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Revealing the inner beauty by 3D structured illumination microscopy

Posted by Hamed Shateri Najafabadi

John W. Sedat and his team at the University of California, San Francisco, have developed a revolutionary method for visualizing the cells. Their new “3D-structured illumination microscopy”, or 3D-SIM, analyzes the changes that happen in the light interference pattern when a fine cellular structure reflects the light, and interprets the image with a resolution of about 100nm, almost twice as good as the resolution of the state-of-the-art confocal laser scanning microscopes – shamefully, that was all I could understand from the physics of this microscope! This technique is fascinating in that, in contrast to the electrone microscopy techniques, it can be used for specific labeling of molecules using the very conventional methods such as labeling with fluorescent antibodies. There is no need to change the protocols that you currently use for preparing the specimens; just the micropscope is different. In a report in Science, Sedat and his team demonstrate the ability of this technique in resolving multicolor images of the nuclear periphery with an unprecedented precision, revealing exciting features such as presence of chromatin-deprived spaces just below the foci of nuclear pore complexes (see figure below).

Simultaneous imaging of DNA, nuclear lamina, and NPC epitopes by 3D-SIM

Some images are so stunning:

Cell division

A nucleus from a mouse-muscle stem cell

P.S. Also see the first comment; Marie-Luise has kindly written a description on the physics behind 3D-SIM.


One thought on “Revealing the inner beauty by 3D structured illumination microscopy

  1. I also read an article, a few days ago, where the Science paper was cited (Christian Meier: Schnappschuss der Zellteilung, spektrumdirekt.de, June 5th, 2008) and where the technique was explained in a somewhat more understandable way than in the original paper. Since I found it quite cool, I would like to share what I understood from that article:

    The physical phenomenon behind the 3D-SIM technique can be compared to what happens when you scan a printed picture.
    During the process of scanning, the original picture is subdivided into a pattern of points (the pixels). If you scan a picture that is printed, it already consists of pixels. Now, if the points that are scanned are not exactly “in line” with the points that are printed, if they are shifted against each other, then you get a new pattern, that looks different. This is the so-called Moiré effect. The Moiré pattern is usually more coarse, bigger than the original pattern. (In everyday life, this effect can be seen when someone is wearing clothes with a fine pattern on TV. Instead of the original pattern you see “dancing” lines.)
    In the new microscpy technique of 3D-SIM, the laser beam that is used for imaging is divided into several components, which are focused on a certain spot in the sample. There, the waves interfere, which leads to the formation of a pattern, which is different from the pattern of the sample, i.e. the substructures of the sample. Both patterns are so small that they cannot be imaged, but the combination of these two patterns leads to the formation of a coarser Moiré pattern, similarly to the example of scanning a printed picture. This Moiré pattern can be registered through the microscope. Since the inteference pattern is known, in theory, you can calculate the substructure from the Moiré pattern. However, in order to gain enough information to be able to calculate and visualize the substructures, it is necessary to image the sample from different angles. (Like in mathematics, where an equation system that contains more variables than equations cannot be solved.)

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