Method and system for guiding geometric and optical magnification in x-ray microscope

Abstract

A user interface presented on a display of the microscope system includes a motion control for moving the object stage subsystem, the source subsystem, and the detector subsystem, and a simulation area; the simulation area displays a resolution curve and a flux curve generated by a zoom tool and displayed on a graphical user interface of the system.

Description

[0001] Related Applications

[0002] This application claims the benefit under 35 USC 119(e) of U.S. Provisional Application No. 63 / 487,068, filed February 27, 2023, which is incorporated by reference in its entirety. BACKGROUND

[0003] X-ray microscopy (XRM) is a powerful imaging technique for analyzing internal structures on the micrometer to nanometer scale. XRM systems provide high-resolution images of a sample, which can be studied in detail for its properties. XRM systems use an x-ray beam to illuminate a sample and then image the sample using a detector. The x-rays are then analyzed to produce an image or projection of the sample.

[0004] X-ray computed tomography (CT) is a non-destructive technique for examining and analyzing the internal structure of a sample. When a sample is scanned at different angles, a tomographic volume data set is reconstructed from a series of these projections by standard CT reconstruction algorithms.

[0005] There are many different configurations of x-ray CT systems. In x-ray microscopy systems, the x-ray source and detector are relatively large, while the sample or object being scanned is typically small, so during acquisition the x-ray source and detector are essentially fixed, while the sample is rotated in the x-ray beam, in contrast to medical CT systems, where the patient is stationary, while the source and detector rotate around the patient.

[0006] X-ray microscopy systems are typically arranged with a relatively simple projection geometry, where x-rays penetrate the sample, and the transmitted x-rays are collected by a detector. With this setup, the geometric magnification of the system is:

[0007]

[0008] where L s is the source-to-sample distance, and L d is the sample-to-detector distance.

[0009] Some systems also or alternatively provide optical magnification through an optical stage. Typically, the detection subsystem comprises a camera detector, e.g. a camera detector based on charge-coupled devices (CCD) or CMOS. A magnification lens or objective system is provided in the optical stage for imaging the light from the scintillator onto the camera. The magnification factor of the overall imaging system is thus distributed between the projection x-ray stage and the optical stage. In preferred embodiments, the magnification factor of the optical stage is typically 0.4x to 40x. The magnification factor of the x-ray stage is typically 1x to 10x. SUMMARY

[0010] One of the biggest challenges in imaging, especially for systems that can employ both geometric and optical magnification factors, is what system geometry and optical magnification factor is best for a given application and sample. Not only is the operational space of possible configurations large, but the definition of "best" can vary from application to application, with some applications demanding resolution and others preferring speed or total scan area / volume. Since there can be multiple combinations to achieve a particular pixel size and field of view required, how to visualize the trade-offs and optimize the setup is a significant challenge.

[0011] For current systems, deciding on the final geometry and optical magnification factor for a sample is an iterative process by moving to those settings and taking images to verify the desired settings. Thus, individual evaluations must be made for each possible solution to make this decision.

[0012] The present invention is directed to helping the user make these decisions by creating an intuitive and interactive interface to explore the possible solution space and suggestions for optimization without having to change the system configuration for each setting change. Geometric collision constraints with the sample can be taken into account and suboptimal solutions can be ignored, thereby reducing the operational space to a more manageable set and allowing the user to focus on the key trade-offs between resolution, throughput, and field of view (FOV) when optimizing the selection.

[0013] Without guidance, the optimal scan setup is not easily achieved. The user's understanding of the impact of geometric constraints on the solution space and the trade-offs between resolution, throughput, and FOV is highly user dependent. Even very experienced users only achieve suboptimal setups and need to manually set up and iterate over the operational space can be very time consuming and error prone.

