High Throughput Tomography (HiTT) on EMBL Beamline P14 on PETRA III

Abstract

Here we present High-Throughput Tomography (HiTT), a fast and versatile phase-contrast imaging platform for life-science samples on the EMBL beamline P14 at DESY in Hamburg, Germany. We use a high photon flux undulator beamline to perform tomographic phase contrast acquisition in about two minutes which is linked to an automated data processing pipeline that delivers a 3D reconstructed data set less than a minute and a half after the completion of the X-ray scan. Combining this workflow with a sophisticated robotic sample changer enables the streamlined collection and reconstruction of X-ray imaging data from potentially hundreds of samples during a beamtime shift. HiTT permits optimal data collection for many different samples and makes possible the imaging of large sample cohorts thus allowing population studies to be attempted. We demonstrate the successful application of HiTT on various soft tissue samples in both liquid (hydrated and also dehydrated) and paraffin embedded preparations. Furthermore, we demonstrate the feasibility of HiTT to be used as a targeting tool for volume electron microscopy (vEM), as well as using HiTT to study plant morphology. We also show how the high throughput nature of the work has allowed large numbers of “identical” samples to be imaged to enable statistically relevant sample volumes to be studied. Synopsis We present HiTT – high throughput tomography – a propagation based phase contrast X-ray imaging technique which can visualise 1 mm 3 biological samples of various types at high resolution. The 3D reconstructions of the imaged volumes are calculated automatically once data collection is complete. The entire process from pressing start on data collection to viewing the final data takes less than 3 minutes. This speed in combination with the use of the automated sample changer to exchange the samples truly enables high throughput X-ray imaging for the first time.

Plant phenotyping relevance

高速・自動3D X線トモグラフィー基盤の開発と、植物形態の画像化への適用が中心であり、植物表現型計測手法として適格です。

Code and data availability

The paper describes the HiTT X-ray tomography pipeline at beamline P14, including an Arabidopsis thaliana seedling stem imaging example, but no public phenotype/trait datasets, plant images, author analysis code, or trained models are deposited or linked. All software (ARAPAHO, TOMO CTF, viewers) is described as in-;no

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