Patent Description:
Microtomes or microtome systems can be used for cutting sections from a specimen like a biological or histological sample. Such microtome systems typically comprise a knife and a sample, which are guided relative to and along each other in order to cut thin slices from the sample. In order to generate even cuts or slices, the knife typically has to be aligned with the specimen or a specimen holder.

Document <CIT> relates to operation of a microtome, in which a knife edge that is turnable around its longitudinal axis is used to cut sections from a specimen by making the specimen pass the knife edge downwards, for facilitating that the distance between the knife edge and the specimen before cutting can be made extremely narrow without the specimen touching the knife, and in which a slit is lit up from below by a light waveguide one end of which is located under the knife edge and is turned with the knife and the other end of which is lit up by a light source movable in relation to the turning of the knife edge.

Document <CIT> describes a microtome that includes a blade located at an end of a trough that defines a cavity for holding a liquid, a sample block in which the at least one sample is suspended, wherein the sample block is moveable relative to the blade such that when the sample block is passed across the blade a section is cut from the sample block. Further, the microtome comprises a plate that includes a support frame defining an opening, a transparent film extending across the opening, the transparent film being transparent to electrons, and a grasper being configured to receive and retain the plate, wherein the grasper is moveable relative to the blade.

Document <CIT> describes a preparation holding device of a microtome that can be pivoted via a ball head. To pivot the preparation holding device, actuators are assigned to the latter as drives. A camera and laser diodes are arranged on the knife carrier of the microtome to detect the shape and positions of the preparation.

Document <CIT> describes a microtome, which comprises a knife and a specimen arm movable relative to the knife. At least one light source with at least one light-emitting diode for illuminating a region around the preparation is also provided.

Document <CIT> relates to a microtome for preparing a specimen, wherein an initial position of a sample and a knife for cutting a sample tube is automatically determined.

In view of the situation described above, there is a need for improvement in microtome systems. According to embodiments of the invention, a microtome system, a method and a computer program with the features of the independent claims are proposed. Advantageous further developments form the subject matter of the dependent claims and of the subsequent description.

An embodiment of the invention relates to a microtome system for cutting sections from a specimen. For example, such microtome system can comprise an ultra-microtome (microtome for cutting very thin or ultra-thin slices from a specimen). The microtome system comprises: a knife having a knife edge configured to cut a section from the specimen, a knife holder holding said knife, a specimen holder configured to hold the specimen, an illumination (or light source), a first actor, a detector, and a controller. The knife holder and the specimen holder are configured to be moveable relative to one preferably, configured to be moveable relative to one another in one or more further directions like a feed direction, as will be explained later. The knife holder or the specimen holder is mounted rotatably about a first axis. Particularly, the cutting direction is parallel to the first axis. Preferably, each of the knife holder and the specimen holder can be mounted to be rotatably about one or more axes, as will be described later. The first actor is configured to cause a rotation of the knife holder or specimen holder (whichever is rotatable about the first axis) about the first axis.

The illumination is configured to illuminate a gap between a front face of the specimen when held by the specimen holder and the knife edge. In this way, a light gap is generated; the measures of the light gap might be different from those of the gap, depending on the way of how the light is reflected between knife and front face (this will be explained in more detail later). The detector is configured to detect at least one geometric feature of the light gap. Such geometric feature can comprise, for example, a length, a width or a parallelism of the light gap or borders of it, or a variability as will be described in more detail later. The controller is configured to a) automatically align the knife edge with the front face of the specimen by controlling the first actor depending on the detected at least one geometric feature of the light gap and/or b) provide indications (e.g., guiding lines) to a user depending on the detected at least one geometric feature of the light gap on how to manually control the first actor in order to align the knife edge with the front face of the specimen.

As mentioned above, the knife or the knife edge of a microtome system and the specimen (or specimen holder) have to be aligned in order to generate even and good cuts or slices from the specimen. In general, such aligning can be performed manually; for example, the light gap mentioned can be monitored visually by the user during adjustment operations like turning different knobs or hand wheels for rotating the knife or the specimen holder. Such manual adjustment, however, requires sufficient experience of the user. With wrong settings, the knife, which often comprise diamond, might be damaged, for example. Also, the sample might be damaged.

