Image restoration in X-ray microscopy: PSF determination and biological applications

Abstract

In this work, we show that digital image processing methods can be applied to enhance the quality of X-ray microscopic images. One application of X-ray microscopy is imaging of biological specimens in their natural aqueous environment. Since X radiation can introduce structural changes in these objects when observing them at room temperature, it is sometimes necessary to take images with short exposure time. The image quality can thus be reduced due to low signal-to-noise ratio (SNR). Digital image processing methods can be applied to reduce image degradation caused by noise. Another example of a digital image processing method we applied to X-ray microscopy images is contrast enhancement of structures near the resolution limit of the microscope. Structures of 20 nm in size, which show weak contrast in the original image, become more clearly visible after restoration. Since image restoration methods are based on the knowledge of the optical transfer function (OTF) or the point spread function (PSF), a handy method for quick PSF determination is presented. An iterative image-restoration method was applied to pictures obtained with the Gottingen transmission X-ray microscope at BESSY. Results of image quality enhancement by this method are shown for images of polytene chromosomes of Chironomus Thummi larvae, test-structures and in situ hybridization on Xist RNA using biotinilated DNA probe.

Characterization of transfer function, resolution and depth of field of a soft X-ray microscope applied to tomography enhancement by Wiener deconvolution

“…To achieve this goal, several methods have been proposed based on: qualitative assessment [5,6], specific contrast decay [7][8][9] and Rayleigh criteria [10,11]. We have favoured this last one because it is obtained using parameters related with the microscope instead of visual inspection or a pure mathematical definition.…”

Electron tomography of amplified nanogold immunolabelling: Improvement of quality based on alignment of projections with sinograms and use of post-reconstruction deconvolution

“…In electron tomography of thick specimens, the image restoration is generally used as a preliminary step before reconstruction in order to correct the Contrast Transfer Function (CTF) and the noise, especially in the case of the transmission electron microscope (TEM) acquisition (Han et al, 1997;Hanai et al, 1997;Winkler and Taylor, 2003). To our knowledge, a post-reconstruction restoration using a PSF in tomography has been described mainly in X-ray microscopy (Rathee et al, 1992;Lehr et al, 1998), but not in the Weld of electron tomography.…”

Quantitative assessment of cone-beam CT system by 3D point-spread function

“…From these facts, we conclude that there exist pitfalls for PSF measurement through direct micro phantom reconstruction. To avoid these pitfalls, we suggest the use of an indirect method, for example, through the use of a macro edge phantom [2,12], as reported below.…”