User-driven-three-dimensional collision avoidance in microscopy system

Abstract

A user interface rendered on a display of a microscopy system comprises motion controls for moving the object stage subsystem, source subsystem, and detector subsystem and a graphic user interface allows the user to outline 'common' sample shapes as well as more irregular sample shapes to create a sample envelope to be then used by the system's collision avoidance app.

Description

[0001] USER-DRIVEN-THREE-DIMENSIONAL COLLISION AVOIDANCE IN MICROSCOPY SYSTEM

[0002] RELATED APPLICATIONS

[0003] [ o o o i ] This application claims the benefit under 35 USC 119(e) of U.S. Provisional Application No. 63 / 487,069, filed on February 27, 2023, which is incorporated herein by reference in its entirety.

[0004] BACKGROUND OF THE INVENTION

[0005]

[0002] X-ray microscopy (XRM) is a powerful imaging technique for analyzing internal structure on the micro to nano scale. XRM systems provide high resolution images of samples, allowing for detailed study of their properties. XRM systems use a beam of x- rays to illuminate the samples, which is then imaged using a detector. The x-rays are then analyzed to produce an image or projection of the sample.

[0006]

[0003] X-ray computed tomography (CT) is a non-destructive technique for inspecting and analyzing internal structures of samples. Tomographic volume data sets are reconstructed from a series of these projections via standard CT reconstruction algorithms, as the samples are scanned at different angles.

[0007]

[0004] There are a number of different configurations for x-ray CT systems. In x-ray microscopy systems, because the x-ray sources and detectors are large and the samples or objects being scanned are typically small, the x-ray sources and detectors are largely fixed, while the samples are rotated in the x-ray beam, in contrast to medical CT systems in which the patient is stationary and the sources and detector rotate around the patient.

[0008]

[0005] X-ray microscopy systems are often arranged in a relatively simple projection geometry, in which the x-rays penetrate the sample, and the transmitted x-rays are collected by the detector. With this setup, the geometrical magnification of the system is: where, Lsis the source to sample distance and the Ld is the sample to detector distance.

[0009]

[0006] In many cases, the samples scanned in X-ray microscopy systems have a priori unknown shapes. Even in the cases where a CAD model is available or the sample is from a dimensionally-known core-sample, for example, the exact alignment of the sample is often unknown. Moreover, the alignment may be changed when different regions of interest are selected and the sample is realigned in the beam path. This leads to the problem that while the sample is moved to be scanned (mostly rotated) or the source or detector are moved for setup, the sample might collide with the scanning setup (the parts of the X-raysource or detector that are most proximate to the sample). The challenge of avoiding collisions is often made more difficult by the fact that the X-ray source and / or the detector will need to be moved into close proximity to the sample for optimal system performance.

[0010]

[0007] Similar setups also exist in other microscopy / tomography systems operating in other regions of the electromagnetic spectrum such as optical coherence tomography and confocal microscopy (optical projection tomography). Still other examples include scanning electron microscopes (SEMs) and focused ion beam (FIB) systems - i.e. charged particle imaging systems.

[0011]

[0008] One of the challenges in X-ray microscopy is to ensure the safety of both the sample and the device. A collision avoidance system that supports accurate system geometrical models is useful, and these models must be able to respond both in real-time and be able to simulate possible collisions based on desired motion sequences. For X-ray microscopy systems that support both geometric and optical magnifications, 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 allowed for a sample of that size and shape. In some existing systems, collisions can be avoided if a 3D model (e.g. a 3D representation such as a mesh or surface data) of the object and a 3D model of the setup are available. One system provides for the generation of an accurate model shape using an automated visual light camera and reconstruction of a sample envelope based on camera’s images as the sample is rotated in the system.

[0012] SUMMARY OF THE INVENTION

[0013]

[0009] The present invention concerns a graphic user interface and the associated XRM system that allows the user to outline ‘common’ sample shapes as well as more irregular sample shapes to create a sample envelope to be then used by the system’s collision avoidance app.