The inventors have recognized that using at least one geometric feature of the light gap detected by a detector can be used to automate the aligning procedure. Such automation can include fully automatic aligning for example, as described for alternative a), and it can also include partial automatic aligning by automatically providing helpful indications or instructions to the user, as described for alternative b). Depending on the alternative used, the first actor can be motorized and/or manually operated. The detected least one geometric feature can be analysed, for example, by means of image or video processing. Such automation also allows unexperienced users to easily and efficiently align the knife or knife edge of the microtome system with the sample. Wrong settings, which might lead to damages, can be avoided or, at least, be reduced.

According to the invention, the controller is configured to control the first actor for arranging the knife edge parallel to the front face of the specimen such that the at least one geometric feature of the detected light gap comprises a constant width along a light gap length. This allows setting the knife edge being parallel to the front face of the specimen.

According to a further embodiment of the invention, the microtome system further comprises a second actor, and the knife holder or the specimen holder is mounted rotatably about a second axis. This can, preferably, correspond to a tilt of the sample holder relative to the knife holder. The second actor is configured to cause a rotation of the knife holder or specimen holder about the second axis, and the controller is configured to control the second actor such that the front face of the specimen is arranged parallel to the cutting direction. In particular, this can be done such that the at least one geometric feature of the detected light gap comprises a dimension that remains constant during relative movement in the cutting direction between the knife edge and the specimen when held by the specimen holder. This allows setting the knife and specimen holder for generating slices having equal thickness along the cutting direction.

According to a further embodiment of the invention, the microtome system further comprises a third actor. The knife holder or the specimen holder is mounted rotatably about a third axis, wherein a feed direction of the specimen holder with respect to the knife holder is parallel to the third axis. The third actor is configured to cause a rotation of the knife holder or specimen holder about the third axis, and the controller is configured to control the third actor such that the upper edge and/or the lower edge of the front face of the specimen is arranged parallel to the knife edge. In particular, this can be done such that, during relative movement in the cutting direction between the knife edge and the specimen when held by the specimen holder, the at least one geometric feature of the detected light gap comprises a dimension that remains constant along the length of the light gap over a predetermined upper region up to the upper edge of the front face of the specimen and then decreases evenly along the length of the light gap and/or over a predetermined lower region down to the lower edge of the front face of the specimen and then decreases evenly along the length of the light gap. This allows setting the knife and specimen holder for cutting to start at the entire edge of the front face at the same time, for example.

According to a further embodiment of the invention, the detector comprises a digital camera configured to image the light gap, i.e., to acquire an image of the light gap. In particular, such image of the light gap comprises the adjacent knife edge and/or at least a part of the front face of the specimen opposed to the knife edge. In this way, the borders or edges of the light gap required for image analysis, for example, can be analysed sufficiently.

According to a further embodiment of the invention, a value of the at least one geometric feature of the light gap is detected by the camera based on a plurality of images acquired at the same relative positions between the knife holder and the sample holder. For example, the intensities of the plurality of images (or of each of the pixels of the images) can be averaged. In this way, the precision of the detected geometric feature can be improved. In particular, a precision that is higher than the actual resolution of the camera provides, can be achieved in this way. Noise in such images can even be of advantage in this case. Note that this way of how to determine a value of the at least one geometric feature can be applied to each of the geometric features mentioned (and for each of the rotations mentioned).

According to a further embodiment of the invention, the detector is configured to detect a plurality of values for the at least one geometric feature of the light gap for a plurality of different relative positions between the sample holder and knife holder. The controller is configured to, based on the plurality of values of the detected features, a) automatically align the knife edge with the front face of the specimen, and/or b) provide the indications to the user. For example, the values for each of the relative positions can be interpolated. In this way, also a value between two detected values (from the interpolation) can be acquired. In this way, a precision that is higher than the actual resolution of the camera provides, can be achieved in this way. Note that this way of how to determine a value of the at least one geometric feature can be applied to each of the geometric features mentioned (and for each of the rotations mentioned).

