Beamline 6-2c at the Stanford Synchrotron Radiation Lightsource (SSRL) is capable of Transmission X-ray Microscopy (TXM) at 30 nm spatial resolution. A transmission X-ray microscope is conceptually identical to a familiar optical microscope, consisting of a light source, a condenser to focus light on the sample, a sample stage, and an objective to focus the transmitted light onto a digital sensor (Figure 1). In this context though, the word refers “light” to synchrotron x-ray radiation, ranging from about 5 to 14 keV per photon. Since X-ray wavelengths are shorter than those of visible light, the X-ray microscope is capable of much higher resolution. from around the world have come to Beamline 6-2 to image a variety of biological and inorganic samples. Depending on the specific TXM technique being used, the user will typically take thousands of images of a single sample. For example, the user might take images at 180 different angles, taking 20 identical pictures per angle, resulting in 3600 images. If the sample is larger than the field of view (FOV) of the microscope, it becomes necessary to construct a mosaic of sub-images at each angle. If it takes five exposures to cover the sample, the total increases to 5*3600 = 18,000 images. Finally, the user will periodically move the sample off to the side and take some reference images (perhaps several hundred). All of these images must be extensively processed before presentation-quality images and 3D models can be obtained. While the details of the image processing depend on the specific TXM technique used, a typical processing workflow is shown in Figure 2. With such massive amounts of data, it is necessary to automate the image processing workflow as much as possible, especially for the alignment of similar images with each other. Not only is it tedious to align images by eye, but a computer should be able to align images much
Beamline 6-2c at the Stanford Synchrotron Radiation Lightsource (SSRL) is capable of Transmission X-ray Microscopy (TXM) at 30 nm spatial resolution. A transmission X-ray microscope is conceptually identical to a familiar optical microscope, consisting of a light source, a condenser to focus light on the sample, a sample stage, and an objective to focus the transmitted light onto a digital sensor (Figure 1). In this context though, the word “light” refers to synchrotron x-ray radiation, ranging from about 5 to 14 keV per photon. Since X-ray wavelengths are shorter than those of visible light, the X-ray microscope is capable of much higher resolution. from around the world have come to Beamline 6-2 to image a variety of biological and inorganic samples. Depending on the specific TXM technique being used, the user will typically take thousands of images of a single sample. For example, the user might take images at 180 different angles, taking 20 identical pictures per angle, resulting in 3600 images. If the sample is larger than the field of view (FOV) of the microscope, it becomes necessary to construct a mosaic of sub-images at each angle. If it takes five exposures to cover the sample, the total increases to 5*3600 = 18,000 images. Finally, the user will periodically move the sample off to the side and take some reference images (perhaps several hundred). All of these images must be extensively processed before presentation-quality images and 3D models can be obtained. While the details of the image processing depend on the specific TXM technique used, a typical processing workflow is shown in Figure 2. With such massive amounts of data, it is necessary to automate the image processing workflow as much as possible, especially for the alignment of similar images with each other. Not only is it tedious to align images by eye, but a computer should be able to align images much
Bolgert_Rough_Draft.docx