[0014] Embodiments of the present invention employ a zoom tool that simulates changes in system geometry and optical magnification to more quickly and optimally determine the geometry and optical magnification. In addition, it can be based on the region of interest (ROI) location, 1) graphically drawn on an overview image in the user interface, or 2) through other means, such as non-graphical input (e.g., from a GUI edit box, or from a file or other data source), rather than having the system first go to the actual location. It also uses sample envelopes such as size and shape to limit the accessible range of parameters so that the user can be confident that the final settings will not result in system conflicts. The overview image can be generated in a number of ways, including from: a physical model of the system and the sample geometry from VLC imaging, a physical model of the sample, volumetric imaging of the sample, projection imaging of the sample, a related imaging modality, and / or volumetric imaging of the sample in conjunction with segmentation for automatic ROI delineation.

[0015] The tool uses the ROI location and size of the sample to determine the field of view required. Next, using simulation, the optical magnification that can be used is determined based on the sample size and shape and the limitations on the geometry magnification available from the stage travel. If multiple options are feasible, one will be recommended for use.

[0016] The zoom tool then uses the selected optical magnification (if any), known details about the objective response, other system performance metrics, typical exposure ranges, and typical total number of projections in a tomographic scan to create simulation curves to describe the resolution response and total scan time response as a function of the achievable FOV and / or pixel size. In addition, depending on the shape of the sample (flat vs. non-flat), there are recommended angular ranges. After these curves are generated, the user can be shown the simulated or calculated field of view and pixel size for the required ROI location. The user will also see "recommended ranges" for the best results under the current settings. For example, "best resolution range" and "fastest scan range".

[0017] The zoom tool takes advantage of the knowledge that the sample is flat or box-like to recommend more optimal acquisition parameters for selection to improve the image quality of the final tomographic scan, for example:

[0018] • variable angle tomography with more projections on the longest sample dimension;

[0019] • variable exposure tomography with higher exposure on the longest sample dimension; and

[0020] • Tomography with 180+ sectors or limited angles (less than 180+ sectors) where the angle range is optimized to have the sample, and even the ROI, closest to the source for faster tomography. Being as close to the source as possible is an important optimization here. For many angle ranges using less than 360 degrees, the sample can be close to the source, but the angle range where the ROI is closest to the source is optimal for the fastest tomography.

[0021] In addition, scanning with limited angles (less than 180+ sectors) can also be done where the projection data is incomplete but a 3D volume can be generated (with potentially acceptable artifacts). These optimization / visualization techniques can also be applied in certain instances.

[0022] Allowing the user to change these settings, such as binning, angle range, and / or selected initial objective, the zoom tool illustrates the effect of the change by generating a new curve for these settings in the graphical user interface. For example, if the user switches to another optical magnification, a new curve is generated. Since the change can not be the best choice to get the best results, the plot can show that the current optical magnification is not suitable for this ROI.

[0023] When the user accepts the final result, the final ROI position, optical and geometric magnification, and all other acquisition parameters can be saved to an actual tomography recipe point, without the user spending time to move the system.

[0024] In general, according to one aspect, the invention features a user interface presented on a display of a microscope system, the microscope system including a computer that processes projection data from the microscope system. The user interface includes a motion control for moving an object stage subsystem, a source subsystem, and a detector subsystem to configure the microscope system to a desired position for imaging a region of interest of a sample; and a simulation region that displays a resolution curve and a throughput curve for imaging the region of interest of the sample.

[0025] Preferably, the simulation region further includes a region of interest marker for displaying a region of interest (ROI). Also, the defined region of interest is specified by graphically defining the region of interest on one or more overview images displayed in one or more panes of the user interface, where the overview images are from a model of the system and / or sample, volumetric imaging of the sample, projection imaging of the sample, a related imaging modality, and / or volumetric imaging of the sample in conjunction with segmentation for automatic ROI definition. However, the ROI can also be specified by non-graphical input (e.g., by a GUI edit box, file, or other data interface).

[0026] The resolution curve and the flux curve can be constrained by sample geometry, stage travel, and collision constraints. In addition, the resolution curve and the flux curve are preferably updated in response to a user change in field of view and pixel size and / or a user change in optical magnification.

[0027] In general, according to another aspect, the application features a method of operating a microscope system that includes a computer that processes projection or image data from the microscope system. The method includes displaying a motion control for moving an object stage subsystem, a source subsystem, and a detector subsystem; and displaying a simulation region that displays a resolution curve and a flux curve.

