A preprocessing package tailored to individual needs

Posted by daviskd2 on Friday, January 3, 2025 in News.

Cryo-electron tomography (cryo-ET) is method for determining structure that relies on tilting a microscope sample stage to collect a wide range of sample views. This unique acquisition technique is especially useful for imaging in the context of cells or intact extracellular particles, allowing researchers to study structure in a near-native environment.

Subtomogram averaging (STA), a process similar to single particle analysis in cryo-electron microscopy, is then used to reconstruct a 3D volume of the sample from the tilt-series data. However, prior to performing STA, tilt series data must be preprocessed for accurate downstream analysis. While many individual preprocessing packages exist, they utilize different design philosophies, inputs, outputs, and file formats, making construction of a complete data pipeline difficult. TOMOMAN (TOMOgram MANager), an extensive MATLAB-based package developed by the Wan lab, aims to address this issue.

TOMOMAN acts as a wrapper for external packages, storing metadata and interfacing the various packages used in each step of cryo-ET preprocessing. It is equipped to import microscope data, generate motion-corrected tilt-series, curate and clean tilt-series data, filter exposure, align tilt-series, estimate contrast transfer function (CTF), and reconstruct and denoise tomograms.

In addition to these preprocessing steps, TOMOMAN also includes an archival module which allows TOMOMAN projects to be exported as “minimal projects” to be deposited in cryo-ET repositories. This allows projects to be revived in their current states, without repeating preprocessing steps, and reduces the project to a file size which can be easily shared.

While other preprocessing pipeline packages exist, TOMOMAN is unique in its flexibility and customization. By establishing its own internal metadata format and interface modules, TOMOMAN allows users to develop their own unique workflow without integrating packages. Further, TOMOMAN minimal projects make sharing well annotated metadata simple, which is vital for collaboration and the development of large data approaches. Altogether, TOMOMAN is a wonderful option for experienced and novice users alike to develop the cryo-ET workflow perfect for their needs.

Check out TOMOMAN here and read more about this exciting package in the Journal of Applied Crystallography!

~ Cameron I. Cohen