Ecdysis period of Rhodnius prolixus head investigated using phase contrast synchrotron microtomography

Performance evaluation of segmentation methods for assessing the lens of the frog Thoropa miliaris from synchrotron-based phase-contrast micro-CT images

PURPOSE

In the context of synchrotron microtomography using propagation-based phase-contrast imaging (XSPCT), we evaluated the performance of semiautomatic and automatic image segmentation of soft biological structures by means of Dice Similarity Coefficient (DSC) and volume quantification.

METHODS

We took advantage of the phase-contrast effects of XSPCT to provide enhanced object boundaries and improved visualization of the lenses of the frog Thoropa miliaris. Then, we applied semiautomatic segmentation methods 1 and 2 (Interpolation and Watershed, respectively) and method 3, an automatic segmentation algorithm using the U-Net architecture, to the reconstructed images. DSC and volume quantification of the lenses were used to quantify the performance of image segmentation methods.

RESULTS

Comparing the lenses segmented by the three methods, the most pronounced difference in volume quantification was between methods 1 and 3: a reduction of 4.24%. Method 1, 2 and 3 obtained the global average DSC of 97.02%, 95.41% and 89.29%, respectively. Although it obtained the lowest DSC, method 3 performed the segmentation in a matter of seconds, while the semiautomatic methods had the average time to segment the lenses around 1 h and 30 min.

CONCLUSIONS

Our results suggest that the performance of U-Net was impaired due to the irregularities of the ROI edges mainly in its lower and upper regions, but it still showed high accuracy (DSC = 89.29%) with significantly reduced segmentation time compared to the semiautomatic methods. Besides, with the present work we have established a baseline for future assessments of Deep Neural Networks applied to XSPCT volumes.

3-Dimensional X-ray microtomography methodology for characterization of monolithic stationary phases and columns for capillary liquid chromatography - A tutorial

In this tutorial we describe a fast, nondestructive, three-dimensional (3-D) view approach to be used in morphology characterization of capillary monoliths and columns by reconstruction from X-ray microtomography (XMT) obtained by acquiring projection images of the sample from a number of different directions. The method comprises imaging acquisition, imaging reconstruction using specific algorithms and imaging analysis by generation of a 3-D image of the sample from radiographic images. The 3-D images show the morphological data for bulk macropore space and skeleton connectivity of the monoliths and were compared with other images from imaging techniques such as scanning electron microscopy (SEM) and field emission scanning electron microscopy (FESEM) and with chromatographic performance. The 3-D XMT methodology is applicable for organic and inorganic capillary chromatographic monolithic materials and it allows the acquisition of many hundreds (in our case 1001 projections) of longitudinal and cross-sectional images in a single session, resolving morphological details with a 3D-view of the monolithic structure, inclusive inside the column in a sectional structure with volume (three dimensions) when compared to the sectional structure area (with only two dimensions) when using SEM and FESEM techniques.

Hard X-ray index of refraction tomography of a whole rabbit knee joint: A feasibility study

We report results of the computed tomography reconstruction of the index of refraction in a whole rabbit knee joint examined at the photon energy of 51keV. Refraction based images make it possible to delineate the bone, cartilage, and soft tissues without adjusting the contrast window width and level. Density variations, which are related to tissue composition and are not visible in absorption X-ray images, are detected in the obtained refraction based images. We discuss why refraction-based images provide better detectability of low contrast features than absorption images.

BMIT facility at the Canadian Light Source: Advances in X-ray phase-sensitive imaging

The BioMedical Imaging and Therapy (BMIT) facility [1,2] located at the Canadian Light Source, provides synchrotron-specific imaging and radiation therapy capabilities. There are two separate beamlines used for experiments: the bending magnet (05B1-1) and the insertion device (05ID-2) beamline. The bending magnet beamline provides access to monochromatic beam spanning a spectral range of 15-40keV, and the beam is 240mm wide in the POE-2 experimental hutch. Users can also perform experiments with polychromatic (pink) beam. The insertion device beamline was officially opened for general user program in 2015. The source for the ID beamline is a multi-pole, superconducting 4.3T wiggler. The high field gives a critical energy over 20keV. The optics hutches prepare a beam that is 220mm wide in the last experimental hutch SOE-1. The monochromatic spectral range spans 25-150+keV. Several different X-ray detectors are available for both beamlines, with resolutions ranging from 2μm to 200μm. BMIT provides a number of imaging techniques including standard absorption X-ray imaging, K-edge subtraction imaging (KES), in-line phase contrast imaging (also known as propagation based imaging, PBI) and Diffraction Enhanced Imaging/Analyzer Based Imaging (DEI/ABI), all in either projection or CT mode. PBI and DEI/ABI are particularly important tools for BMIT users since these techniques enable visualization of soft tissue and allow for low dose imaging.