[0010] Common shapes can include cylindrical, spherical, flat, or box shapes, to list a few examples.

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

[0015]

[0012] The knowledge that a sample is flat or box shaped allows more optimized acquisition parameters to be selected 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 exposures on longest edge, and 180+fan acquisition with angle ranges optimized to keep the sample closest to the source for faster tomographies.

[0016]

[0013] In general, according to one aspect, the invention features a user interface rendered on a display of a microscopy system including a computer that processes projection data from the microscopy system. This interface comprises camera pane for displaying images of a sample held in the microscopy system taken by a camera and an overlay allowing a user to size bounding boxes for the sample displayed on the images.

[0017]

[0014] The sized bounding boxes can then be used during an entire rotation of the sample to determine the closest source and detector distances that can be used for specified angle ranges of a tomography.

[0018]

[0015] The user interface might further enable the user to select between ‘ common’ sample shapes, including cylindrical / spherical and box / flat samples. It can further implement a workflow in which the device geometries are first changed to a known ‘safe’ state in which there is no collision or danger of collision between the sample and the microscopy system by reference to a model of the sample and a model of the microscopy system. A maximum sample envelope can further be displayed as an overlay.

[0019]

[0016] In general, according to another aspect, the invention features an X-ray microscopy system comprising an X-ray source subsystem of generating X-rays, an object stage subsystem for positioning and holding a sample in the X-rays, and a detector subsystem for detecting the X-rays after interaction 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 object stage subsystem, a source subsystem, and a detector subsystem. The interface further includes a camera pane for displaying images of a sample held in the microscopy system taken by the optical camera and an overlay allowing a user to size bounding boxes for the sample displayed on the images.

[0020]

[0017] The above and other features of the invention including various novel details of construction and combinations of parts, and other advantages, will now be more particularly described with reference to the accompanying drawings and pointed out in the claims. It will be understood that the particular method and device embodying the invention are shown by way of illustration and not as a limitation of the invention. The principles and features of this invention may be employed in various and numerous embodiments without departing from the scope of the invention.

[0021] BRIEF DESCRIPTION OF THE DRAWINGS

[0022]

[0018] In the accompanying drawings, reference characters refer to the same parts throughout the different views. The drawings are not necessarily to scale; emphasis has instead been placed upon illustrating the principles of the invention. Of the drawings:

[0023]

[0019] Fig. 1 is a schematic diagram of an x-ray microscopy system to which the present invention is applied in one embodiment; and

[0024]

[0020] Figs. 2 through 25 show a user interface generated by the x-ray microscopy system for display on its display device.

[0025] DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0021] The invention now will be described more fully hereinafter with reference to the accompanying drawings, in which illustrative embodiments of the invention are shown. This invention 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 will fully convey the scope of the invention to those skilled in the art.

[0026]

[0022] As used herein, the term "and / or" includes any and all combinations of one or more of the associated listed items. Further, the singular forms and the articles "a", "an" and "the" are intended to include the plural forms as well, unless expressly stated otherwise. It will be further understood that the terms: includes, comprises, including and / or comprising, 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. Further, it will be understood that when an element, including component or subsystem, is referred to and / or shown as being connected or coupled to another element, it can be directly connected or coupled to the other element or intervening elements may be present.

[0027]

[0023] 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 invention 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.

[0028]

[0024] Fig. 1 is a schematic diagram of a XRM system 200 to which the present invention is applicable.

[0029]

[0025] The illustrated microscopy 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 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 beam 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 optics table 107, provides a stable foundation for the microscopy system 200 and its subsystems.