[0028] In general, according to another aspect, the application features a method of operating a microscope system that includes a computer that processes projection or image data from the microscope system. The method includes displaying a motion control for moving an object stage subsystem, a source subsystem, and a detector subsystem; and displaying a simulation region that displays a resolution curve and a flux curve.

[0029] The above and other features of the application, including various novel details of structure and combinations of parts, and others will now be more apparent to those skilled in the art upon reading the following detailed description, taken in conjunction with the accompanying drawings. It is to be understood that the phraseology and terminology employed herein are for the purpose of description and not of limitation. The principles and features of the application can be employed in various arrangements without departing from the scope of the application. BRIEF DESCRIPTION OF DRAWINGS

[0030] In the drawings:

[0031] Figure 1 Schematic diagram of an x-ray microscope system embodying the application in one embodiment;

[0032] Figure 2 , Figure 3 , Figure 4 , Figure 5 , Figure 6 , Figure 7 , Figure 8 , Figure 9 and Figure 10 A user interface generated by the x-ray microscope system is shown. DETAILED DESCRIPTION

[0033] The present application will be described more fully hereinafter with reference to the accompanying drawings, in which example embodiments of the application are shown. The application may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will be thorough and complete, and fully convey the scope of the application to those skilled in the art.

[0034] As used herein, the term "and / or" includes any and all combinations of one or more of the associated listed items. In addition, unless otherwise indicated, singular forms and singular forms of reference such as "a", "an" and "the" are intended to include the plural forms as well. It will be further understood that the terms "comprises", "comprising", "includes" and / or "including", when used in this specification, specify the presence of stated features, integers, steps, operations, elements, and / or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and / or groups thereof. Furthermore, it is to be understood that where the term "comprises" is used in the specification, it is taken to mean that something is included, but not to the exclusion of anything else; that is, it allows for elements, functionalities, and / or operations that "comprise", include, are included in, but are not limited to, as well as anything that is / are similar.

[0035] Unless otherwise defined, all terms (including technical and scientific terms) used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this application belongs. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the relevant art and will not be interpreted in an idealized or overly formal sense unless expressly so defined herein.

[0036] Figure 1 Schematic diagram of an XRM system 200 suitable for use with the present application.

[0037] The illustrated microscope system 200 is an X-ray CT system, and generally includes several subsystems. An X-ray source subsystem 102 generates a polychromatic or possibly monochromatic X-ray beam 103. An object stage subsystem 110 with an object holder 112 fixes a sample or object 114 in the beam and positions and repositions it to enable scanning of the sample 114 in the fixed beam 103, 105. One or more detector subsystems 118 detect the beam 105 after it has been modulated by the sample. A base, such as a platform or optical table 107, provides a stable foundation for the microscope system 200 and its subsystems. In some instances, there are multiple detector subsystems. One has all the lenses and magnifications from 0.4x to 40x. The other has a flat essentially 1x, but it generally has a larger field of view than the lenses.

[0038] In general, the object stage subsystem 110 has the ability to position and rotate the sample 114 in the beam of rays 103. Thus, the object stage subsystem 110 typically includes a linear stage and a rotational stage. The illustrated example has a precision 3-axis stage 150 that translates and positions the sample very precisely along the x, y, and z axes, but only over a relatively small range of travel. This enables the region of interest of the object 114 to be within the beam of rays 103 / 105. The 3-axis stage 150 is mounted on a theta stage 152 that rotates the 3-axis stage 150, thereby rotating the sample 114 in the beam of rays about the y axis. The theta stage 152, in turn, is mounted on the base 107.

[0039] Thus, the frame of reference or coordinate system of the 3-axis stage 150 is related to the frame of reference or coordinate system 10 of the microscope system 200 by the angular position of the theta stage 152.

[0040] In some embodiments, the source subsystem 102 is typically a synchrotron x-ray radiation source or a "laboratory x-ray source".

