Karyotyping human chromosomes by optical and X-ray ptychography methods

Quantitative phase measurements of human cell nuclei using X-ray ptychography

The human cell nucleus serves as an important organelle holding the genetic blueprint for life. In this work, X-ray ptychography was applied to assess the masses of human cell nuclei using its unique phase shift information. Measurements were carried out at the I13-1 beamline at the Diamond Light Source that has extremely large transverse coherence properties. The ptychographic diffractive imaging approach allowed imaging of large structures that gave quantitative measurements of the phase shift in 2D projections. In this paper a modified ptychography algorithm that improves the quality of the reconstruction for weak scattering samples is presented. The application of this approach to calculate the mass of several human nuclei is also demonstrated.

Combining Multicolor FISH with Fluorescence Lifetime Imaging for Chromosomal Identification and Chromosomal Sub Structure Investigation

Understanding the structure of chromatin in chromosomes during normal and diseased state of cells is still one of the key challenges in structural biology. Using DAPI staining alone together with Fluorescence lifetime imaging (FLIM), the environment of chromatin in chromosomes can be explored. Fluorescence lifetime can be used to probe the environment of a fluorophore such as energy transfer, pH and viscosity. Multicolor FISH (M-FISH) is a technique that allows individual chromosome identification, classification as well as assessment of the entire genome. Here we describe a combined approach using DAPI as a DNA environment sensor together with FLIM and M-FISH to understand the nanometer structure of all 46 chromosomes in the nucleus covering the entire human genome at the single cell level. Upon DAPI binding to DNA minor groove followed by fluorescence lifetime measurement and imaging by multiphoton excitation, structural differences in the chromosomes can be studied and observed. This manuscript provides a blow by blow account of the protocol required to perform M-FISH-FLIM of whole chromosomes.

X-ray Ptychography Imaging of Human Chromosomes After Low-dose Irradiation

Studies of the structural and functional role of chromosomes in cytogenetics have spanned more than 10 decades. In this work, we take advantage of the coherent X-rays available at the latest synchrotron sources to extract the individual masses of all 46 chromosomes of metaphase human B and T cells using hard X-ray ptychography. We have produced 'X-ray karyotypes' of both heavy metal-stained and unstained spreads to determine the gain or loss of genetic material upon low-level X-ray irradiation doses due to radiation damage. The experiments were performed at the I-13 beamline, Diamond Light Source, Didcot, UK, using the phase-sensitive X-ray ptychography method.

Joint estimation of object and probes in vectorial ptychography

Vectorial ptychography has been recently introduced to reconstruct the Jones matrix of an anisotropic object by means of series of ptychographic measurements performed using a set of polarized illumination probes in conjugation with various analyzers. So far, the probes were assumed to be completely known (amplitude, wavefront, state of polarization), which is rarely the case in practice. Here we address the issue of the joint estimating of the set of polarized illumination probes together with the Jones matrix of an anisotropic object in vectorial ptychography. We propose an algorithm based on a conjugate gradient strategy. Experimental results are reported, showing an improvement on the object estimate, in addition to a precise reconstruction of the probes.

Angle-resolved light scattering of single human chromosomes: experiments and simulations

Angle-resolved light scattering measurements of human metaphase chromosomes were compared to the results of numerical light scattering simulations with geometrical models based on atomic force microscopy (AFM) measurements of the same chromosomes. The simulations were conducted using the discrete dipole approximation method (DDA), which solves Maxwell's equations for induced dipoles, positioned in a discrete lattice. A remarkable agreement between the light scattering simulations and measurements of all 6 studied chromosomes was found. Additionally, the influence of small changes in the orientation of a complex scatterer geometry on its angle-resolved scattering pattern is shown. A method is presented to approximate such variations in the scatterer's orientation by a linear shift of the angular scattering pattern. This method provides an initial guess on the scatterers orientation, reducing the amount of simulations needed considerably. It was validated on simulations of a cuboid and successfully applied in the evaluation of the chromosome measurements.

Coherent amplitude modulation imaging based on partially saturated diffraction pattern

A single-shot phase retrieval algorithm based on a random aperture and partially saturated diffraction pattern is proposed. The diffraction pattern in the saturated area could be retrieved during the iterative process, which circumvents the problem of limited dynamic range of the detector. Besides, the random aperture is easier to be manufactured and if the accuracy of the random aperture is high enough, the design value could be used directly for iterations. It has the potential to be adapted for different wavelengths without additional transmission measurement of the wave modulator. The validity has been demonstrated by simulations and experiment.