[0030]

[0026] In general, the object stage subsystem 110 has the ability to position and rotate the sample 114 in the beam 103. Thus, the object stage subsystem 110 will typically include linear and rotation stages. The illustrated example has a precision 3-axis stage 150 that translates and positions the sample along the x, y, and z axes, very precisely but only over relatively small ranges of travel. This allows a region of interest of the object 114 to be located within the beam 103 / 105. The 3-axis stage 150 is mounted on a theta stage 152 that rotates the 3-axis stage 150 and thus sample 114 in the beam around the y-axis. The theta stage 152 is in turn mounted on the base 107.

[0027] 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 microscopy system 200 by the angular position of the theta stage 152.

[0031]

[0028] The source subsystem 102 will typically be either a synchrotron x-ray radiation source or alternatively a “laboratory x-ray source” in some embodiments.

[0032]

[0029] As used herein, a “laboratory x-ray source” is any suitable source of x-rays that is not a synchrotron x-ray radiation source. 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 piece of metal, with x-rays being emitted as the electrons decelerate in the metal. Typically, such sources produce a continuous spectrum of background x-rays combined with sharp peaks in intensity at certain energies that derive from the characteristic lines of the selected target, depending on the type of metal target used.

[0033]

[0030] In one example, source subsystem 102 is a rotating anode (reflective target) type or micro-focused source, with a Tungsten target. Targets that include Molybdenum, Gold, Platinum, Silver or Copper also can be employed. Preferably a transmission-target configuration is used in which the electron beam strikes the thin target from its backside. The x-rays emitted from the other side of the target are used as the beam 103.

[0034]

[0031] The x-ray beam generated by source subsystem 102 is often conditioned to suppress unwanted energies or wavelengths of radiation. For example, undesired wavelengths present in the beam are eliminated or attenuated, using, for instance, energy filters (designed to select a desired x-ray energy range (bandwidth)) held in a filter wheel 160. These energy filters typically include an 'air' filter corresponding to no filter along with a set of low energy filters for filtering lower energy x-rays and high energy filters for filtering higher energy x-rays.

[0035]

[0032] When the object 114 is exposed to the X-ray beam 103, the X-ray photons or particles, which propagate through the sample 114, form a modulated beam 105 that is received by the detector subsystem 118. In some other examples, an objective lens is used to form an image onto the detector subsystem 118 of the microscopy system 200.

[0036]

[0033] Typically, a magnified projection image of the object 114 is formed on the detector subsystem 118. The 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.

[0034] To achieve high resolution, an embodiment of the x-ray CT system 200 further utilizes several optical objectives offering different optical magnifications. In one example, the detection system includes a very high resolution detector 124-1. In one example, this high-resolution detector 124-1 has camera, a scintillator, and a microscope objective to provide additional optical magnification in a range between 2x and lOOx, or more. The scintillator converts the x-rays into an optical image that are magnified by the microscope objective and then detected by the camera.

[0037]

[0035] Other detectors are often included as part of the detector subsystem 118. For example, the detector subsystem 118 can include a lower resolution detector 124-2. This could be a scintillator and flat panel detector or a camera with a lower magnification microscope objective, in examples. Configurations of one, two, or even more detectors 124 of the detector subsystem 118 are possible.

[0038]

[0036] Preferably, the two or more 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.

[0039]

[0037] 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 lower precision, high travel -range stages that allow the source subsystem 102 and the detector subsystem 118 to be moved into position, often very close to the object during scanning and then be retracted to allow the object to be removed from, a new object to be loaded onto, and / or the object to be repositioned on the object holder 112 of the object stage subsystem 110.

[0040]

[0038] The present microscopy system 200 has an optical camera 210 such as a video camera that collects image data of the sample 114 held in the object holder 112. This camera is typically mounted directly or indirectly to the system base 107 via a mounting system 215, such as a bracket. Typically, optical camera 210 collects the images in the visible portion of the spectrum and / or in the adjacent spectral regions such as the infrared. Usually, the optical camera 210 has a CCD or CMOS image sensor. Also included is a light source 212 that illuminates the object in the spectral regions employed by the optical camera.

