User-driven three-dimensional collision avoidance in microscope system

Abstract

A user interface presented on a display of the microscope system includes motion controls for moving the stage subsystem, the source subsystem, and the detector subsystem, and a graphical user interface allows a user to delineate "common" sample shapes as well as more irregular sample shapes to create a sample envelope that is subsequently used by a collision avoidance application of the system.

Description

[0001] Related applications

[0002] This application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 63 / 487,069, filed on February 27, 2023, the entire contents of which are incorporated herein by reference. Background Art

[0003] X-ray microscopy (XRM) is a powerful imaging technique used to analyze internal structures at the micrometer to nanometer scale. XRM systems provide high-resolution images of samples, allowing their properties to be studied in detail. XRM systems use an X-ray beam to illuminate the sample and then image it 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 used to examine and analyze the internal structure of a sample. When a sample is scanned at different angles, a tomographic data set is reconstructed from a series of these projections using standard CT reconstruction algorithms.

[0005] There are many different configurations for x-ray CT systems. In x-ray microscopy systems, because the x-ray source and detector are large and the sample or object being scanned is typically small, the x-ray source and detector are largely stationary while the sample rotates in the x-ray beam, in contrast to medical CT systems where the patient is stationary and the source and detector rotate around the patient.

[0006] X-ray microscope systems are typically arranged in 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] Among them, L s is the distance from the source to the sample, L d is the distance from the sample to the detector.

[0009] In many cases, the sample scanned in an X-ray microscope system has an a priori unknown shape. For example, even in cases where a CAD (Computer-Aided Design) model is available or the sample comes from a core sample of known dimensions, the exact alignment of the sample is often unknown. Furthermore, the alignment can change when different regions of interest are selected and the sample is realigned in the beam path. This leads to the following problem: the sample may collide with the scanning setup (the part of the X-ray source or detector that is closest to the sample) when the sample is moved to be scanned (mostly rotated) or when the source or detector is moved for the setup. The challenge of collision avoidance is often made more difficult by the fact that the X-ray source and / or detector will need to be moved very close to the sample for optimal system performance.

[0010] Similar setups exist for other microscope / tomography systems operating in other regions of the electromagnetic spectrum, such as optical coherence tomography and confocal microscopes (optical projection tomography). Still other examples include scanning electron microscopes (SEMs) and focused ion beam (FIB) systems, i.e., charged particle imaging systems.

[0011] One of the challenges in X-ray microscopy is to ensure the safety of both the sample and the equipment. Collision avoidance systems that support accurate system geometric models are useful, and these models must be able to respond in real time and be able to simulate possible collisions based on the expected motion sequence. For X-ray microscopy systems that support both geometric and optical magnification, the size and shape of the sample can be used to optimize throughput resolution or field of view based on the possible range of system geometries that allow samples of that size and shape. In some existing systems, collisions can be avoided if a 3D model of the object (e.g., a 3D representation such as a mesh or surface data) and a 3D model of the setup are available. One system provides for the use of an automated visual light camera to generate the accurate model shape and to reconstruct the sample envelope based on images of the camera as the sample is rotated in the system. Summary of the Invention

[0012] The present invention relates to a graphical user interface and associated XRM system that allows a user to outline "common" sample shapes as well as more irregular sample shapes to create a sample envelope that is subsequently used by the system's collision avoidance application.

[0013] Common shapes may include cylindrical, spherical, flat, or box shapes, to name a few examples.

[0014] On the other hand, if the shape is irregular, the same approach can be used, but more images from a visible light camera or a larger field of view x-ray detector will be needed to properly outline the sample. The collision avoidance application provides a workflow to use this knowledge and guide the user to safely define these differently shaped samples.

[0015] The knowledge that the sample is flat or box-shaped allows the selection of more optimized acquisition parameters to improve the image quality of the final tomography, such as variable angle tomography with more projections through the longest edge, variable exposure tomography with higher exposure on the longest edge, and 180+ sector acquisition where the angular range is optimized to keep the sample closest to the source for faster tomography.

