X-ray tomographic reconstruction and segmentation pipeline for the long-wavelength macromolecular crystallography beamline at Diamond Light Source

Abstract

In this paper a practical solution for the reconstruction and segmentation of low-contrast X-ray tomographic data of protein crystals from the long-wavelength macromolecular crystallography beamline I23 at Diamond Light Source is provided. The resulting segmented data will provide the path lengths through both diffracting and non-diffracting materials as basis for analytical absorption corrections for X-ray diffraction data taken in the same sample environment ahead of the tomography experiment. X-ray tomography data from protein crystals can be difficult to analyse due to very low or absent contrast between the different materials: the crystal, the sample holder and the surrounding mother liquor. The proposed data processing pipeline consists of two major sequential operations: model-based iterative reconstruction to improve contrast and minimize the influence of noise and artefacts, followed by segmentation. The segmentation aims to partition the reconstructed data into four phases: the crystal, mother liquor, loop and vacuum. In this study three different semi-automated segmentation methods are experimented with by using Gaussian mixture models, geodesic distance thresholding and a novel morphological method, RegionGrow, implemented specifically for the task. The complete reconstruction-segmentation pipeline is integrated into the MPI-based data analysis and reconstruction framework Savu, which is used to reduce computation time through parallelization across a computing cluster and makes the developed methods easily accessible.

Research on the optimization of local lane segmentation in BEV based on dynamic serpentine convolution

“…The main innovation of this paper, as shown in Figure 2, is the architectural improvement that delicately reconstructs the traditional ResNet extraction network. By introducing Ghost convolution [11] , this method first generates a smaller number of convolution outputs (i.e., "ghost" feature maps), and then completes the remaining feature maps through cost-effective linear transformation operations. This strategy effectively reduces the number of direct convolution operations, significantly lowering the computational complexity of the model.…”

Ray-tracing analytical absorption correction for X-ray crystallography based on tomographic reconstructions

“…The invacuum sample environment comprises the cylindrical P12M detector and a multi-axis goniometer to enable collection of complete diffraction data from crystals in low-symmetry space groups even at the longest wavelengths. A tomography camera is integrated into the beamline sample environment, allowing easy transition between the two experimental modes (Kazantsev et al, 2021). The sample preparation for invacuum data collection followed the standard protocol for beamline I23 (Duman et al, 2021).…”

“…The tomography data were processed using the SAVU pipeline (Kazantsev et al, 2022), with a processing routine consisting of standard flat-field correction, followed by ring artefact removal (Vo et al, 2018) and reconstruction. For OmpK36, the reconstruction step was performed by iterative methods via the ToMoBAR module in SAVU (Kazantsev et al, 2021), as its edge-enhancing properties gave improved results. For Cld, where the data showed better contrast, the filter-back projection (TomoPy) module (Gu ¨rsoy et al, 2014) was used instead.…”

Software and algorithms for high-throughput multimodal experiments at advanced synchrotron light sources

“…A recent study 28 that integrates the segmentation steps into the reconstruction pipeline with contrast enhancement and artifact removal is also worth mentioning. This work compared their novel model-based iterative reconstruction (MBIR) approach to multiple solutions including the methods based on thresholding and image growth.…”

“…They called it "Savu 29,30 ". This software had a parallel computing architecture that utilized the so-called Message Passing Interface (MPI) protocol 28 . The processed data of Savu was in hdf5 format and could be visualized with another open source software Dawn 31 .…”