[0039] The operation of the microscopy system 200 and the scanning of the object 114 is controlled by a computer subsystem 224 that often includes an image processor 220 and a controller 222.

[0041]

[0040] The computer system 224 includes one or more processors 260 along with their data storage resources such as disc or solid-state drives, and memory MEM. The processors 260 execute an operating system 262 and various applications run on that operating system 262 to allow for user control and operation of the microscopy system 200. Particularly, a user interface application 250 executes on the operating system 262 and generates a user interface that is rendered on a display device 236 connected to the computer subsystem 224. The user interface enables the operator to control the system and view projection, images and tomographic reconstructions. User input device(s) 235 such as a touch screen, computer mouse, and / or keyboard enable interaction between the operator and the computer subsystem 124. A collision avoidance app 252 allows the user to define the physical extent of the sample 114 and then monitors the movement of the x-ray source subsystem 102, the object stage subsystem 110, and the detector subsystem to ensure that the subsystems do not collide with the sample 114 or with each other.

[0042]

[0041] To this end, the collision avoidance app 252 maintains complete collision models. In particular, a system model 252-1 includes all of the currently installed hardware of the system, in their actual and current positions. In addition, a sample model 252-2, often loaded into the system by the user, includes a solid model of the currently loaded sample at the moment, which further includes bounding boxes added by the user. To create the sample model, the sample is loaded into the system by the user and then the user draws boxes or other lines or shapes around the sample on the interface and the software generates the sample model.

[0043]

[0042] Based on the system model 252-1 and the sample model 252-2, the collision avoidance app 252 models in real time for any collisions for any requested motor moves of any hardware of the sample and / or the system. The app further optimizes hardware acquisition geometries and predict whether or not a collision will occur for a full tomography.

[0044]

[0043] The controller 222 allows the computer subsystem 224 to control and manage components in the X-ray CT microscope 200 under software control. The controller might be a separate computer system adapted to handle realtime operations or an application program executing on the processor 260. The source subsystem 102 includes a control interface 130 allowing for its control and monitoring by the controller 222. Similarly, the object stage subsystem 110 and the detector subsystem 118 have respective control interfaces 132, 134 for allowing for their control and monitoring by the computer subsystem 224 via the controller 222.

[0045]

[0044] To configure the microscopy system 200 to scan the sample and to adjust other parameters such as the geometrical magnification, the operator utilizes the user interface rendered on the display device 236 and generated by the user interface application 250 to first define the sample using the collision avoidance app 252. Then, the user can safely adjust the source-to-obj ect distance 202 and the source-to-detector distance 204 by respective operation of the source stage 154 and detector stage 156 to achieve the desired scanning setup. Note that typically, at this stage the sample or a region of interest on the sample is located on the axis of rotation. So moving the sample (object) stage will change that and thus will change the scanning region. Therefore, usually, the adjustments are done only with the source and detector stages.

[0046]

[0045] Specifically, the source stage 154 and detector stage 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 the detector subsystem 118 to specified positions via the control interfaces 130, 134. Further, the source stage 154 and detector stage 156 signal the controller 222 of their actual positions.

[0047]

[0046] The operator of the system under automatic control operates the object stage subsystem 110 to perform the CT scan via computer subsystem, the controller 222 and the control interfaces 130, 132, 134. Typically, the object stage subsystem 110 will position the object by rotating the object about an axis that is orthogonal to the optical axis of the x- ray beam 103, 105 by controlling the theta stage 152 and / or position the sample in the x, y, z axes directions using stage 150.

