Abstract: Systems or techniques are provided for spectral analysis. In various embodiments, a system can comprise a memory that stores computer executable components and a processor that executes the computer executable components stored in the memory. The computer executable components can comprise a graph generation component that generates a class neighborhood graph for a lamella milling processes, wherein the graph generation component generates the class neighborhood graph by: classifying structures within a region of interest of a design schematic of a sample; and generating a directed graph of the region of interest, wherein the directed graph comprises nodes representing the classified structures and weighted directed edges between the nodes representing distances between the classified structures.

Abstract: The disclosure relates to a method for micromachining a biological sample for creating a lamella for analysis in a Cryo-Charged Particle Microscope (Cryo-CPM). The method comprising the steps of providing a biological sample on a sample carrier; Locating a sample area on the sample carrier, said sample area comprising a region of interest having biological material from which a lamella can be created; and Micromachining at least part of the biological sample so as to remove material in a part of the sample area surrounding the region of interest, in order to increase a visual contrast between the biological material in the region of interest and its surroundings. With the increased visual contrast a location for a potential lamella can be identified.

Abstract: A computer-implemented method for generating synthetic data describing a sample can comprise processing, by a system operatively coupled to a processor, sample information describing a set of original features of a sample, resulting in processed model input information, and generating, by an analytical model, synthetic image data, usable to generate a synthetic image, and describing at least a portion of the set of original features and based on the processed model input information. The computer-implemented method further can comprise generating, by the system, the synthetic image of a pseudo-sample, based on the synthetic image data, having at least one pseudo-feature that is different from and based on the set of original features.

Abstract: Disclosed herein are scientific instrument support systems, as well as related methods, computing devices, and computer-readable media. For example, in some embodiments, a support apparatus is provided for a charged particle microscope. The support apparatus is configured to apply automated image processing to an image representing a lamella sample to segment the image into a plurality of segmented classes. The support apparatus is also configured to identify, based on the plurality of segmented classes, a subset of candidate structures-of-interest in the lamella sample and to select, from the subset of candidate structures-of-interest in the lamella sample, a selected structure-of-interest for milling. The support apparatus is also configured to set, based on the selected structure-of-interest for milling, at least one milling parameter for the scientific instrument. An automated method performed via a computing device for providing such scientific instrument support is also provided.

Abstract: Methods and apparatus apply focus stacking to sample preparation, improving accuracy of analytic tasks, facilitating automation, and improving throughput. Focus stacking is applied to a set of sample images having different focus depths, to produce a composite image in which features at different depths are in focus and, optionally, a depth map. A sample location is selected from the composite image and a localized material removal, measurement, or imaging operation is performed based on the sample location. A depth value from the depth map is used to set a working depth of a tool for performing the localized operation. Applications include lamella preparation for cryogenic TEM analysis of biological samples. Other applications, techniques, and variations are disclosed.

Abstract: Methods and apparatus apply focus stacking to sample preparation, improving accuracy of analytic tasks, facilitating automation, and improving throughput. Focus stacking is applied to a set of sample images having different focus depths, to produce a composite image in which features at different depths are in focus and, optionally, a depth map. A sample location is selected from the composite image and a localized material removal, measurement, or imaging operation is performed based on the sample location. A depth value from the depth map is used to set a working depth of a tool for performing the localized operation. Applications include lamella preparation for cryogenic TEM analysis of biological samples. Other applications, techniques, and variations are disclosed.

Abstract: A sample is milled to expose the region of interest (ROI) within the sample, while being held by a sample stage in a microscopy system. The sample is milled based on the ROI location determined with sample images acquired with light beam irradiating from different axes. The sample images are acquired while the sample is held using the same sample stage for milling.

Abstract: The disclosure relates to a method for micromachining a biological sample for creating a lamella for analysis in a Cryo-Charged Particle Microscope (Cryo-CPM). The method comprising the steps of providing a biological sample on a sample carrier; Locating a sample area on the sample carrier, said sample area comprising a region of interest having biological material from which a lamella can be created; and Micromachining at least part of the biological sample so as to remove material in a part of the sample area surrounding the region of interest, in order to increase a visual contrast between the biological material in the region of interest and its surroundings. With the increased visual contrast a location for a potential lamella can be identified.

Abstract: Disclosed herein are scientific instrument support systems, as well as related methods, computing devices, and computer-readable media. For example, in some embodiments, a support apparatus is provided for a charged particle microscope. The support apparatus is configured to apply automated image processing to an image representing a lamella sample to segment the image into a plurality of segmented classes. The support apparatus is also configured to identify, based on the plurality of segmented classes, a subset of candidate structures-of-interest in the lamella sample and to select, from the subset of candidate structures-of-interest in the lamella sample, a selected structure-of-interest for milling. The support apparatus is also configured to set, based on the selected structure-of-interest for milling, at least one milling parameter for the scientific instrument. An automated method performed via a computing device for providing such scientific instrument support is also provided.