu reconstruction

The following Ot2Rec plugins are also covered, but may be stubs or less stable:

• CTFSim
• CTFFind4
• Richardson-Lucy deconvolution with RedlionFish.

If you have any ideas on what you'd like included in the reports, file an issue and we will do our best to add it. Or if you'd like to get involved, feel free to make a pull request.

Installation

We highly recommend using a virtual environment, e.g., conda

conda create -n ot2rec_report pip python=3.10
conda activate ot2rec_report

To install from PyPI:

pip install ot2rec-report

To install from source:

git clone https://github.com/rosalindfranklininstitute/ot2rec_report.git
conda create -n o2r_report
conda activate o2r_report
pip install -e .

If you encounter any issues with pydot, with your conda environment activated:

conda install -c conda-forge graphviz

Usage

In your terminal, navigate to the folder where your Ot2Rec processing has been done (hint: this is where the o2r_plugin.log files live.

Once you're there:

o2r.report.run

A GUI will pop up to capture your input:

• Project name is the project name of your experiment, same as you'd have used for Ot2Rec. This is normally the first part of the filename, e.g. TS would be the project name for TS_001_0.0.mrc.
• Choice of sections to include in the report. Hold down Ctrl to select more than one.
• Export to html: If you'd like this Jupyter notebook without the code as a html report. Your report.html will be created in the same directory. You can print this as a pdf if you'd like to.
• Export to slides: This creates a report.slides.html file which you can view and present in your browser.

By default, a Jupyter notebook report.ipynb is produced which contains the report.

Contributing

Contributions are very welcome, it does not have to be through code! If you have any suggestions, you can raise an issue. Pull requests are also welcome, though you may want to raise an issue first to make sure we're not duplicating effort.

Citing

If you have found Ot2Rec useful, please cite us:

Ot2Rec: A Semi-Automatic, Extensible, Multi-Software Tomographic Reconstruction Workflow Neville B.-y. Yee, Elaine M. L. Ho, Win Tun, Jake L. R. Smith, Maud Dumoux, Michael Grange, Michele C. Darrow, Mark Basham bioRxiv 2022.12.15.520632; doi: https://doi.org/10.1101/2022.12.15.520632

Funding

This project was funded as part of the Electrifying Life Sciences project at the Rosalind Franklin Institute.