Another embodiment of the invention relates to a method for aligning a knife edge of a knife with a front face of a specimen for cutting sections from the specimen. The knife is held by a knife holder, and the specimen is held by a specimen holder. The knife holder or the specimen holder is mounted rotatably about a first axis, and a first actor is configured to cause a rotation of the knife holder or specimen holder about the first axis. Said method comprises: illuminating, by a light source, a gap between a front face of the specimen and the knife edge, in order to generate a light gap; detecting, by a detector, at least one geometric feature of the light gap, and a) automatically aligning the knife edge with the front face of the specimen by controlling, with a controller, the first actor depending on the detected at least one geometric feature of the light gap, and/or b) providing, by a controller, instructions to a user depending on the detected at least one geometric feature of the light gap on how to manually control the first actor in order to align the knife edge with the front face of the specimen. The method is characterised in that the controller is configured to control the first actor for arranging the knife edge parallel to the front face of the specimen such that the at least one geometric feature of the detected light gap comprises a constant width along a light gap length.

Another embodiment of the invention relates a computer program according to claim <NUM>.

With respect to advantages and further embodiments of the method and the computer program, it is referred to the above description of embodiments of the microtome system and its features and advantages, which apply here correspondingly.

Further advantages and embodiments of the invention will become apparent from the description and the appended figures.

It should be noted that the previously mentioned features and the features to be further described in the following are usable not only in the respectively indicated combination, but also in further combinations or taken alone, without departing from the scope of the present invention as defined in the appended claims.

<FIG> schematically illustrates a microtome system <NUM> according to an embodiment of the invention, in a perspective view. The microtome system <NUM> is, preferably, an ultra-microtome system or comprises an ultra-microtome. The microtome system <NUM> comprises a knife holder <NUM> and a specimen holder <NUM>. Note that a typical microtome comprises further components like a housing and the like, which are not shown in <FIG> for illustration purposes.

The knife holder <NUM> holds a knife <NUM>; the knife <NUM> has a knife edge <NUM> at the top right of the knife <NUM>. In addition, a reception box <NUM> can be arranged at or on the knife <NUM>, for example. The specimen holder <NUM> is configured to hold a specimen <NUM>. For example, such specimen <NUM> can have the form of a block, which can be mounted into the specimen holder <NUM> such that a front face <NUM> of the specimen <NUM> is oriented towards the knife <NUM>.

The operating mechanism of such microtome system <NUM> is, in general, that the specimen <NUM> is moved along a cutting direction c relative to the knife edged <NUM> when the specimen is properly aligned with the knife edge. The knife edge <NUM> is configured to cut a section (or slice) from the specimen <NUM>. A section that has been cut off the specimen <NUM> can be collected in the collection box <NUM>, for example. In order to provide such movement, the knife holder <NUM> and the specimen holder <NUM> are configured to be moveable relative to one another in the cutting direction c. Basically, either or both of the knife holder <NUM> and the specimen holder <NUM> can be configured to be movable along cutting direction c. In an embodiment, (only) specimen holder <NUM> is configured to be movable in cutting direction c (in both ways, up and down). In addition, the knife holder <NUM> and the specimen holder <NUM> can be configured to be movable relative to one another in feed direction b, in order to bring the knife edge <NUM> in contact with the specimen <NUM> and, in particular, to feed the specimen <NUM> after a section or slice has been cut from the specimen <NUM>.

In an embodiment, the knife holder <NUM> and, thus, the knife <NUM>, is configured to be movable in the feed direction b, i.e., towards (and also away from) the specimen <NUM> or the specimen holder <NUM>. Basically, however, also the specimen holder <NUM> might be configured to be movable in (or against) the feed direction b towards the knife <NUM>.

As mentioned earlier, in order to generate proper and precise sections cut from the specimen, the knife <NUM> or knife edge <NUM> and the specimen <NUM> or specimen holder <NUM> have to be aligned prior to cutting.

This can require that the knife holder <NUM> or the specimen holder <NUM> is to be mounted rotatably about at least one axis. In <FIG>, four axes are shown for illustration purposes: a first axis z', a second axis x, a third axis y, and a further axis z. Rotating the knife holder <NUM> and/or the specimen holder <NUM> around one or more of these axis allows aligning the knife edge <NUM> with the front face <NUM> of the specimen <NUM> as will be described in more detail later.

