RESUMEN

X-ray tomography is widely used for three-dimensional structure determination in many areas of science, from the millimeter to the nanometer scale. The resolution and quality of the 3D reconstruction is limited by the availability of alignment parameters that correct for the mechanical shifts of the sample or sample stage for the images that constitute a scan. In this paper we describe an algorithm for marker-free, fully automated and accurately aligned and reconstructed X-ray tomography data. Our approach solves the tomographic reconstruction jointly with projection data alignment based on a rigid-body deformation model. We demonstrate the robustness of our method on both synthetic phantom and experimental data and show that our method is highly efficient in recovering relatively large alignment errors without prior knowledge of a low resolution approximation of the 3D structure or a reasonable estimate of alignment parameters.

RESUMEN

Molluscs often possess complex calcified elements in addition to the shell, but how these elements function and relate to other tissues is often poorly understood. Dorid nudibranchs typically possess innumerable calcareous spicules arranged in complex networks. To describe how these spicules interact with muscles and connective tissue, we reconstructed tomographic digital models using serial sections and synchrotron micro-computed tomography. In two species with dramatically different spicule network morphologies, musculature was divided into a dorsal layer of crossed fibres, a ventral layer of branching radial fibres, and scattered dorsoventral fibres in between. These two species differed in the size of their dorsal tubercles, which was reflected in the organization of dorsal musculature, and in the amount and organization of connective tissue. In Platydoris sanguinea Bergh, 1905, dense mats of spicules sandwiched a layer of connective tissue with fewer spicules and muscle insertions only onto the ventral spicules. In Cadlina luteomarginata MacFarland, 1966, thick tracts of spicules are surrounded by a sheath of connective tissue. Muscles surround and insert into the dorsal tubercle spicule layer. Thus, both species appear to use the spicule network for muscle antagonism and transfer of motion, but the different arrangement of elements suggests that they use this skeleton in quite different ways.

Les mollusques présentent fréquemment des éléments calcifiés complexes en plus de leur coquille, mais le fonctionnement de ces éléments et leur relation avec d'autres tissus ne sont souvent pas bien compris. Les nudibranches doridiens possèdent typiquement d'innombrables spicules calcaires disposés en réseaux complexes. Pour décrire l'interaction de ces spicules avec les muscles et les tissus conjonctifs, nous avons reconstitué des modèles numériques tomographiques en utilisant des séries de coupes et la microtomodensitométrie par synchrotron. Chez deux espèces dont les réseaux de spicules présentent des morphologies très différentes, la musculature est divisée en une couche dorsale de fibres entrecroisées, une couche ventrale de fibres radiales ramifiées et, entre les deux, des fibres dorsoventrales dispersées. Ces deux espèces diffèrent sur le plan de la taille de leurs tubercules dorsaux, ce qui se reflète dans l'organisation de la musculature dorsale, et de la quantité et de l'organisation du tissu conjonctif. Chez Platydoris sanguinea Bergh, 1905, de denses tapis de spicules bordent de part et d'autre une couche de tissu conjonctif comptant moins de spicules et des insertions de muscles seulement sur les spicules ventraux. Chez Cadlina luteomarginata MacFarland, 1966, d'épais faisceaux de spicules sont entourés d'une gaine de tissu conjonctif. Des muscles entourent la couche de spicules du tubercule dorsal et la pénètrent. Ainsi, les deux espèces semblent utiliser le réseau de spicules pour l'antagonisme de muscles et le transfert de mouvement, mais les différentes configurations d'éléments indiqueraient qu'elles utilisent ce squelette de manières très différentes.

RESUMEN

Three-dimensional imaging of human stem cells using transmission soft X-ray tomography (SXT) is presented for the first time. Major organelle types--nuclei, nucleoli, mitochondria, lysosomes and vesicles--were discriminated at approximately 50 nm spatial resolution without the use of contrast agents, on the basis of measured linear X-ray absorption coefficients and comparison of the size and shape of structures to transmission electron microscopy (TEM) images. In addition, SXT was used to visualize the distribution of a cell surface protein using gold-labelled antibody staining. We present the strengths of SXT, which include excellent spatial resolution (intermediate between that of TEM and light microscopy), the lack of the requirement for fixative or contrast agent that might perturb cellular morphology or produce imaging artefacts, and the ability to produce three-dimensional images of cells without microtome sectioning. Possible applications to studying the differentiation of human stem cells are discussed.

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RESUMEN

We employ a coded aperture pattern in front of a pixilated charge couple device detector to image fluorescent x-rays (6-25 KeV) from samples irradiated with synchrotron radiation. Coded apertures encode the angular direction of x-rays, and given a known source plane, allow for a large numerical aperture x-ray imaging system. The algorithm to develop and fabricate the free standing No-Two-Holes-Touching aperture pattern was developed. The algorithms to reconstruct the x-ray image from the recorded encoded pattern were developed by means of a ray tracing technique and confirmed by experiments on standard samples.