[0016] In general, according to one aspect, the invention features a user interface presented on a display of a microscope system including a computer that processes projection data from the microscope system. The interface includes a camera pane for displaying an image of a sample held in the microscope system captured by a camera, and an overlay that allows a user to size the boundaries of the sample displayed in the image.

[0017] The sized bounding box can then be used throughout the rotation of the sample to determine the closest source and detector distances that can be used for a specified angular range of tomographic scanning.

[0018] The user interface can further enable the user to select between "common" sample shapes, including cylindrical / spherical and box-shaped / flat samples. It can further implement a workflow in which, by referencing a model of the sample and a model of the microscope system, the device geometry is first changed to a known "safe" state in which there is no collision or risk of collision between the sample and the microscope system. The maximum sample envelope can further be presented as an overlay.

[0019] In general, according to another aspect, the present invention features an X-ray microscope system comprising an X-ray source subsystem for generating X-rays, a stage subsystem for positioning and holding a sample in the X-rays, and a detector subsystem for detecting the X-rays after interacting with the sample. A computer is provided for receiving projections from the detector subsystem and images from an optical camera and generating a user interface including motion controls for moving the stage subsystem, the source subsystem, and the detector subsystem. The interface also includes a camera pane for displaying an image of a sample held in the microscope system taken by the optical camera, and an overlay that allows a user to size the boundaries of the sample displayed on the image.

[0020] The above and other features of the present invention (including various novel construction details and component combinations) and other advantages will now be described in more detail with reference to the accompanying drawings and will be pointed out in the claims. It will be understood that the specific methods and devices embodying the present invention are shown by way of illustration and not as limitations of the present invention. The principles and features of the present invention may be used in various and numerous embodiments without departing from the scope of the present invention. BRIEF DESCRIPTION OF THE DRAWINGS

[0021] In the accompanying drawings, reference numerals refer to the same parts throughout the different views. The drawings are not necessarily drawn to scale, emphasis instead being placed upon illustrating the principles of the invention. In the drawings:

[0022] Figure 1 is a schematic diagram of an x-ray microscope system employing the present invention in one embodiment; and

[0023] Figures 2 to 25 A user interface generated by an x-ray microscope system for display on a display device thereof is shown. DETAILED DESCRIPTION

[0024] The present invention will now be described more fully hereinafter with reference to the accompanying drawings, in which illustrative embodiments of the invention are shown. However, the invention may 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 will fully convey the scope of the invention to those skilled in the art.

[0025] As used herein, the term "and / or" includes any and all combinations of one or more of the associated listed items. In addition, unless expressly stated otherwise, the singular form and the articles "a", "an" and "the" are also intended to include the plural form. It should also be understood that the terms include, contain, cover and / or encompass when used in this specification specify the presence of the features, wholes, steps, operations, elements and / or parts, but do not exclude the presence or addition of one or more other features, wholes, steps, operations, elements, parts and / or combinations thereof. Further, it will be understood that when an element comprising a component or subsystem is mentioned and / or shown as connected or coupled to another element, it may be directly connected or coupled to the other element, or there may be intermediate elements.

[0026] 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 the present invention belongs. It will be further understood that terms (such as those defined in commonly used dictionaries, etc.) should be interpreted as having a meaning consistent with their meaning in the context of the relevant art, and not in an idealized or overly formal sense, unless explicitly defined as such herein.

[0027] Figure 1 is a schematic diagram of an XRM system 200 to which the present invention is applicable.

[0028] The microscope system 200 shown is an X-ray computed tomography (CT) system and generally includes several subsystems. An X-ray source subsystem 102 generates a polychromatic or possibly monochromatic X-ray beam 103. A stage subsystem 110 with an object holder 112 holds a sample or object 114 in the beam and positions and repositions it to enable scanning of the sample 114 in the beams 103, 105. A detector subsystem 118 detects 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.

