Imaging samples larger than the field of view: the SLS experience

Ioannis Vogiatzis Oikonomidis,Marco Stampanoni,Goran Lovric,Tiziana P Cremona,Filippo Arcadu,Johannes C Schittny,Alessandra Patera

doi:10.1088/1742-6596/849/1/012004

Abstract

Volumetric datasets with micrometer spatial and sub-second temporal resolutions are nowadays routinely acquired using synchrotron X-ray tomographic microscopy (SRXTM). Although SRXTM technology allows the examination of multiple samples with short scan times, many specimens are larger than the field-of-view (FOV) provided by the detector. The extension of the FOV in the direction perpendicular to the rotation axis remains non-trivial. We present a method that can efficiently increase the FOV merging volumetric datasets obtained by region-of-interest tomographies in different 3D positions of the sample with a minimal amount of artefacts and with the ability to handle large amounts of data. The method has been successfully applied for the three-dimensional imaging of a small number of mouse lung acini of intact animals, where pixel sizes down to the micrometer range and short exposure times are required.

Highlights

Synchrotron X-ray tomographic microscopy (SRXTM) is an effective technique that can provide the three-dimensional (3D) structural information of samples in a non-destructive manner and with high throughput
synchrotron X-ray tomographic microscopy (SRXTM) technology allows the examination of multiple samples with short scan times, many specimens are larger than the field-of-view (FOV) provided by the detector
We discuss the case of a mouse lung that resulted in approximately 4500 × 4500 pixels shown in figure 2e

Summary

Introduction

Synchrotron X-ray tomographic microscopy (SRXTM) is an effective technique that can provide the three-dimensional (3D) structural information of samples in a non-destructive manner and with high throughput. The simplest method is to combine single X-ray projection images (radiographs) that cover the whole sample and use the larger composite images to conduct the 3D reconstruction [1]. This leads to long acquisition times and increases computational complexity for the CT reconstruction. Such an approach is very prone to misalignment artefacts in the radiography space, since they are propagated along the entire volume when reconstructing the 3D volume with the standard filtered back projection method [2]. Not having the entire object within the FOV leads to a change in the mean value of the image and low-frequency artefacts [3]

Methods

Results

Conclusion