As can be seen from <FIG>, in general, the specimen holder <NUM> might be configured to be rotatable around each of three different axes x, y, and z, for example. Similarly, the knife holder <NUM> might be configured to be rotatable around each of three different axes, for example, from which only axis z' is shown (similar, axes x' and y' might be used). Note that the axes shown are oriented according to a Cartesian coordinate system, as is typical for such microtome systems; however, this is for illustration purposes only and other ways of defining such axes are possible. Rotating the knife holder <NUM> and the specimen holder <NUM> around three different axes each, allows many degrees of freedom for aligning the knife edge <NUM> and the specimen front face <NUM>. Nevertheless, three different axes in total for both, the knife holder <NUM> and the specimen holder <NUM> can be sufficient for providing alignment in sufficiently many ways.

In an embodiment, the knife holder <NUM> is mounted rotatably around the first axis z', wherein the first axis z' is parallel to the cutting direction c. The specimen holder <NUM> is mounted rotatably around the second axis x and the third axis y. The third axis y is parallel to the feed direction b. As can be seen from <FIG>, an equivalent to the knife holder <NUM> being mounted rotatably around the first axis z', would be the specimen holder <NUM> being mounted rotatably around the axis z. In both alternatives, the knife edge <NUM> can be rotated relative to the specimen <NUM> or its front face <NUM> in the same or an equivalent way. Similarly, the knife holder <NUM> might be rotatable around further axis x' and/or y '(not shown in <FIG>), which would be equivalent to the specimen holder being rotatable around axis x and/or y. Which component of knife holder and specimen holder is to be rotatable around which axes might be chosen depending on a preferred way of implementation in the specific microtome system.

Further, it is noted that, basically, only one or two axes around which one of knife holder and specimen holder are rotatable, can be sufficient to align the knife edge <NUM> and the specimen front face <NUM>. Note that actors can be provided to the knife holder <NUM> and/or specimen holder <NUM> in order to facilitate the required rotation around the respective axis. This will be described later.

<FIG> schematically illustrates a microtome system <NUM> according to a further embodiment of the invention. Microtome system <NUM> basically corresponds to microtome system <NUM> of <FIG>. In contrast to <FIG>, the microtome system is shown in a sectional view and rotated (positions of knife holder and specimen holder are exchanged). The axes and directions shown in <FIG> correspond to the ones shown in <FIG>. Note that some components of microtome <NUM> of <FIG> are not shown in <FIG>, some are shown (with identical reference numerals) and some further components are shown.

In particular, the microtome system <NUM> comprises, besides the knife holder <NUM> with knife <NUM> and the specimen holder <NUM> with specimen <NUM>, an illumination <NUM>, a detector <NUM>, and a controller <NUM>. The illumination <NUM> comprises, in an embodiment, a LED or other light source <NUM> and a diffusion element or filter <NUM> in order to provide even illumination by means of the light source <NUM>. In an embodiment, the detector <NUM> can comprise a camera.

The illumination <NUM> is arranged such that a light beam <NUM>, which is emitted from the illumination <NUM> (or the light source <NUM>), is directed to the region where the front face <NUM> of the specimen <NUM> and the knife edge <NUM> are arranged. Light passing the gap <NUM> between the front face <NUM> of the specimen <NUM> and the knife edge <NUM> reaches the detector <NUM>. In this way, a light gap <NUM> is produced, which is or can be detected by the detector <NUM>. Depending on the current alignment or arrangement of the knife <NUM> and the specimen <NUM>, the light of the light beam <NUM> might be reflected on a side surface <NUM> of the knife <NUM> and/or on the front face <NUM> of the specimen <NUM>.

<FIG> illustrates a way of how the light gap <NUM> can be produced, in an embodiment, in more detail. Some components from <FIG> are illustrated enlarged in <FIG>. Light emitted from the light source <NUM> and passing the diffusion element <NUM> is reflected at the side surface <NUM> of the knife <NUM> and then at the front face <NUM> of the specimen <NUM>. Light of the light beam <NUM> then reaches the detector <NUM>. Thus, the detector detects, as a border of the light gap <NUM>, a mirrored knife edge <NUM>' of a mirrored knife <NUM>', which is generated by the knife edge <NUM> and the knife <NUM> mirroring in the front face <NUM>. A width W of the light gap <NUM> is, thus, formed by the distance of the knife edge <NUM> and the mirrored knife edge <NUM>'. The width W is approximately twice of the width d of the actual gap <NUM> between the front face <NUM> and the knife edge <NUM>, depending on an angle of the slight inclination of light beam <NUM> between the front face <NUM> and the detector <NUM>.

