High Throughput Tomography (HiTT) on EMBL beamline P14 on PETRA III.

Abstract

Here, 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, is presented. A high-photon-flux undulator beamline is used 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 beam-time 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. The successful application of HiTT on various soft tissue samples in both liquid (hydrated and also dehydrated) and paraffin-embedded preparations is demonstrated. Furthermore, the feasibility of HiTT to be used as a targeting tool for volume electron microscopy, as well as using HiTT to study plant morphology, is demonstrated. It is also shown 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.

Plant phenotyping relevance

高速X線トモグラフィー、ロボット試料交換、自動再構成を統合した高スループット画像化プラットフォームが主題であり、植物形態の画像計測への適用も明示されている。

Code and data availability

This paper describes the HiTT high-throughput X-ray tomography beamline setup at EMBL P14, applied mainly to soft-tissue (murine organ) samples, with only a passing mention of plant morphology. No public plant-phenotype datasets, plant images, author analysis code repositories, or trained models are described. All URLs

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