[0041] As used herein, a "laboratory x-ray source" refers to any suitable x-ray source that is not a synchrotron x-ray radiation source. The laboratory x-ray source 102 can be an x-ray tube in which electrons are accelerated in a vacuum by an electric field and shot into a target metal sheet, emitting x-rays as the electrons decelerate in the metal. Typically, depending on the type of metal target used, such a source will produce a continuous background x-ray spectrum combined with certain energies of sharp peaks from characteristic lines of the selected target.

[0042] In one example, the source subsystem 102 is a rotating anode (bouncing target) type or microfocus source with a tungsten target. Targets including molybdenum, gold, platinum, silver, or copper can also be used. Preferably, a transmission target configuration is used in which the electron beam hits a thin target from the back side of the thin target. The x-rays emitted from the other side of the target are used as the beam of rays 103.

[0043] The beam of x-rays produced by the source subsystem 102 is typically conditioned to suppress unwanted radiation energies or wavelengths. For example, energy filters, such as those fixed in a filter wheel 160, designed to select a desired range of x-ray energies (bandwidth), are used to eliminate or attenuate unwanted wavelengths present in the beam of rays. These energy filters typically include an "air" filter corresponding to no filter, and a set of low energy filters for filtering lower energy x-rays and high energy filters for filtering higher energy x-rays.

[0044] When the object 114 is exposed to the x-ray beam 103, the x-ray photons that pass through the sample 114 form a modulated beam 105, which is received by the detector subsystem 118. Optionally, an optical magnification stage (including at least one objective lens) is used to form an image on the detector subsystem 118 of the microscope system 200.

[0045] Typically, a geometric and / or optically magnified projection image of the object 114 is formed on the detector subsystem 118. The geometric magnification of the x-ray stage is equal to the inverse ratio of the source-to-object distance 202 and the source-to-detector distance 204.

[0046] To achieve high resolution, one embodiment of the x-ray CT system 200 also utilizes multiple optical objectives that provide different optical magnification in the optical stage. In one example, the detection system includes a very high resolution detector 124-1. In one example, this high resolution detector 124-1 has a camera, a scintillator, and a microscope objective to provide additional optical magnification in a range of 0.4x to 100x or more. The scintillator converts the x-rays to an optical image that is magnified by the microscope objective and then detected by the camera.

[0047] Other detectors are typically included as part of the detector subsystem 118. For example, the detector subsystem 118 can include a lower resolution detector 124-2. This can be a scintillator and flat panel detector, for example, or a camera with a lower magnification microscope objective. Configurations of one, two, or even more detectors 124 of the detector subsystem 118 are possible.

[0048] Preferably, the detectors 124-1, 124-2 are mounted on a turret 122 of the detector subsystem 118 so that they can be alternately rotated into the path of the modulated beam 105 from the sample 114.

[0049] Typically, the source subsystem 102 and the detector subsystem 118 are mounted on respective z-axis stages. For example, in the illustrated example, the source subsystem 102 is mounted to the base 107 via a source stage 154, and the detector subsystem 118 is mounted to the base 107 via a detector stage 156. In practice, the source stage 154 and the detector stage 156 are low precision, high travel range stages that allow the source subsystem 102 and the detector subsystem 118 to be moved to positions that are typically very close to the object during scanning, and then to be retracted to allow removal of the object from the object holder 112 of the object stage subsystem 110, loading of a new object, and / or repositioning of the object.

[0050] The microscope system 200 has an optical camera 210, e.g. a video camera, which collects image data of the sample 114 fixed in the object holder 112. The camera is typically mounted directly or indirectly to the system base 107 by a mounting system 215, such as a stand. Typically, the optical camera 210 collects images in the visible part of the spectrum and / or adjacent spectral regions, such as infrared. Typically, the optical camera 210 has a CCD or CMOS image sensor. Also included is a light source 212, which illuminates the object in the spectral region employed by the optical camera.

[0051] The operation of the microscope system 200 and the scanning of the object 114 is controlled by a computer subsystem 224, which typically comprises an image processor 220 and a controller 222.