[0029] Generally speaking, the stage subsystem 110 has the ability to position and rotate the sample 114 within the beam 103. Thus, the stage subsystem 110 typically includes a linear stage and a rotational stage. The illustrated example features a precise three-axis stage 150 that translates and positions the sample along the x, y, and z axes with great precision, but within a relatively small range of travel. This allows the region of interest of the object 114 to be located within the beams 103 / 105. The three-axis stage 150 is mounted on a theta stage 152, which rotates the three-axis stage 150, thereby rotating the sample 114 within the beam about the y-axis. The theta stage 152 is, in turn, mounted on the base 107.

[0030] Thus, the reference frame or coordinate system of the three-axis stage 150 is related to the reference frame or coordinate system 10 of the microscope system 200 through the angular position of the θ stage 152 .

[0031] In some embodiments, source subsystem 102 will typically be a synchrotron x-ray radiation source or alternatively a "laboratory x-ray source."

[0032] As used herein, a "laboratory x-ray source" is any suitable x-ray source that is not a synchrotron x-ray radiation source. Laboratory x-ray source 102 may be an x-ray tube in which electrons are accelerated in a vacuum by an electric field and injected into a metal target, emitting x-rays as the electrons decelerate in the metal. Typically, depending on the type of metal target used, such a source produces a continuum of background x-rays that incorporates sharp peaks in intensity at certain energies derived from characteristic lines of the selected target.

[0033] In one example, the source subsystem 102 is a rotating anode (reflective target) type or microfocus source with a tungsten target. Targets comprising molybdenum, gold, platinum, silver, or copper may also be used. Preferably, a transmission target configuration is used, in which the electron beam strikes the thin target from the back side. X-rays emitted from the other side of the target are used as the beam 103.

[0034] The x-ray beam generated by the source subsystem 102 is typically conditioned to suppress undesirable radiation energies or wavelengths. For example, energy filters, such as those held in the filter wheel 160 and designed to select a desired x-ray energy range (bandwidth), are used to eliminate or attenuate undesirable wavelengths present in the beam. These energy filters typically include an "air" filter, which corresponds to no filter, as well as a set of low-energy filters for filtering lower-energy x-rays and a set of high-energy filters for filtering higher-energy x-rays.

[0035] When object 114 is exposed to X-ray beam 103, X-ray photons or particles propagating through sample 114 form a modulated beam 105 that is received by detector subsystem 118. In some other examples, an image is formed on detector subsystem 118 of microscope system 200 using an objective lens.

[0036] Typically, a magnified projected image of the object 114 is formed on the detector subsystem 118. The magnification of the x-ray table is equal to the inverse ratio of the source-to-object distance 202 and the source-to-detector distance 204.

[0037] To achieve high resolution, embodiments of the x-ray CT system 200 further utilize several optical objectives that provide different optical magnifications. In one example, the detection system includes a very high resolution detector 124-1. In one example, the high resolution detector 124-1 includes a camera, a scintillator, and a microscope objective to provide additional optical magnification in the range of 2x to 100x, or greater. The scintillator converts x-rays into an optical image, which is magnified by the microscope objective and then detected by the camera.

[0038] Other detectors are often included as part of the detector subsystem 118. For example, the detector subsystem 118 may include a lower resolution detector 124-2. In examples, this may be a scintillator and a flat panel detector or a camera with a lower magnification microscope objective. Configurations of the detector subsystem 118 with one, two, or more detectors 124 are possible.

[0039] Preferably, two or more detectors 124 - 1 , 124 - 2 are mounted on a turntable 122 of the detector subsystem 118 so that they can be alternately rotated into the path of the modulated light beam 105 from the sample 114 .

[0040] 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, while 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, typically very close to the object during scanning, and then retracted to allow the object to be removed from the object holder 112 of the stage subsystem 110, a new object to be loaded onto the object holder 112 of the stage subsystem 110, and / or the object to be repositioned on the object holder 112 of the stage subsystem 110.