[0048]

[0047] Using the user interface rendered on the display device 236 by the user interface app 250, the operator defines / selects scanning set up including the acquisition parameters via the UI devices 235. These acquisition parameters include x-ray source voltage settings that help to determine the X-ray energy spectrum and 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 upon the sample 114, the number of X-ray projection images to create for the sample 114, and the detector 124-1, 124-2 selected. Generally, the acquisition parameters include X-ray source voltage, X-ray source filtration, camera exposure time, number of frames, and overall number of projections and the scanning setup includes the angles to rotate the sample by the stage subsystem 110. In addition, the source-to-object distance 202 and the source-to-detector distance 204 are often specified and these are converted to the necessary positions or settings for the source stage 154 and detector stage 156 as part of the scanning setup.

[0049]

[0048] Operation and workflow:

[0050]

[0049] Fig. 2 shows the user interface 500 generated by the user interface app 250 executing on the operating system 262 of the computer system 224 and typically rendered on the display device 236.

[0051]

[0050] In the illustrated mode, the user interface 500 includes an optical camera pane 318. This displays the current live image or video data received from the optical camera 210.

[0052]

[0051] Sample motion controls are located at the bottom of the window. A sample x- position control area 330 enables the movement of the object holder 112 and thus the sample or object 114 along the x-axis by control of the x-axis stage of the 3-axis stage 150, a sample y-position control area 332 enables the movement along the y-axis by control of the y-axis stage of the 3-axis stage 150, a sample z-position control area 334 enables the movement along the z-axis by control of the z-axis stage of the 3-axis stage 150, sample theta control area 336 enables the rotation of the object holder 112, 3-axis stage 150, and thus the sample or object 114 by control of the theta stage 152.

[0053]

[0052] Source Z stage control functions 338 are located to the left. These includes a step size indicator indicating the steps that the source stage 154 will move in response to each user input. It includes a current position display. Also included is a user data entry line along with a "Go" button that allows the user to enter a desired absolute position for the source stage 154.

[0054]

[0053] There are similar detector control functions 340 for the detector stage 156 providing Z-axis control functions to the right. Here again, it includes a step size indicator indicating the steps that the source stage will move. Also included is a current position display. Finally, the user can enter a desired absolute position.

[0054] Each of the control areas 330, 332, 334, 336, 338, and 340 include separate step size indicators 392. Here, the user can enter the desired step size using the user interface devices. Also included are movement controls 394, back and forward, that allow the decrease or increase of the associated stage. These further include a pause button that will arrest the movement of the corresponding stage. The current position of the corresponding stage is indicated by an absolute location indicator 398. Finally, the user can move to a desired absolute position by entering in the desired position in a data entry line 396 and then selecting the associated "Go” button using the user interface devices 235.

[0055]

[0055] In addition, the user interface includes a coordinate overlay 380 that is a graphical set of indicators that are overlaid on top of the image data from camera 210 in the optical camera pane 318 by the user interface app 250. This overlay indicates the relative direction within the frame of reference of the system 200 and user for the respective axes of the 3-axis stage 150. This is important information since each of the Z-axis and the X- axis of the 3-axis stage 150 are dependent on the current angular position of the theta stage 152.

[0056]

[0056] The coordinate overlay 380 is useful because the operator cannot generally look at the sample 114 in the image data from the optical camera pane 210 and know in which direction the X axis and Z axis of the 3-axis stage 150 are pointed unless they also are aware of the current angle of the theta stage and mentally apply the transformation between the coordinate system of the system to the coordinate system of the 3-axis stage 150. Now, this information is provided by the coordinate overlay 380.

[0057]

[0057] In a dialog portion 310 of the display, the user is able to select a manual mode to create a sample protection envelope using the collision avoidance app 252.

[0058]

[0058] The collision avoidance app 252 helps to avoid collisions of the sample 114 with parts of the system 200 during operation of the source stage 154, the detector stage 156, the 3-axis stage 150, and theta stage 152. Thus, it will predict possible collisions of the sample to the device during an entire rotation of a tomography for the angles specified in the tomography, i.e. full 360 degree rotation, 180 degree + fan, etc. by reference to the system model 252-1 and sample model 252-2. The collision avoidance app 252 uses the size of the sample 114 to determine the closest source and detector distances that can be used for specified angle ranges of a tomography. These values can be used to determine the system geometry and objective type to use to obtain a full field of view 2D image from any angle for a specified angle range tomography.