It is noted that light passing the gap <NUM> without reflection at either the side surface <NUM> or the front face <NUM> will not contribute to the light gap to be detected in this example.

The controller <NUM> can be electrically and/or communicatively coupled to the detector <NUM> in order to receive data or information detected or acquired by the detector <NUM>. In an embodiment, the controller <NUM> can also be electrically and/or communicatively coupled to the illumination <NUM>.

In an embodiment, the microtome system <NUM> further comprises a first actor <NUM>, a second actor <NUM>, and a third actor <NUM>. Note that, if only one or two axes are used about which the knife holder <NUM> and/or the specimen holder <NUM> are rotatably mounted, one or two actors would be sufficient.

The first actor <NUM> is configured to cause a rotation of the knife holder <NUM> about the first axis z'. Note that in <FIG>, the knife holder <NUM> is not shown, however, it is clear from <FIG> and <FIG> that a rotation of the knife holder results in a corresponding rotation of the knife <NUM> around axis z'. The second actor <NUM> is configured to cause a rotation of the specimen holder <NUM> about the second axis x; such rotation corresponds to a tilt of the specimen holder <NUM> and, thus, of the specimen <NUM>. The third actor <NUM> is configured to cause a rotation of the specimen holder <NUM> about the third axis y. Each of the first, second and third actor <NUM>, <NUM>, <NUM> can be motorized. The controller <NUM> can be electrically and/or communicatively coupled to each of the first, second and third actor <NUM>, <NUM>, <NUM> in order to operate them and, thus, to cause the mentioned rotation about the respective axis.

In an embodiment, one or two of the first, second and third actor <NUM>, <NUM>, <NUM> can also be un-motorized but be configured to be actuated or operated manually, for example, like a hand wheel, in order to cause the mentioned rotation. Also, one or more of the first, second and third actor <NUM>, <NUM>, <NUM> can be motorized but configured for manual operation, for example, such that a user has to actuate an operating element like a switch in order to actuate the actuator.

In an embodiment, the microtome system <NUM> comprises a hand wheel or actuation wheel <NUM>. The hand wheel <NUM> is configured (particularly, by means of a mechanism not shown here) to cause a cutting movement such that the specimen holder <NUM> moves in the cutting direction c, up and down, in order to cut sections from the specimen. The hand wheel <NUM> can also be configured to cause a feed movement (of the knife holder <NUM>, for example) in the feed direction b. Both movements, cutting movement and feed movement, can be coupled such that efficient cutting of several slices is possible. The hand wheel <NUM> can be motorized and/or configured for manual operation. In case the hand wheel is motorized, an automated cutting movement is possible, such that the hand wheel might be used only for additional and/or correctional movements.

In addition, a side movement in a direction of second axis x might be possible in order to move the specimen, after a section or slice has been cut, in order to cut another section or slice next to the first one. The hand wheel <NUM> can also be configured to provide such side movement. Also, such side movement could be implemented in another way, for example by an additional (motorized) hand wheel.

<FIG> schematically illustrates a microtome system <NUM> according to a further embodiment of the invention. Microtome system <NUM> basically corresponds to microtome system <NUM> of <FIG> and microtome system <NUM> of <FIG>, <FIG>. In addition to <FIG> and <FIG>, <FIG>, a housing <NUM> of the microtome system <NUM> is shown, in which housing <NUM> the required components are arranged. It is noted that some components of microtome <NUM> of <FIG> and of microtome system <NUM> of <FIG>, <FIG>. are not shown in <FIG>, some are shown (with identical reference numerals) and some further components are shown.

Microtome system <NUM> further comprises, in an embodiment, a microscope <NUM>, which is arranged at the housing <NUM> and is configured such that a user can look at (and inspect) the region of the specimen <NUM> and the knife <NUM> (with knife edge <NUM>, not shown in <FIG>). For example, a user might inspect the cutting movement and/or the quality of the knife edge <NUM>, in this way. The light gap, generated by the illumination <NUM> by illuminating the (physical) gap between the specimen <NUM> (or its front face <NUM>) and the knife <NUM> (or its knife edge <NUM>) is detected by the detector <NUM>. This might require appropriate arrangement and/or orientation of the detector <NUM>.