[0041] The microscope system 200 includes an optical camera 210, such as a video camera, that collects image data of a sample 114 held in an object holder 112. The camera is typically mounted directly or indirectly to the system base 107 via a mounting system 215, such as a bracket. Typically, the optical camera 210 collects images in the visible portion of the spectrum and / or in adjacent spectral regions, such as infrared. Typically, the optical camera 210 includes a charge coupled device (CCD) or complementary metal oxide semiconductor (CMOS) image sensor. A light source 212 is also included to illuminate the object in the spectral region used by the optical camera.

[0042] The operation of the microscope system 200 and the scanning of the object 114 are controlled by a computer subsystem 224 , which generally includes an image processor 220 and a controller 222 .

[0043] The computer system 224 includes one or more processors 260 and its data storage resources (such as disks or solid-state drives) and memory MEM (MEM). The processor 260 executes an operating system 262 and various applications running on the operating system 262 to allow the user to control and operate the microscope system 200. Specifically, the user interface application 250 executes on the operating system 262 and generates a user interface presented on the display device 236 connected to the computer subsystem 224. The user interface enables the operator to control the system and observe 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 124. The collision avoidance application 252 allows the user to define the physical range of the sample 114 and then monitors the movement of the x-ray source subsystem 102, the stage subsystem 110, and the detector subsystem to ensure that the subsystems do not collide with the sample 114 or with each other.

[0044] To this end, the collision avoidance application 252 maintains a complete collision model. Specifically, a system model 252-1 includes all currently installed hardware of the system in their actual and current positions. In addition, a sample model 252-2, typically loaded into the system by a user, includes a solid model of the then-currently loaded sample, which further includes bounding boxes added by the user. To create a sample model, the user loads the sample into the system, and then the user draws a box or other line or shape around the sample on the interface, and the software generates the sample model.

[0045] Based on the system model 252-1 and the sample model 252-2, the collision avoidance application 252 models in real time any collisions of the sample and / or any requested motor movements of any hardware of the system. The application further optimizes the hardware acquisition geometry and predicts whether a collision will occur for the full tomographic scan.

[0046] Controller 222 allows computer subsystem 224 to control and manage components within X-ray CT microscope 200 under software control. Controller 222 may be a separate computer system suitable for handling real-time operations or an application program executed on processor 260. Source subsystem 102 includes control interface 130, which allows controller 222 to control and monitor it. Similarly, stage subsystem 110 and detector subsystem 118 have corresponding control interfaces 132, 134, which allow computer subsystem 224 to control and monitor them via controller 222.

[0047] To configure the microscope system 200 to scan a sample and adjust other parameters (such as geometric magnification, etc.), the operator first defines the sample using the collision avoidance application 252 using a user interface presented on the display device 236 and generated by the user interface application 250. The user can then safely adjust the source-to-object distance 202 and the source-to-detector distance 204 by corresponding operation of the source stage 154 and the detector stage 156 to achieve the desired scan settings. Note that typically, in this stage, the sample or the region of interest on the sample is located on the axis of rotation. Therefore, moving the sample (object) stage will change this and, therefore, the scan area. Therefore, typically, only the source and detector stages are used for adjustments.

[0048] Specifically, the source table 154 and the detector table 156 include respective motor encoder systems or other actuator systems that allow the computer system 224, via the controller 222, to position the respective x-ray source subsystem 102 and detector subsystem 118 to designated positions via the control interfaces 130, 134. Further, the source table 154 and the detector table 156 signal the controller 222 of their actual positions.

[0049] An operator of the system under automated control operates stage subsystem 110 to perform a CT scan via the computer subsystem, controller 222, and control interfaces 130, 132, 134. Typically, stage subsystem 110 positions an object by rotating the object about an axis orthogonal to the optical axes of x-ray beams 103, 105 using stage 152, and / or positions the sample in the x, y, and z directions using stage 150.

