Patent ID: 12219286

DETAILED DESCRIPTION

An example of an image scanning apparatus1is shown inFIG.1. This comprises a sample holder6, such as a stage, adapted to hold a sample3contained on a microscope slide. The sample holder6is optically aligned with imaging optics4and a detector array2such as a line scan detector. The imaging optics4and detector array2may together form an integral unit such as a line scan camera.

The sample holder6is adapted to move relative to the detector array2as shown by the horizontal arrows inFIG.1. A light source7, comprising one or more LEDs, is provided so that light from the light source7illuminates the sample3and arrives at the detector array2through the imaging optics4.

A controller5is provided and configured to issue position control signals so as to control the relative movement between the sample holder6and the detector array2. In the present example the sample holder6is moved whilst the remainder of the microscope scanner1, including the detector array2, remains stationary. The detector array2(together with the imaging optics4) may be moved instead as only relative movement between this and the sample3is required. Typically the sample holder6is moved relative to the detector array, perpendicular to the optical axis11of the scanner1, by a drive mechanism (not shown) that may include a motor and tracks. This is because the sample holder6is usually lighter than the camera and thus has a lower inertia.

Coordinate axes are also provided inFIGS.1and4for reference. The ordinate z-axis is aligned with the optical axis11of the microscope scanner1, whereas the abscissa x-axis represents the scan direction (parallel to the horizontal arrow inFIG.1). The surface of the sample3is aligned with the xy plane.

The sample holder6is configured to move along the x-axis during an imaging scan path. The image acquired by the movement of the apparatus across the image scan path forms a swathe. The method finds particular use when implemented using a line scan detector or a ‘line scanner’. Line scan detectors typically comprise a photodetector array in the form of a narrow strip or line of pixels. Alternatively an area scanner, which is essentially a two dimensional line scanner, could be used. The array detector is typically configured to be incrementally moved between locations on the surface target, parallel to the narrow direction of the array (in the event that a line scanner is used) so as to acquire additional scan lines for each location. Once a complete swathe has been obtained the sample holder may be returned to its initial position and laterally offset (in the y-direction) so as to obtain additional swathes such that the target3is fully imaged.

The operation of the image scanning apparatus1in performing a first example method will now be described with reference toFIGS.1and2. With reference to the flow diagram ofFIG.2, the method begins at step100where any set-up and initialisation procedures are performed including positioning the sample3under the imaging optics4so that the scan area of the sample3, which is selected by a user, is just outside the field of view of the detector. The scan starts as the scan area is moved into the field of view of the detector.

Once the image scan has commenced a first image of the sample is captured by the detector array2at step101in response to a position control signal issued by the controller5. The controller5then issues a position control signal to a motor so as to move the sample holder6along an image scan path on a track aligned with the x-axis. In the first example method a stepper motor is used to drive relative movement between the detector array2and the sample3. Stepper motors can be commanded to rotate specified amounts without the need for a feedback sensor. A stepper motor divides a full rotation into a number of equal steps known as the step count. Thus the image capture may be triggered in accordance with this step count; for example to occur every thousand steps. This corresponds to fixed distal intervals on a predetermined target velocity profile or velocity-time trajectory stored on a memory that is accessed by the controller and includes any accelerating, constant velocity and decelerating phases of the sample motion.

Typically the target locations on the image scan path are distally separated from one another by a distance d on the sample approximately equal to the field of view of the detector. The field of view depends on the detector used and the resolution or magnification selected by a user, however it is typically between 0.25 micrometres and 0.2 micrometres for line scan detectors. In the event that an area scanner is used instead, the field of view will typically be between 1 and 5 millimetres. For example, a line scan camera with an optical magnification of 40× would typically use a 10 micrometre pixel size sensor to produce a pixel size of 0.25 micrometres at the sample. The scanning system would then be instructed to capture an image line for every 0.25 micrometres moved.

Once the controller has determined that a threshold number of steps have been reached, it issues a position control signal causing the detector to capture a second image of the sample. Steps101and102are then repeated until the end of the sample is reached i.e. a complete image swathe is formed. The sample holder6is continuously moved during the scan and images are obtained by the line scan detector2whilst the sample3is in motion. For a suitable choice of array detector it is not necessary to stop the movement of the sample3so that an image can be captured. In addition to this movement, the focal height of the system (in the z-direction) may be automatically adjusted during the scan so that the sample3is kept in focus. This focus control may be performed using the controller5and a dedicated drive mechanism.

Once a complete image swathe has been obtained, in the event that a, rectangular scan area, larger than the area by the swathe is selected, the moveable stage6is returned to the initialisation position and laterally offset in the y-direction by a distance equal to the field of view of the detector array2. Steps101and102are then repeated for yet un-imaged areas of the sample to form additional adjacent swathes until the entire desired area of the sample is imaged. This is performed at step103. Non-rectangular scan areas may be desired instead, in which case an appropriate, alternative movement will be made. At step104each image or “image tile” obtained at the plurality of target positions during the imaging scan is combined together so as to form an aggregate image of the sample. This aggregated image of the sample may then be analysed by a system user or technician.