[0052] The computer system 224 comprises one or more processors 260 and their data storage resources, such as disks or solid state drives, and a memory MEM. The processor 260 executes an operating system 262, and on this operating system 262 various applications are run to allow a user to control and operate the microscope system 200. In particular, a user interface application 250 is executed on the operating system 262 and generates a user interface that is presented on a display device 236 connected to the computer subsystem 224. The user interface enables an operator to control the system and view projections, images and tomographic reconstructions. User input devices 235, such as a touch screen, computer mouse and / or keyboard, enable interaction between the operator and the computer subsystem 224. A zoom tool application 252 generates analog information for display on the display device 236.

[0053] The controller 222 allows the computer subsystem 224 to control and manage the components in the X-ray CT microscope 200 under software control. The controller can be a separate computer system adapted to handle real-time operations or an application executed on the processor 260. The source subsystem 102 comprises a control interface 130, which allows the controller 222 to control and monitor it. Similarly, the object stage subsystem 110 and the detector subsystem 118 have respective control interfaces 132, 134 for allowing the computer subsystem 224 to control and monitor them through the controller 222.

[0054] To configure the microscope system 200 to scan a sample and adjust other parameters, such as the geometric magnification, the operator uses the user interface presented on the display device 236 and generated by the user interface application 250 to adjust the source-to-object distance 202 and the source-to-detector distance 204 by operating the source stage 154 and the detector stage 156, respectively, to achieve the desired scanning setup.

[0055] In particular, the source stage 154 and the detector stage 156 include respective motor encoder systems or other actuator systems that allow the computer system 224 to position the respective X-ray source subsystem 102 and detector subsystem 118 through the control interface 130, 134 to a specified position through the controller 222. In addition, the source stage 154 and the detector stage 156 signal the controller 222 of their actual position.

[0056] The system operator under automatic control operates the object stage subsystem 110 to perform a CT scan through the computer subsystem, the controller 222 and the control interface 130, 132, 134. Typically, the object stage subsystem 110 will position the object by controlling the theta stage 152 to rotate the object about an axis orthogonal to the optical axis of the X-ray beam 103, 105 and / or use the stage 150 to position the sample in the x, y, z axis directions.

[0057] Using the user interface presented on the display device 236 using the user interface application 250, the operator defines / chooses scan settings including acquisition parameters through the UI device 235. Typically, the source to object distance 202 and the source to detector distance 204 are specified and converted to the necessary position or setting of the source stage 154 and the detector stage 156 as part of the scan settings. These acquisition parameters include the X-ray source voltage setting that helps determine the X-ray energy spectrum generated by the X-ray source subsystem 102. Other parameters include the exposure time and the number of frames. The operator will also typically select other settings such as the field of view of the X-ray beam 103 incident on the sample 114, the number of X-ray projection images created for the sample 114 and the selected detectors 124-1, 124-2. Typically, the acquisition parameters include the X-ray source voltage, X-ray source filtration, camera exposure time, number of frames and total number of projections and the scan settings include the angle through which the sample is rotated by the stage subsystem 110.

[0058] Operation:

[0059] Figure 2 A user interface 500 generated and presented on the display device 236 by the user interface application 250 executing on the operating system 262 of the computer system 224 is shown.

[0060] In the illustrated mode, the user interface 500 includes two projection panes 310A, 310B in which overview images are displayed. In the illustrated example, the overview images are projections captured by the detector subsystem 118 at two different theta angles for the sample. In other examples, the overview images can be generated in a variety of ways, including: a physical model of the system and sample geometry for VLC imaging, a physical model of the sample, volumetric imaging of the sample, projection imaging of the sample, a related imaging modality, and / or volumetric imaging of the sample in conjunction with segmentation for automated ROI delineation.

[0061] The user interface 500 also includes an optical camera panel 318. This displays current image data received from the optical camera 210. In addition, the user interface 500 includes controls for configuring the x-ray microscope system 200 to the desired position for imaging the sample.

[0062] The source z stage control function 338 is located in the lower right region. This includes a step indicator, indicating the step size that the source stage 154 will move in response to each user input. It includes a current position display. Also included are user data entry lines as well as a "Go" button, which allows the user to enter a desired absolute position for the source stage 154.