[0050] Using a user interface presented on a display device 236 by a user interface application 250, an operator defines / selects a scan setup, including acquisition parameters, via a UI (user interface) device 235. These acquisition parameters include x-ray source voltage settings that help determine the x-ray energy spectrum, as well as the exposure time and number of frames on the x-ray source subsystem 102. The operator also typically selects 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 to be created for the sample 114, and the selected detectors 124-1 and 124-2. Typically, acquisition parameters include x-ray source voltage, x-ray source filtering, camera exposure time, number of frames, and total number of projections, and the scan setup includes the angle by which the sample is rotated by the stage subsystem 110. Additionally, a source-to-object distance 202 and a source-to-detector distance 204 are typically specified, and these are translated into the necessary positions or settings for the source stage 154 and detector stage 156 as part of the scan setup.

[0051] Operation and Workflow:

[0052] Figure 2A user interface 500 is shown generated by a user interface application 250 executing on an operating system 262 of a computer system 224 and typically presented on a display device 236 .

[0053] In the illustrated mode, the user interface 500 includes an optical camera pane 318. This displays the current real-time image or video data being received from the optical camera 210.

[0054] The sample motion controls are located at the bottom of the window. The sample x position control section 330 controls the x-axis stage of the three-axis stage 150 to move the object holder 112, thereby moving the sample or object 114 along the x-axis. The sample y position control section 332 controls the y-axis stage of the three-axis stage 150 to move the sample along the y-axis. The sample z position control section 334 controls the z-axis stage of the three-axis stage 150 to move the sample along the z-axis. The sample theta control section 336 controls the theta stage 152 to rotate the object holder 112 and the three-axis stage 150, thereby rotating the sample or object 114.

[0055] The source Z stage control functions 338 are located on the left. These include a step size indicator that indicates the step size that the source stage 154 will move in response to each user input. It includes a current position display. It also includes a user data input line and a "Go" button that allows the user to enter the desired absolute position of the source stage 154.

[0056] Similar detector control functionality 340 exists for the detector stage 156, providing Z-axis control functionality to the right. Here again, it includes a step size indicator indicating the step size the source stage will move. It also includes a current position display. Finally, the user can enter the desired absolute position.

[0057] Each of the control areas 330, 332, 334, 336, 338, and 340 includes a separate step size indicator 392. Here, the user can enter the desired step size using the user interface device. Also included are controls 394 that allow for decreasing or increasing the forward and backward movement of the associated stage. These also include a pause button that will stop the 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 the desired absolute position by entering the desired position in the data input line 396 and then selecting the associated "forward" button using the user interface device 235.

[0058] In addition, the user interface includes a coordinate overlay 380, which is a graphical collection of indicators superimposed by the user interface application 250 on top of the image data from the camera 210 in the optical camera pane 318. This overlay indicates the relative orientation of the respective axes of the three-axis stage 150 within the reference frames of the system 200 and the user. This is important information because the Z and X axes of the three-axis stage 150 each depend on the current angular position of the theta stage 152.

[0059] Coordinate overlay 380 is useful because an operator cannot typically view specimen 114 in the image data from optical camera pane 210 and know which direction the X and Z axes of three-axis stage 150 are pointing unless they also know the current angle of the theta stage and mentally apply a transformation between the coordinate system of that system and the coordinate system of three-axis stage 150. This information is now provided by coordinate overlay 380.

[0060] In the dialog portion 310 of the display, the user can select a manual mode to create a sample protection envelope using the collision avoidance application 252 .