[0059]

[0059] As shown in Fig. 3, the collision avoidance app 252 first changes the device geometries and source filter selection to a known ‘safe’ state in which there is no collision or danger of collision between the sample and the system by reference to the system model 252-1 and sample model 252-2. This operation is described in the dialog portion 310.

[0060]

[0060] A sample bounding box overlay 382 is displayed as a graphic overlaid on top of the image data provided in the optical camera pane 318.

[0061]

[0061] Here, a maximum size for the sample is outlined by the bounding box overlay 382 in the visual light camera image show displayed in the optical camera pane 318. This allows the user to augment the sample model 252-2.

[0062]

[0062] As shown in Figs. 4 and 5, the collision avoidance app 252 in the dialog portion 310 instructs the user about the process and limitations. Those instructions note that the sample must be less than 100 millimeters in diameter and fit within the green bounding box. It also notes that the following types of samples may not be compatible such as dark transparent highly reflective and shiny samples, samples generally not visible with the live camera and samples of 1 millimeter or smaller in size or thickness.

[0063]

[0063] As shown in Fig. 6, the collision avoidance app 252 in the dialog portion 310 instructs the user rotate the sample 360 degrees to ensure that the sample remains in the bounding box 382. This auto-rotation provides a visual confirmation of acceptable sample size.

[0064]

[0064] As shown in Fig. 7, the collision avoidance app 252 in the dialog portion 310 allows the user to select from ‘common’ sample shapes, including cylindrical / spherical and box / flat samples. The collision avoidance app 252 also allows the user to create a collision envelope based on unlimited number of angles, and the user creates sample envelope annotations at each angle to create a custom sample. This can be used for more irregular shapes.

[0065]

[0065] If the user selects a common shape that is a cylinder / spherical or flat / box, the user is instructed to outline the sample using ‘outline bounding boxes’ that are rectangular in shape and can be re-sized to match the sample. The bounding boxes also separate the sample holder 112 from the sample 114.

[0066] Figs. 8 and 9 shows the outline bounding box 384 displayed overlaid on the images form the optical camera 210. These are "manually" sized by the user selecting the dots on the box 384 with a mouse or touchscreen user interface device 238 to thereby augment the sample model 252-2.

[0066]

[0067] In the dialog portion 310, the user is instructed to rotate the sample to orthogonal views in order to ensure that the sample remains in the outline bounding box 384.

[0067]

[0068] As shown in Fig. 10, for flat / box samples, the dialog portion 310 provides a workflow that step-by-step guides the user first to rotate the sample to the widest view first and adjust the bounding box to identify the sample holder and sample.

[0068]

[0069] As shown in Fig. 11, the collision avoidance app 252 then rotates the sample 114 to 90 degrees away from the widest angle, and the user will adjust the outline bounding boxes 384 to fit the ‘thin’ view.

[0069]

[0070] For Custom shapes, the collision avoidance app 252 allows the user to go to as many angles as needed to properly define the shape. Instructions in the dialog section 310 to first go to the widest view ensures that the widest view is captured, then go to the thinnest view and save.

[0070]

[0071] As shown in Fig. 12, the collision avoidance app 252 enables the user to add views from any angles needed to define the shape accurately enough to define the correct envelope. The more irregular the sample, the more angles are needed.

[0071]

[0072] After shaping the bounding boxes to augment the sample model 252-2, as shown in Fig. 13, the collision avoidance app 252 enables the generation the sample envelope as in the dialog section 310. The model 252-2 knows that the sample is either cylindrical, flat / box, or custom when creating the sample envelope.