FIG.3illustrates a velocity profile that may be achieved according to a second example method. The second example method of the disclosure broadly matches the first example however a servomotor is used instead of a stepper motor to drive relative movement between the sample holder6and the detector array2.

A velocity profile shows the relationship of the displacement of the sample3(dictated by movement of the sample holder6) with time. The sample holder6is configured to move to a plurality of target positions during an imaging scan. These target positions are shown by the smooth dotted line or ‘target velocity profile’ shown inFIG.3. This target velocity profile may be stored on a memory that is accessed by the controller during the imaging scan so as to drive movement of the sample holder6in accordance with this profile. The actual achieved position of the sample holder6(or sample3) is shown by the continuous line that oscillates about the target velocity profile. In practice this position is not known by the system.

Unlike the prior art methods the present disclosure allows for image capture to occur during the accelerating and decelerating phases of the sample motion. This is shown by the increasing gradient of the solid line inFIG.3. Rather than necessarily being linked to time, image capture may instead be linked to the distance moved by the sample holder6whilst the image capture occurs at a variable frequency dictated by the position control signals.FIG.3illustrates an example in which image capture occurs at distances d1, d2, d3and d4which correspond to times t1, t2, t3and t4respectively. As shown, the distances d1to d4are each approximately equal, whereas the times t1to t4are not. It is further shown that although the motion of the sample3is in accordance with the target velocity profile, in practice due to the limitations of the slide scanner1it can be difficult to exactly match this profile and thus the actual achieved position or velocity profile oscillates about this target. Thus a spatial distortion in the image may still occur due to the sample not being exactly at the target position at the time which the image is captured.

In the second example method (illustrated inFIG.3) the motor used to drive relative motion between the sample holder6and the detector array2is a servomotor. Servomotors allow for precise control of velocity and acceleration and comprise a motor coupled to a sensor for position of velocity which is fed back via a closed loop to the motor. Thus a sensor may monitor either the position or velocity of the sample holder6and continuously feed this information back to the motor in order to adjust the power supplied by the motor so as to match the target profile. This feedback is evident by the oscillation about the target velocity profile.

A second example of a microscope scanner1′ according to the disclosure is illustrated inFIG.4. The features of this example broadly match those of the first example apparatus however the detector is moved instead of the sample holder during the image scan. The apparatus1′ comprises a scan head2′, such as a line scan detector, comprising a photo-detector array and imaging optics4′. A sample holder or platen6′ is provided upon which is positioned a target to be scanned3′. The target is typically a biological tissue sample. The scan head2′ is attached to a track8′ enabling it to be moved with respect to the remainder of the apparatus1′ along the x-axis, as indicated by the arrows9′. Motion of the scan head2′ is driven by a servomotor configured to operate according to a target velocity profile stored in memory.

The track8′ and the scan head2′ are coupled to a linear incremental encoder configured to monitor the position of the scan head2′ relative to the sample holder along a scan path. The track8′ also allows the scan head to be offset in the y-direction for imaging adjacent swathes. The image scanning apparatus1′ is controlled using a controller5′ which may comprise programmable logic, a dedicated processor or a computer system. In this example a light source7′ is situated beneath the platen6′ such that light may pass through the sample3′, along the optical axis11′ of the detector array. The light source7′ is connected to the controller5′ and the intensity of the light output may be controlled by the controller5′.

A third example of a method for performing the disclosure will now be discussed primarily with reference toFIG.5which illustrates a flow diagram for performing the method and with reference to the apparatus shown inFIG.4and with reference toFIGS.6and7. The start-up initialisation procedures are performed at step200before the imaging scan commences. At step201the imaging scan begins and the first image of the sample3′ is captured by the scan head2′. At step201the position of the scan head2′ in the x-axis along the image scan path is measured using a linear encoder (not shown) coupled to the track8′ for allowing movement along the image scan path (in the x-direction). Alternatively, a rotary encoder coupled to the motor may be used. This monitored position is recorded by the controller5′ and stored in a memory referenced with the respective image for that position. At step202the servomotor (not shown) is instructed by the controller5′ to move the scan head2′ by distance d along the image scan path. At this point, steps201to203are repeated until the end of the sample3′ is reached for that image swathe; again with the position of the sample holder relative to the optical axis11of the scan head2′ being monitored for each image. The scan head2′ is then moved back to its starting position at step200and a lateral offset in the y-direction is made for the scan head2′ (or alternatively, the sample holder6′). Steps201to203are repeated for adjacent image swathes until the desired surface area of the sample3′ is imaged by the scanner1′.

Due to positional errors that can result from the impact of external vibration on the system1or limitations in the equipment used, the images obtained at the plurality of target locations from the imaging scan may not actually each be at exactly equal spaced distal intervals on the sample3′. These discrepancies are illustrated byFIG.3. Where this occurs, an irregular image grid of spatial distortions may be produced by aggregating the images. At step205a controller maps the irregular image grid the imaging scan onto a regular image grid for images obtained at exactly or substantially equal distances along the image scan path. This is done using an interpolation technique within the controller by one or more processors using software stored in memory.