[0061] The collision avoidance application 252 helps avoid collisions between the sample 114 and parts of the system 200 during operation of the source stage 154, the detector stage 156, the three-axis stage 150, and the theta stage 152. Thus, by referencing the system model 252-1 and the sample model 252-2, potential collisions between the sample and the device are predicted for the entire rotation of the tomographic scan (i.e., a full 360-degree rotation, 180 degrees + a sector, etc.) specified in the tomographic scan. The collision avoidance application 252 uses the dimensions of the sample 114 to determine the closest source and detector distances that can be used for the specified angular range of the tomographic scan. These values ​​can be used to determine the system geometry and objective lens type used to obtain a full-field 2D image from any angle within the specified angular range of the tomographic scan.

[0062] like Figure 3 As shown, by referring to the system model 252-1 and the sample model 252-2, the collision avoidance application 252 first changes the device geometry and source filter selection to a known "safe" state in which there is no collision or collision risk between the sample and the system. This operation is described in the dialogue section 310.

[0063] The sample bounding box overlay 382 is displayed as a graphic superimposed on top of the image data provided in the optical camera pane 318 .

[0064] Here, the maximum size of the specimen is outlined by a bounding box overlay 382 in the visual light camera image display shown in the optical camera pane 318. This allows the user to augment the specimen model 252-2.

[0065] like Figure 4and Figure 5 As shown, the collision avoidance application 252 in the dialogue portion 310 instructs the user about the process and limitations. Those instructions note that the sample must be less than 100 mm in diameter and fit within the green bounding box. It should also be noted that the following types of samples may not be compatible, such as dark transparent highly reflective and shiny samples, samples that are not normally visible with a real-time camera, and samples that are 1 mm or less in size or thickness.

[0066] like Figure 6 As shown, the collision avoidance application 252 in the dialogue portion 310 instructs the user to rotate the sample 360 ​​degrees to ensure that the sample remains within the bounding box 382. This automatic rotation provides visual confirmation of an acceptable sample size.

[0067] like Figure 7 As shown, the collision avoidance application 252 in the dialog section 310 allows the user to select from "common" sample shapes, including cylindrical / spherical samples and box / flat samples. The collision avoidance application 252 also allows the user to create collision envelopes based on an unlimited number of angles, and the user can create sample envelope annotations at each angle to create custom samples. This can be used for more irregular shapes.

[0068] If the user selects the common shapes of cylindrical / spherical or flat / box, the user is instructed to outline the sample using an "outline bounding box," which is rectangular in shape and can be resized to fit the sample. The bounding box also separates the sample holder 112 from the sample 114.

[0069] Figure 8 and Figure 9 An outline bounding box 384 is shown displayed on the image from the optical camera 210. The sample model 252-2 is augmented by the user selecting points on the box 384 with a mouse or touch screen user interface device 238 to "manually" size the points.

[0070] In the dialog portion 310 , the user is instructed to rotate the sample to an orthographic view in order to ensure that the sample remains within the outline bounding box 384 .

[0071] like Figure 10 As shown, for flat / box-shaped samples, the dialog portion 310 provides a workflow that steps the user through first rotating the sample to the widest view and adjusting the bounding box to identify the sample holder and sample.

[0072] like Figure 11 As shown, the collision avoidance application 252 would then rotate the sample 114 90 degrees away from the widest angle, and the user would adjust the outline bounding box 384 to fit the "thin" view.

[0073] For custom shapes, the collision avoidance application 252 allows the user to go to as many angles as needed to properly define the shape. The instructions in the dialog portion 310 are to go to the widest view first, ensure the widest view is captured, then go to the thinnest view and save.

[0074] like Figure 12 As shown, the collision avoidance application 252 enables the user to add views from any angle that accurately define the shape to define the correct envelope. The more irregular the sample, the more angles are needed.

[0075] After reshaping the bounding box to enhance the sample model 252-2, as shown in Figure 13 As shown, the collision avoidance application 252 enables the generation of a sample envelope as in the dialog portion 310. When creating the sample envelope, the model 252-2 knows whether the sample is cylindrical, flat / box-shaped, or custom.