[0072]

[0073] As shown in Figs. 14 and 15, the collision avoidance app 252 presents the maximum sample envelope size 386 to the user visually as an overlay in the optical camera pane 318. In addition, the collision avoidance app 252 provides the user with given tools to easily determine if the sample envelope represents the sample accurately, for example allowing automatic repeated sample rotation to assure the sample stays within the maximum envelope size.

[0074] As shown in Figs. 16 and 17, the collision avoidance app 252 here presents a model view pane 388. It shows the sample model envelope at the current system geometries, and the user can move the sample stage and the model envelope will continue to reflect where the sample currently is. The user can rotate or move the sample to ensure that the model correctly matches the sample.

[0073]

[0075] Using the sample envelope, the collision avoidance app 252 calculates the system geometry and objective settings to best image the full sample at all tomography angles, called a Full Field of View (FFOV) or ‘overview image’ as shown in Fig. 18.

[0074]

[0076] As shown in Figs. 19 and 20, the collision avoidance app 252 also allows the user to indicate the height to use as the center of the overview scan using a height annotation, shown here as a circle overlay in the 392 in the optical camera pane 318.

[0075]

[0077] As shown in Figs. 21 and 22, the collision avoidance app 252 automatically moves the system safely and automatically to the overview image settings.

[0076]

[0078] As shown in Figs. 23, 24, and 25, the user can navigate to page and verify that the system geometries and objective type do confirm that the full sample is in the field of view.

[0077]

[0079] While this invention has been particularly shown and described with references 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 encompassed by the appended claims.

Claims

CLAIMSWhat is claimed is:

1. A user interface rendered on a display of a microscopy system including a computer that processes projection data from the microscopy system, the user interface comprising: a camera pane for displaying images of a sample held in the microscopy system taken by a camera; and an overlay allowing a user to size bounding boxes for the sample displayed on the images.

2. The user interface as claimed in claim 1, wherein the sized bounding boxes are used during a rotation of the sample to determine the closest source and detector distances that can be used for specified angle ranges of a tomography.

3. The user interface as claimed in any of claims 1 or 2, further comprising enabling the user to select between ‘common’ sample shapes, including cylindrical / spherical and box / flat samples.

4. The user interface as claimed in any of claims 1-3, implementing a workflow in which the device geometries of the microscopy system are first changed to a known ‘safe’ state in which there is no collision or danger of collision between the sample and the microscopy system by reference to a model of the sample and a model of the microscopy system.

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

6. The user interface as claimed in any of claims 1-5, further presenting a model view.

7. The user interface as claimed in any of claims 1-6, further displaying a workflow that step-by-step guides the user to arrange the sample.

8. An X-ray microscopy system, comprising: an X-ray source subsystem of generating X-rays;an object stage subsystem for holding 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 images from an optical camera and generating a user interface including motion controls for moving the object stage subsystem, a source subsystem, and a detector subsystem, and a camera pane for displaying images of a sample held in the microscopy system taken by the optical camera and an overlay allowing a user to size bounding boxes for the sample displayed on the images.

9. The system as claimed in claim 8, wherein the sized bounding boxes are used by the computer during a rotation of the sample to determine the closest source and detector distances that can be used for specified angle ranges of a tomography.

10. The system as claimed in any of claims 8 or 9, wherein the computer enables the user to select between ‘common’ sample shapes, including cylindrical / spherical and box / flat samples.

11. The system as claimed in any of claims 8-10, implementing a workflow in which the device geometries of the system are first changed to a known ‘safe’ state in which there is no collision or danger of collision between the sample and the microscopy system by reference to a model of the sample and a model of the microscopy system.

12. The system as claimed in any of claims 8-11, wherein the computer further presents a maximum sample envelope size as an overlay.

13. The system as claimed in any of claims 8-12, wherein the computer further provides a model view.

14. The system as claimed in any of claims 8-13, wherein the computer further displays a workflow that step-by-step guides the user to arrange the sample.

Images