Ot2Rec

Ot2Rec software allows for the automatic reconstruction of tomograms, 2D images that can be reassembled to reveal 3D structures. 

Cryo-electron microscopes are collecting terabytes of data per day, and processing images at this scale is computationally challenging. There are several tools available for each processing stage, and exchanging data between these tools is not straightforward. Ot2Rec is a framework with which scientists can easily configure custom processing workflows, run them automatically on large datasets, and visualise the results. Streamlined processing of tomography with Ot2Rec enables us to handle the high throughput we are expecting from our microscopes, whilst providing a platform to prototype and deploy novel image processing solutions. 

Ot2Rec enables scientists to reproducibly process their data as all the metadata for each stage of the processing is recorded automatically. A report is also generated which is useful for comparison of the results of different software tools on the same data (see video). Ot2Rec is also developer-friendly as new techniques can be easily prototyped within the Ot2Rec plugin system, so tools can be quickly tested in full reconstruction workflows.  

To learn more about Ot2Rec, please see our publication or our Github page. 

Project Leadership  
Michele Darrow
Mark Basham

Project Members at the Franklin 
Elaine Ho
Neville Yee
Maud Dumoux

Collaborating Institutes
Thermofisher Scientific

Funded by 
Wellcome Trust (Electrifying Life Sciences)