Lensless Imaging of Whole Biologic Cells Developed Utilizing Soft X-Rays

Scientists are utilizing X-ray diffraction microscopy to generate images of whole yeast cells, achieving the highest resolution--11-13 nanometers-- the first ever obtained with this method for biologic specimens. Their success indicates that full three-dimensional (3D) tomography of whole cells at an equivalent resolution should soon be possible.

The team of scientists is working on their project at beamline 9.0.1 of the Advanced Light Source (ALS) at the U.S. Department of Energy's (DOE) Lawrence Berkeley National Laboratory (Berkeley, CA, USA). "We have demonstrated that lensless imaging techniques can achieve very high resolution while overcoming the limitations of X-ray optics--limitations that include requiring 20 to 50 times the radiation exposure to get a magnified image of the sample,” said Dr. Chris Jacobsen, formerly of Stony Brook University (Stony Brook, NY, USA), now of Argonne National Laboratory (Argonne, IL, USA) and Northwestern University (Evanston, IL, USA), who designed the lensless-imaging research program at beamline 9.0.1. "While at present it takes us a long time to image a single specimen--and full 3D imaging of hydrated cells will take even more work--this is a big step in the right direction.”

Three-dimensional imaging of whole cells under conditions close to those in nature, specifically a hydrated (watery) environment, was already achieved at the U.S. National Center for X-Ray Tomography at ALS beamline 2.1, under the direction of Dr. Carolyn Larabell of Berkeley Lab's physical biosciences division, where large numbers of cells can be processed in a short time at resolutions of 40-60 nm. The ability to increase resolution to the 10-nm range would considerably advance research in both biology and materials sciences. "Ten-nanometer resolution is easy to achieve with an electron microscope,” said Janos Kirz of the ALS, codesigner with Dr. Jacobsen of the lensless-imaging program. "The problem is that electron microscopy is limited to very thin samples, a few hundred nanometers or less--so you can't use it to look through a whole cell.”

Whereas X-rays have the ability to look deep into thick specimens, or right through them, imaging with a lens has its own difficulties. Even the best X-ray microscope lenses (concentric circles of metal known as Fresnel zone plates), cannot focus X-rays with high efficiency, so to get an image means using such intense radiation that it more quickly damages biological specimens. At the same time, the geometry of the highest-resolution zone plates makes for an extremely narrow depth of focus.

To get around these hurdles, a research team led by Dr. Jacobsen's students Johanna Nelson, Xiaojing Huang, and Jan Steinbrener--also of Stony Brook--utilized a lensless X-ray diffraction microscopy. To produce a high-resolution diffraction pattern from noncrystalline structures such as the membranes and organelles of a cell, the light has to be coherent, meaning, laser-like, having all the same frequency and phase. Beamline 9.0.1 was built to supply this kind of light.

As the scientists proceed through the cell, the coherent X-rays are scattered and differentially absorbed by the cell's internal structures. There is no lens either in front or behind the sample as the light passes through the cell and reaches the detector, so there is nothing to limit resolution or efficiency. However, the result looks nothing like an image. Instead, it is a pattern of dark and light speckles, the traces of the scattered X-rays. A computer, which acts as the "lens” in lensless imaging, uses these patterns to create an image. Dr. Stefano Marchesini, ALS beamline scientist for beamline 9.0.1, remarked, "The challenge of the lensless technique is that essentially the preparation and quality of the sample have to be perfect--and, ideally, completely isolated in the beam.”

The principle cannot be reached in reality, since the sample has to be supported. Furthermore, to image hydrated cells, the specimen has to be frozen, which introduces misleading data from the presence of ice. In November 2009, Dr. Jacobsen's team utilized the beamline 9.0.1 to image a frozen, fully hydrated yeast cell at a resolution of 25 nm--a resolution limited by ice. The current experiment's 10-13-nm resolution required using unhydrated, freeze-dried cells at room temperature.

Until recently, to produce an image, researchers had to know the precise shape of the sample's support and have a pretty good idea of the shape of the sample itself, before the computer could even start solving the diffraction patterns. A new algorithm written by Dr. Marchesini called "shrinkwrap” converges on the diffraction data through subsequent iterations, and finally differentiates and subtracts the support from the sample image.

Nevertheless, tens of thousands of iterations with both algorithms and manual modifications of the cell boundaries were needed to produce the current study's final image of a pair of yeast cells. Details emerged when the computer was instructed to represent differences in absorption with differences in image brightness, and differences in the phase of the light, altered by scattering, with differences in image color.

The relationship of a cell's internal structures can only be determined accurately by full 3D tomography. In a 2D image, these features are stacked one on top of another, and separating the planes is partly a matter of conjecture. Short of true 3D, it is possible to gain some sense of how the internal structures are arranged by focusing on different depths in the structure, then comparing these images with others of the same object made with different techniques.

In the current project, additional images of the same freeze-dried cells were made first by scanning transmission X-ray microscopy (using a lens), which was of lower resolution but helped validate features at different planes, and then by scanning electron microscopy, which was of higher resolution but could only show surface details such as sugar molecules in the cell walls, which the researchers had labeled with gold particles to serve as position markers.

"True 3D of whole, hydrated, frozen cells at this very high resolution is our next step,” stated Dr. Jacobsen. "One ingredient is to rotate the frozen sample in the beam to get more depth information. Another is to scan the beam across the sample.”

Dr. Jacobsen's team is making progress using both techniques at beamline 9.0.1, but the present set-up, extraordinary as it is, requires what he calls "heroic” experimental efforts. To harvest the full benefits of lensless imaging with X-ray diffraction microscopy, he noted, will require a source of intense coherent light that can yield a thousand times the current data rate. "We'll want to readily tune the frequency of the light, and tune its energy to the optimum. And we'll need a sample stage that can easily tilt and rotate frozen samples, holding them in the beam for many exposures. These advances would mean we could do our experiments reasonably rather than heroically, and on a wider range of materials.”

In the meantime, X-ray diffraction microscopy at beamline 9.0.1 is showing the way to what lensless imaging can do, according to the investigators.

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Lawrence Berkeley National Laboratory