2005年12月5日
Computer scientists and biologists at the Department of Energy'sLawrence Berkeley National Laboratory已经开发了可以快速和自动自动从电子微封印中选择数以万计的生物分子的高质量图像的软件，其精度接近经验丰富的人类分析师。
根据电子显微镜的数据，新的算法被描述为“通过分割进行粒子进行分割”，有望大大提高在高分辨率下确定生物结构的速度和功率。
当需要的是一个大而复杂的生物分子的高分辨率结构时 - 核糖体（例如，结合蛋白质和RNA），或者很容易在水中散开并且难以结晶的膜蛋白 - 生物学家通常会转向冷冻电子显微镜（Cryo-EM）执行单粒子重建。
Understanding structure is often the key to devising antibiotics and other therapies that can interfere with unwanted biological activity -- for example, the ability of infectious bacteria to synthesize proteins can be wrecked by jamming their ribosomes, if the ribosome structure is known in detail. Single-particle reconstruction with cryo-EM holds the promise of providing many high-resolution structures which may be difficult or impossible to obtain otherwise.
Instead of trying to coax molecules to arrange themselves in a repeating crystalline structure, as is necessary for x-ray crystallography, cryo-EM uses individual molecules frozen in random orientations. Capturing two-dimensional images of the molecule from many different angles allows powerful computers to recreate the structure in three dimensions, a process molecular biologist Robert Glaeser of Berkeley Lab's Physical Biosciences and Life Sciences Divisions, who is also a professor of biochemistry and molecular biology at the University of California at Berkeley, calls "crystallization in silico."
"In theory, you need twice as many particles as the molecular weight of what you want to image," explains Umesh Adiga, a member of Glaeser's laboratory and a staff scientist in the Physical Biosciences Division. Molecular weight roughly corresponds to the number of atoms in the molecule. "So for a molecule with half a million atoms, you need a million particle images -- thousands for each orientation."
These must be chosen from many millions of candidates, and each must show the whole particle and nothing but the particle. A typical micrograph may show fifteen hundred or more particles, but picking them out isn't easy. The microscope's electron beam has to be kept at low power to prevent radiation damage, so the signal-to-noise ratio is low and the particles are barely perceptible shapes in a field of gray.
已经设计了自动颗粒方法来应对这一挑战，但直到现在，最佳产量超过30％的假阳性 - 颗粒的质量质量较差，或者完全是其他东西，例如碎片或背景噪声。欧洲杯猜球平台因此，“一个人仍然必须经历他们，挑选好人，”阿迪加说。
Adiga and his colleagues decided that concentrating too much attention on the particle itself in the early stages of picking -- for example, approximating its shape and creating a template into which real images are forced to fit, a process common to all previous automatic methods -- simply added to the difficulty. "We decided that if there's noise, there's noise, so at first let's not deal with the particle but with the noise," he says. "If the particle is the foreground, we deal with the background."
通过首先建立感兴趣的颗粒的平均灰度范围，可以保持对比度的良好质地。欧洲杯猜球平台然后减去平滑背景。
The next steps involve a procedure called segmentation, developed by Adiga and his colleagues. After the background is subtracted, the micrograph is rendered in high contrast. Only shapes of a certain size and brightness are retained; all the rest are thrown away in a step called binarization, or thresholding. "You need not know how the particle looks before you set out to pick good images of it, only how big it is," says Adiga.
The thresholding procedure is iterative, but eventually the processed high-contrast particle images can be matched unambiguously with their originals in the more highly detailed, low-contrast micrograph. Some images may still remain problematic -- for example, some particles may be so close together they appear to be touching; in these cases, an additional procedure called "pinch-off" separates candidates that aren't actually connected and discards those that are. Boxes are drawn around the final picks and their image quality is enhanced by an operation called "shrink-wrapping."
如果相邻粒子的一部分突出到盒子中，则将其自动丢弃并用像其他背景一样纹理的图案代替。在此过程的这个结束阶段（尽管不是在开始时），使用模板（包括粒子的形状信息）来完善标识可能是有利的。
Scores of micrographs are needed to supply the hundreds of thousands of particles in a typical large-molecule reconstruction, but a program user needs to set parameters like particle size and gray-scale range only once, on a single micrograph. Thereafter the program runs on its own, sorting through each micrograph in about ten minutes.
阿迪加（Adiga）和他的同事通过使用该算法从奥尔巴尼纽约州卫生部沃兹沃思中心（Wadsworth Center）提供的55个显微照片中，从130,000多个核糖体颗粒中挑选出图像，从而测试了新算法。欧洲杯猜球平台Adiga通过眼睛和“手动”选定的粒子分别检查了55个显微照片，其中80％以上的粒子与该程序挑选的粒子相同。欧洲杯猜球平台该程序选择的图像中只有不到10％是误报。
http://www.lbl.gov/