Also, the microscope <NUM> might be arranged and/or oriented such that this light gap is visible by means of the microscope <NUM>. Further, the microscope <NUM> does not need to be an optical microscope but can use the detector <NUM> in order to provide an image of the region on an integrated display. In an embodiment, the detector <NUM> can also be integrated into the microscope <NUM>.

Microtome system <NUM> further comprises, in an embodiment, a display <NUM>, on which information about the cutting process and/or indications <NUM> for the alignment of the knife edge <NUM> with the front face <NUM> of the specimen <NUM> can be displayed to the user. In an embodiment, the microtome system <NUM> is also configured to render a user interface or graphical user interface, in particular, by using the display <NUM>. In addition, input devices like switches, buttons, a keyboard and a computer mouse might be used. Also, display <NUM> can comprise a touch screen.

<FIG>, <FIG> illustrate the light gap <NUM> and the respective relative positions of front face <NUM> and knife edge <NUM> for explanation of embodiments of the invention. In addition, first axis z', second axis x and third axis y as well as cutting direction c are shown in these Figs. The orientations of these axes and direction are in accordance with the previous Figs.

In <FIG>, the light gap <NUM> is illustrated in a top view like it is seen by the microscope <NUM> of <FIG> for example, or from detector <NUM>, for example. This view is approximately along the cutting direction c, in particular along light beam <NUM> as illustrated in <FIG>, <FIG>. As mentioned, the light beam <NUM> can be slightly inclined versus the cutting direction c. The light gap <NUM>, in an embodiment, has a length or light gap length L. The length L is, for example, defined along the knife edge <NUM>. The length L, typically, corresponds to the length of the front face <NUM> in this direction. In addition, the light gap has a width W. The width W, for example, corresponds to the distance of the knife edge <NUM> from the mirrored knife edge <NUM>' (i.e., the reflection of knife edge <NUM> at the front face <NUM>) as illustrated in <FIG>. As mentioned for <FIG>, the width W is approximately twice the distance d between the knife edge <NUM> and the front face <NUM>. It is noted that the mirrored knife edge <NUM>' appears at the front face <NUM>.

In order to cut sections or slices from the specimen <NUM>, which are of constant or even thickness, the knife edge <NUM> shall be aligned with the front face <NUM> such that the knife edge <NUM> is parallel to the front face <NUM>. As can be seen from <FIG>, the knife edge <NUM> being parallel to the front face <NUM> corresponds to or results in the width W having the same or a constant value along the entire length L. If a value of the width W was smaller, for example, on the left end of length L (in <FIG>) than on the right end of length L, knife edge <NUM> would not be parallel to the front face <NUM>.

In that a geometric feature like the width W along the length L is detected with the detector and analyzed, this allows for aligning the knife edged <NUM> with the front face <NUM>. The first actor can be controlled so as to rotate the knife holder and, thus, the knife <NUM> and the knife edge <NUM>, around the first axis z' until the width W detected is constant along the length L. From <FIG> it is clear that rotation the knife edge <NUM> about the first axis z' results in changing the width W at every position along the length L.

It is noted that this constant width W along the length L is one of the geometric features of the detected light gap <NUM>, which is used to align the knife edge <NUM> with the front face <NUM>. Another possible geometric feature might be an angle between the long edges <NUM>, <NUM> of the light gap <NUM>, i.e., the edge <NUM> at or corresponding to the knife edge <NUM> and the edge <NUM> corresponding to the mirrored knife edge <NUM>'. As mentioned, the mirrored knife edge <NUM>' and, thus, the edge <NUM> appear on the front face <NUM>. If such an angle is zero, these two edges are parallel. Consequently, the knife edge <NUM> and the front face <NUM> are parallel to each other. Another possible geometric feature might be a variability of the width W; such variability should then be zero, i.e., the width should not vary after final alignment.

While in an embodiment, such aligning can be performed automatically, in another embodiment, indications might be generated from the geometric feature and provided to the user, for example, on the display shown in <FIG>. If a value of the width W was smaller, for example, on the left end of length L (in <FIG>) than on the right end of length L, such indication might include the instruction for the user to operate the first actor such that the knife holder <NUM> (and, thus, the knife <NUM> and the knife edge <NUM>) is rotated about the first axis z' in a certain direction (clockwise, for example). In addition, such instruction could include a measure of how much or how far the knife holder has to be rotated about the first axis z'.