[0063] The detector stage 156 has a similar detector control function 340, providing Z-axis control functionality. Here again, it includes a step indicator, indicating the step size that the source stage will move. Also included is a current position display. Finally, the user can enter a desired absolute position.

[0064] Sample motion controls are located at the bottom of the window. The sample x-position control region 330 enables movement of the object holder 112 and the sample or object 114 along the x-axis by controlling the x-axis stage of the 3-axis stage 150, the sample y-position control region 332 enables movement along the y-axis by controlling the y-axis stage of the 3-axis stage 150, the sample z-position control region 334 enables movement along the z-axis by controlling the z-axis stage of the 3-axis stage 150, and the sample theta control region 336 enables rotation of the object holder 112, 3-axis stage 150, and thus the sample or object 114 by controlling the theta stage 152.

[0065] Each of the control areas 330, 332, 334, and 336 includes a separate step indicator 392. Here, the user can input the desired step using the user interface device. Also included are back and forward motion controls 394 that allow for a decrease or increase of the associated stage. These also include a pause button for stopping movement of the corresponding stage. The current position of the corresponding stage is indicated by an absolute position indicator 398. Finally, the user can move to a desired absolute position by entering the desired position in the data entry line 396 and then selecting the associated "Run" button using the user interface device 235.

[0066] Figure 3 Another mode of the user interface 500 is shown in which both projection panes 310A, 310B have ROI markers rendered on the overview image. A user- movable and resizable ROI marker 408 is used to specify the desired location and field of view or pixel size. This ROI marker is resized and moved by the user through the user interface device 235. In other instances, the ROI is specified by a non-graphical input modality. For example, in these instances, the ROI is specified by the user from a GUI edit box or from a file or other data interface. In any case, the ROI marker is still rendered in the overview image as a visual confirmation of the ROI.

[0067] Figure 4 Another mode of the user interface 500 is shown, which shows the recommended objective that can be used to achieve this field of view at this ROI location. Specifically, one of the projection panes is used as a dialog pane 312 that suggests using a 4x objective or a number of other objectives that correspond to the detector 124-1, 124-2 or more and to the selected ROI. Figure 1

[0068] Figure 5 Another mode of the user interface 500 is shown, which shows the resolution 410 and flux 412 curves of the simulation performed by the zoom tool 252 rendered in the dialog pane 312.

[0069] The zoom tool also generates the exact location of the required ROI size 414 on these curves. The displayed possible operating space curves have been constrained by the sample geometry, stage travel, and collision constraints. The dialog pane 312 also displays only the best cone angle, source, and detector settings at each FOV, ignoring sub-optimal flux solutions that can achieve similar resolution but can take longer at a given FOV.

[0070] ​More generally, the zoom tool analyzes the cross-sectional aspect ratio of the sample envelope. If the aspect ratio is high, it means it is a planar sample, and the tool calculates based on a 180+ sector theta range. Otherwise, it simply rotates the sample the usual 360 degrees as the default angular range, but the user can select a different range.

[0071] In the calculation, the sample is "rotated" through angles to form the total envelope used to determine the closest source and detector approach. From this, the tool calculates the range of possible FOVs, resolutions, and relative scan times.

[0072] The geometric zoom setting for the currently selected FOV is based on the sample size and shape (envelope), and is calculated to make the selected angular range at that location collision-free. These curves also show the recommended range for the best result, as well as the best resolution range and the fastest scan range.

[0073] Figure 6 Another mode of the user interface 500 is shown, illustrating the curves for resolution 410 and flux 412 from the simulation in the dialog pane 312 as the user changes the field of view and pixel size with the slider bar 414. In this case, the initially requested ROI size is within the best resolution range, but if the user wants to scan faster, the bar can be moved into the fastest scan range. Note that as the user moves the slider bar 414, the size of the white dashed ROI marker changes, as does the data in the dialog pane 312.

[0074] Figure 7 Another mode of the user interface 500 is shown, illustrating that the user can also make changes to many of the settings (such as the optical magnification) and generate new curves for the ROI location and size 414. In some cases, the initially requested ROI size cannot be maintained with the new optical magnification, which is indicated both visually with the white dashed ROI marker and with the pixel size and field of view presented in the dialog pane 312. In some cases, the new manually requested optical magnification does not have a "recommended range."