[0076] like Figure 14 and Figure 15 As shown, the collision avoidance application 252 visually presents the maximum sample envelope size 386 to the user as an overlay in the optical camera pane 318. Furthermore, the collision avoidance application 252 provides the user with given tools to easily and accurately determine whether the sample envelope represents the sample, such as allowing for automatic repetition of sample rotation to ensure that the sample remains within the maximum envelope size.

[0077] like Figure 16 and Figure 17 As shown in , the collision avoidance application 252 presents a model view pane 388. It shows the sample model envelope at the current system geometry, and the user can move the sample stage and the model envelope will continue to reflect where the current sample is. The user can rotate or move the sample to ensure that the model fits the sample correctly.

[0078] Using the sample envelope, the collision avoidance application 252 calculates the system geometry and objective lens settings to optimally image the complete sample at all tomographic angles, e.g. Figure 18 As shown, it is called the Full Field of View (FFOV) or "overview image".

[0079] like Figure 19 and Figure 20 As shown, the collision avoidance application 252 also allows the user to indicate an altitude to use as the center of the overview scan using an altitude annotation, shown here as a circle overlay at 392 in the optical camera pane 318 .

[0080] like Figure 21 and Figure 22 As shown, the collision avoidance application 252 automatically and safely moves the system to the overview image setting.

[0081] like Figure 23 、 Figure 24 and Figure 25 As shown, the user can navigate to the page and verify that the system geometry and target type indeed confirm that the entire sample is in view.

[0082] While the invention has been particularly shown and described with reference to preferred embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention as encompassed by the appended claims.

Claims

1. 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 comprising: a camera pane for displaying an image captured by a camera of a sample held in the microscope system; as well as An overlay that allows the user to size the bounds of the sample displayed on the image.

2. The user interface according to claim 1, wherein During rotation of the sample, the sized bounding box is used to determine the closest source and detector distances that can be used for a specified angular range of tomographic scanning.

3. The user interface according to claim 1 or 2, further comprising: Enables the user to select between "common" sample shapes, including cylindrical / spherical samples and box / flat samples.

4. A user interface according to any one of claims 1-3, implementing a workflow in which the device geometry of the microscope system is first changed to a known "safe" state by reference to a model of the sample and a model of the microscope system, in which there is no collision or risk of collision between the sample and the microscope system.

5. The user interface of any one of claims 1-4, further comprising presenting a maximum sample envelope size as an overlay.

6. The user interface according to any one of claims 1-5, further presenting a model view. 7 . The user interface according to claim 1 , further comprising displaying a workflow that guides the user step by step in arranging the sample.

8. An X-ray microscope system comprising: An X-ray source subsystem for generating X-rays; a stage subsystem for holding the sample in the X-ray; a detector subsystem for detecting the X-rays after interacting with the sample; as well as a computer for receiving projections from the detector subsystem and images from the optical camera and generating a user interface, the user interface comprising: motion controls for moving the stage subsystem, source subsystem, and detector subsystem, a camera pane for displaying an image of a sample held in the microscope system taken by the optical camera, and an overlay allowing a user to size a bounding box of the sample displayed on the image.

9. The system according to claim 8, wherein: During rotation of the sample, the computer uses the sized bounding box to determine the closest source and detector distances that can be used for a specified angular range of tomographic scanning.

10. The system according to any one of claims 8 or 9, wherein: The computer enables the user to select between "common" sample shapes, including cylindrical / spherical samples and box / flat samples.

11. A system according to any one of claims 8-10, implementing a workflow in which the device geometry of the system is first changed to a known "safe" state by reference to a model of the sample and a model of the microscope system, in which there is no collision or risk of collision between the sample and the microscope system.

12. The system according to any one of claims 8 to 11, wherein: The computer further presents the maximum sample envelope size as an overlay.

13. The system according to any one of claims 8 to 12, wherein: The computer further provides a view of the model.

14. The system according to any one of claims 8 to 13, wherein: The computer further displays a workflow that guides the user step by step to arrange the samples.

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