Quantitative imaging of anisotropic material properties with vectorial ptychography

Following the recent establishment of the formalism of vectorial ptychography [Opt. Lett.40, 5144 (2015)OPLEDP0146-959210.1364/OL.40.005144], first measurements, to the best of our knowledge, are reported in the optical range, demonstrating the capability of the proposed method to map the four parameters of the Jones matrix of an anisotropic specimen, and therefore to quantify a wide range of optical material properties, including power transmittance, optical path difference, diattenuation, retardance, and fast-axis orientation.

Procedures for cryogenic X-ray ptychographic imaging of biological samples

Biological sample-preparation procedures have been developed for imaging human chromosomes under cryogenic conditions. A new experimental setup, developed for imaging frozen samples using beamline I13 at Diamond Light Source, is described. This manuscript describes the equipment and experimental procedures as well as the authors' first ptychographic reconstructions using X-rays.

Nuclear incorporation of iron during the eukaryotic cell cycle

Scanning X-ray fluorescence microscopy has been used to probe the distribution of S, P and Fe within cell nuclei. Nuclei, which may have originated at different phases of the cell cycle, are found to show very different levels of Fe present with a strongly inhomogeneous distribution. P and S signals, presumably from DNA and associated nucleosomes, are high and relatively uniform across all the nuclei; these agree with X-ray phase contrast projection microscopy images of the same samples. Possible reasons for the Fe incorporation are discussed.

Tomography of a Cryo-immobilized Yeast Cell Using Ptychographic Coherent X-Ray Diffractive Imaging

The structural investigation of noncrystalline, soft biological matter using x-rays is of rapidly increasing interest. Large-scale x-ray sources, such as synchrotrons and x-ray free electron lasers, are becoming ever brighter and make the study of such weakly scattering materials more feasible. Variants of coherent diffractive imaging (CDI) are particularly attractive, as the absence of an objective lens between sample and detector ensures that no x-ray photons scattered by a sample are lost in a limited-efficiency imaging system. Furthermore, the reconstructed complex image contains quantitative density information, most directly accessible through its phase, which is proportional to the projected electron density of the sample. If applied in three dimensions, CDI can thus recover the sample's electron density distribution. As the extension to three dimensions is accompanied by a considerable dose applied to the sample, cryogenic cooling is necessary to optimize the structural preservation of a unique sample in the beam. This, however, imposes considerable technical challenges on the experimental realization. Here, we show a route toward the solution of these challenges using ptychographic CDI (PCDI), a scanning variant of coherent imaging. We present an experimental demonstration of the combination of three-dimensional structure determination through PCDI with a cryogenically cooled biological sample—a budding yeast cell (Saccharomyces cerevisiae)—using hard (7.9 keV) synchrotron x-rays. This proof-of-principle demonstration in particular illustrates the potential of PCDI for highly sensitive, quantitative three-dimensional density determination of cryogenically cooled, hydrated, and unstained biological matter and paves the way to future studies of unique, nonreproducible biological cells at higher resolution.

Multimodality hard-x-ray imaging of a chromosome with nanoscale spatial resolution

We developed a scanning hard x-ray microscope using a new class of x-ray nano-focusing optic called a multilayer Laue lens and imaged a chromosome with nanoscale spatial resolution. The combination of the hard x-ray’s superior penetration power, high sensitivity to elemental composition, high spatial-resolution and quantitative analysis creates a unique tool with capabilities that other microscopy techniques cannot provide. Using this microscope, we simultaneously obtained absorption-, phase-, and fluorescence-contrast images of Pt-stained human chromosome samples. The high spatial-resolution of the microscope and its multi-modality imaging capabilities enabled us to observe the internal ultra-structures of a thick chromosome without sectioning it.

Ptychography in anisotropic media

This letter describes ptychography in the context of polarized light probing anisotropic specimen (i.e., showing properties of birefringence and/or diattenuation). We established an optimization strategy using a vectorial formalism. We propose a measurement scheme using a set of linearly polarized probes and linear polarization analyzers, which allows the retrieval of the full anisotropy map of the specimen.

Coherent diffraction imaging of non-isolated object with apodized illumination

Coherent diffraction imaging (CDI) is an established lensless imaging method widely used at the x-ray regime applicable to the imaging of non-periodic materials. Conventional CDI can practically image isolated objects only, which hinders the broader application of the method. We present the imaging of non-isolated objects by employing recently proposed "non-scanning" apodized-illumination CDI at an optical wavelength. We realized isolated apodized illumination with a specially designed optical configuration and succeeded in imaging phase objects as well as amplitude objects. The non-scanning nature of the method is important particularly in imaging live cells and tissues, where fast imaging is required for non-isolated objects, and is an advantage over ptychography. We believe that our result of phase contrast imaging at an optical wavelength can be extended to the quantitative phase imaging of cells and tissues. The method also provides the feasibility of the lensless single-shot imaging of extended objects with x-ray free-electron lasers.