[0075] Figure 8 Another mode of the user interface 500 is shown, illustrating that the user can also change the sort, creating new simulation curves.

[0076] Figure 9 Another mode of the user interface 500 is shown, also in Figure 6 illustrating that the zoom tool 252 can also be used to simulate and optimize advanced acquisition settings for variable angle tomography and 180+ sector range tomography if the sample has a planar or box-like shape.

[0077] After the zoom tool is completed, the selected parameters can be saved into the tomography recipe by pressing the updated recipe point 416.

[0078] Figure 10 Another mode of the user interface 500 is shown, illustrating that the user can use the "Go To Positions" button 380 shown in the zoom tool to move to the positions selected with the zoom tool, and because the zoom tool simulates curves under the known geometric constraints for a given setup, it is ensured that the updated recipe is collision-free for the full tomography, and that the go-to-positions move is safe for the device and sample. The user can then take an image at the newly moved-to positions to verify that the ROIs are in the correct positions, and that the field of view and pixel size match what was required in the zoom tool 252. Figure 2

[0079] For X-ray imaging systems where the detector resolution is comparable to the X-ray source spot size, the process of achieving optimal resolution is iterative and non-intuitive. In systems with multiple detectors and variable source spot sizes, the ability to obtain the fastest scan at a particular resolution is challenging for many users. Given a particular set of geometric collision constraints and desired FOV selection, the ability to quickly visualize the multi-dimensional solution space and understand the tradeoffs between FOV, resolution, and throughput is non-trivial. Systems that can image a variety of sample sizes and types add to the confusion. The user must determine the positions of the source and detectors in order to obtain the desired resolution in the shortest amount of time without colliding the sample with system components during the scan. The present system addresses these issues with an intuitive and interactive graphical interface to illustrate the interaction of different requirements for FOV, resolution, and scan time while avoiding collision constraints and sub-optimal solutions.

[0080] In summary, the system can provide a number of innovations:

[0081] • The ability to generate resolution and throughput maps from sample and system knowledge and simulated data. These include source spot size, detector pixel size, and the X-ray and optical response of these detectors.

[0082] • The application of geometric constraints (such as collision constraints with the sample or system components or travel limit constraints) to the theoretical solution space to reduce the displayed solutions to those that do not violate the constraints.

[0083] • Algorithmic exclusion of sub-optimal solutions. For example, while there can be many geometric solutions that will produce a certain FOV at a resolution, only the highest throughput of these solutions will be displayed.

[0084] ​• Knowledge of the source and detector configuration closest to the sample according to the sample size and shape.

[0085] • Transferring the simulated optimal conditions from the graphical interface to the parameters used in the scanning process.

[0086] • Ability to graphically position the region of interest in the sample and visualize the selected FOV boundaries around the region of interest.

[0087] At the same time, some of the features are not always critical. These include:

[0088] • Sample shape based tomography parameter suggestions. For example, 180+ fan tomography for a planar sample.

[0089] • Initial overview scan.

[0090] • Numerical display of predicted performance parameters updated with the slider position.

[0091] It should be further noted that other alternative embodiments, for example:

[0092] • The way the graphs are presented can be different. For example, the horizontal axis does not have to be the field of view, it can be pixel size, source / detector position, geometric magnification, etc. The vertical axis can be detectability of detail, MTF, frame rate, etc.

[0093] • The method for inputting the sample size constraints into the system can be different. For example, using a system generated three-dimensional collision model, but simpler methods include determining the user specified sample diameter outside the system.

[0094] • The specific inputs and algorithms used to simulate the performance parameters displayed on the vertical axis of the graphs can be different. For example, resolution can be simulated with geometric methods, empirical look-up tables, etc. The overview image can be generated in a number of ways, including: a physical model of the system and the sample geometry of the VLC imaging, a physical model of the sample, volumetric imaging of the sample, projection imaging of the sample, a related imaging modality, and / or volumetric imaging of the sample combined with segmentation for automatic ROI delimitation.