Step205is further illustrated byFIG.6which shows an example of an irregular and a regular image grid in one dimension. The ‘measured values’ displayed on the top graph show image data acquired by the imaging scan at each measured position, whilst the ‘interpolated values’ shown below display the result of the interpolation performed at step205.

As shown, the mapping is performed using the monitored positional information recorded for each image during the scan and uses an interpolation technique. There are various interpolation techniques that may be used and which are known in the art. A discussion and comparison of various interpolation techniques that are utilised with a contouring and 3D surface mapping program known as Surfer™, is provided in Yang, Kao, Lee and Hung,Twelve Different Interpolation Methods: A Case Study of Surfer8.0Proceedings of the XXth ISPRS Congress,2004, 778-785. Most of these techniques can be simplified for this application as the data is only irregularly spaced in one axis (along the image scan path). In addition to this, the spacing can be assumed to be regular over a small number of images. InFIG.6the interpolation technique used is cubic interpolation with sample points being taken from the four nearest neighbours.

FIG.7illustrates a flow diagram of fourth example method wherein a sample is moved relative to a camera during an imaging scan and interpolation is used to correct for spatial distortions in the aggregate image. The sample is imaged as before with images being acquired by the camera based on position control signals but with varied actual distances between each image being obtained due to inherent limitations of the apparatus. A position sensor monitors the position of the moving sample during the scan and outputs this data to a controller (not shown). The position data for each image is used in combination with the image data and positional discrepancies between the target position and the actual positions are corrected for so as to interpolate data for a regular image grid. The regular aggregate image grid is then output for analysis.

Interpolation, when applied in this context, provides a number of associated advantages over the prior art. First, any errors in the sampling position are corrected during the interpolation process. There is thus a tolerance to velocity based errors that may arise from the limitations in the equipment used. Second, the scanner1′ has an increased tolerance to external vibration. Errors in the sampling position are corrected for through interpolation thus increasing the reliability of the system and the images obtained from it. Third, similar to the first example image capture can begin before the slide has reached a constant velocity; enabling the scan to ultimately be performed over a shorter timescale.

The relative position of the sample holder and detector could be monitored and any errors in the position corrected for after the scan has occurred through interpolation using prior art scanners for which image capture is triggered by a timing source rather than a demand position. However the combination of these features and triggering image capture by position control signals provides an ultimately improved method for digitising microscope samples. The position of the image capture may be more closely controlled and any discrepancies between the demand position and its actual position or any discrepancies that result from external vibration may be later corrected for through interpolation. The continuity of the aggregate image obtained as a result is thus greatly improved.

In the present disclosure, the verb “may” is used to designate optionality/noncompulsoriness. In other words, something that “may” can, but need not. In the present disclosure, the verb “comprise” may be understood in the sense of including. Accordingly, the verb “comprise” does not exclude the presence of other elements/actions. In the present disclosure, relational terms such as “first,” “second,” “top,” “bottom” and the like may be used solely to distinguish one entity or action from another entity or action without necessarily requiring or implying any actual such relationship or order between such entities or actions.

In the present disclosure, the term “any” may be understood as designating any number of the respective elements, e.g. as designating one, at least one, at least two, each or all of the respective elements. Similarly, the term “any” may be understood as designating any collection(s) of the respective elements, e.g. as designating one or more collections of the respective elements, a collection comprising one, at least one, at least two, each or all of the respective elements. The respective collections need not comprise the same number of elements.

In the present disclosure, the expression “at least one” is used to designate any (integer) number or range of (integer) numbers (that is technically reasonable in the given context). As such, the expression “at least one” may, inter alia, be understood as one, two, three, four, five, ten, fifteen, twenty or one hundred. Similarly, the expression “at least one” may, inter alia, be understood as “one or more,” “two or more” or “five or more.”

In the present disclosure, expressions in parentheses may be understood as being optional. As used in the present disclosure, quotation marks may emphasize that the expression in quotation marks may also be understood in a figurative sense. As used in the present disclosure, quotation marks may identify a particular expression under discussion.

In the present disclosure, many features are described as being optional, e.g. through the use of the verb “may” or the use of parentheses. For the sake of brevity and legibility, the present disclosure does not explicitly recite each and every permutation that may be obtained by choosing from the set of optional features. However, the present disclosure is to be interpreted as explicitly disclosing all such permutations. For example, a system described as having three optional features may be embodied in seven different ways, namely with just one of the three possible features, with any two of the three possible features or with all three of the three possible features.

Further, in describing representative embodiments of the subject disclosure, the specification may have presented the method and/or process of the present invention as a particular sequence of steps. However, to the extent that the method or process does not rely on the particular order of steps set forth herein, the method or process should not be limited to the particular sequence of steps described. As one of ordinary skill in the art would appreciate, other sequences of steps may be possible. Therefore, the particular order of the steps set forth in the specification should not be construed as limitations on the claims. In addition, the claims directed to the method and/or process of the subject disclosure should not be limited to the performance of their steps in the order written, and one skilled in the art can readily appreciate that the sequences may be varied and still remain within the spirit and scope of the subject disclosure.