[0095] Thus, the present system can facilitate more efficient imaging, avoiding the laborious imaging parameter iterative exploration or learning from experience with imaging parameters to optimize the scan according to user preferences, and avoiding the laborious iterative process of moving the sample and system components to check for collisions and understand the geometric operating space.

[0096] While the application has been particularly shown and described with reference to particular embodiments thereof, it will be understood by those skilled in the art that various changes in the details of the application can be made without departing from the scope of the application as encompassed by the appended claims.

Claims

1. A user interface rendered on a display of a microscope system, the microscope system comprising a computer processing projection or image data from the microscope system, the user interface comprising: motion controls for moving an object stage subsystem, a source subsystem, and a detector subsystem to configure the microscope system to a desired position to image a region of interest of a sample; and a simulation region displaying a resolution curve and a throughput curve for imaging the region of interest of the sample.

2. The user interface of claim 1, wherein the simulation region further comprises a region of interest marker displaying the region of interest.

3. The user interface of any one of claims 1 or 2, wherein the region of interest is specified by a GUI edit box or by a file or other data interface.

4. The user interface of any one of claims 1 or 2, wherein, 4. The user interface of any one of claims 1-3, wherein the region of interest is specified by delineating the region of interest on one or more overview images displayed in one or more panes of the user interface, wherein the overview images are from a model of the system and / or sample, volumetric imaging of the sample, projection imaging of the sample, a related imaging modality, and / or volumetric imaging of the sample in conjunction with segmentation for automatic ROI delineation.

5. The user interface of any one of claims 1-4, wherein the resolution curve and the throughput curve are constrained by sample geometry, stage travel, and collision constraints.

6. The user interface of any one of claims 1 to 5, wherein, 6. The user interface of any one of claims 1-5, wherein the resolution curve and the throughput curve are updated in response to a user change to field of view and / or pixel size.

7. The user interface of any of claims 1-6, wherein, 7. The user interface of any one of claims 1-6, wherein the resolution curve and the throughput curve are updated in response to a user change to optical magnification, sorting, or angular range.

8. An X-ray microscope system comprising: an X-ray source subsystem for generating X-rays; an object stage subsystem for fixing a sample in the X-rays; a detector subsystem for detecting the X-rays after interaction with the sample; and a computer for receiving projections from the detector subsystem and generating a user interface, the user interface comprising motion controls for moving the object stage subsystem, source subsystem, and detector subsystem; and a simulation region displaying a resolution curve and a throughput curve.

9. The X-ray microscope system of claim 8, wherein the X-ray microscope system comprises the user interface of any one of claims 1-7.

10. A method of operating a microscope system, the microscope system comprising a computer processing projection or image data from the microscope system, the method comprising: displaying motion controls for moving an object stage subsystem, a source subsystem, and a detector subsystem to configure the microscope system to a desired position to image a region of interest of a sample; and displaying a simulation region displaying a resolution curve and a throughput curve for imaging the region of interest of the sample.

11. The method of claim 10, wherein the simulation region further comprises a region of interest marker that displays the region of interest.

12. The method of any one of claims 10 or 11, wherein the region of interest is specified by a GUI edit box, or by a file or other data interface.

13. The method of any one of claims 10 or 11, wherein, specifying the region of interest by delineating a region of interest on one or more overview images displayed in one or more panes of the user interface, wherein the overview images are from a model of the system and / or sample, volumetric imaging of the sample, projection imaging of the sample, a related imaging modality, and / or volumetric imaging of the sample in conjunction with segmentation for automated ROI delineation.

14. The method of any one of claims 10 to 13, wherein the method further comprises constraining the resolution curve and the throughput curve by sample geometry, stage travel, and collision constraints.

15. The method of any one of claims 10 to 14, wherein the method further comprises updating the resolution curve and the throughput curve in response to user changes to field of view and / or pixel size.

16. The method of any one of claims 10 to 15, wherein the method further comprises updating the resolution curve and the throughput curve in response to user changes to optical magnification, sorting, or angular range.

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