In an embodiment, the cutting process can include cutting sections or slices from the specimen <NUM> with different positions of the specimen <NUM> relative to the knife in a side direction by moving the knife <NUM> in a direction parallel to the third axis x by a certain amount after each or after a certain number of cuts. For every new or new certain number of sections to be cut, the knife <NUM> can then be moved in such side movement along the direction of axis x by a certain distance (e.g., <NUM> or the like).

In this case, it is of advantage if the knife <NUM> is aligned such that the width W is constant over the entire length M of the knife edge <NUM> but not only along the length of the front face <NUM>, which corresponds to the length L of the light gap. It is noted that, in practice, the entire length M of the knife edge <NUM> is a multiple of the length of the front face <NUM> or the length L (other than in the example of <FIG>). This might require moving the knife along the direction of axis x in order to acquire values for the width W at the required positions.

In <FIG>, the light gap <NUM> is illustrated in a side view like along axis x. There are two different situations shown, one on the left side and one on the right side. Both situations can correspond to a view along A-A as indicated in <FIG>. In both situations, the specimen <NUM> and the knife <NUM> with knife edge <NUM> are shown. An upper edge <NUM> and a lower edge <NUM> of the front face <NUM> of the specimen <NUM> are indicated.

On the left side, the relative position between the specimen <NUM> and the knife <NUM> (and, thus, between the specimen holder <NUM> and the knife holder <NUM>) is such that almost the entire front face <NUM> is located above the knife edge <NUM>, viewed in the cutting direction c.

The width W of the light gap <NUM> is indicated, in addition to the distance d of the (physical) gap (see <FIG> for how the width W can be determined). On the right side, the relative position between the specimen <NUM> and the knife <NUM> (and, thus, between the specimen holder <NUM> and the knife holder <NUM>) is such that almost the entire front face <NUM> is located below the knife edge <NUM>, viewed in the cutting direction c. The width W of the light gap and the distance d of the (physical) gap are indicated again.

In order to cut sections or slices from the specimen <NUM>, which are of constant or even thickness, the knife edge <NUM> shall be aligned with the front face <NUM> such that the front face <NUM> of the specimen <NUM> is arranged parallel to the cutting direction c. As can be seen from <FIG>, the front face <NUM> being parallel to the cutting direction c corresponds to or results in the width W having the same or a constant value during relative movement in the cutting direction c between the knife edge <NUM> and the specimen <NUM> when held by the specimen holder <NUM>. This corresponds to the width W having the same or a constant value for different relative positions between the knife edge <NUM> and the specimen <NUM> along the cutting direction c. Two of these different positions are illustrated with the two situations in <FIG>. Note that this also results in the distance d having the same or a constant value during relative movement in the cutting direction c between the knife edge <NUM> and the specimen <NUM> when held by the specimen holder <NUM>.

Such relative movement in the cutting direction c between the knife edge <NUM> and the specimen <NUM> when held by the specimen holder <NUM> and, thus, different relative positions at which a value for the width W can be detected or acquired, can be achieved by means of operating the hand wheel <NUM> mentioned above, for example. This might be manually or automatically, for example.

If a value of the width W was smaller, for example, near the lower edge <NUM> (see left side of <FIG>) than near the upper edge <NUM> (see right side of <FIG>), the front face <NUM> would not be parallel to the cutting direction c. In that a geometric feature like the width W during relative movement in the cutting direction c between the knife edge <NUM> and the specimen <NUM> when held by the specimen holder <NUM> is detected with the detector and analyzed, this allows for aligning the front face <NUM> to be parallel with the cutting direction c. This corresponds to the width W having the same or a constant value for different relative positions between the knife edge <NUM> and the specimen <NUM> along the cutting direction c.

The second actor can be controlled so as to rotate the specimen holder <NUM> and, thus, the specimen <NUM> with its front face <NUM>, around the second axis x until the width W detected is constant for different relative positions along the cutting direction c. From <FIG> it is clear that rotation of the specimen holder <NUM> (and, thus, of the front face <NUM>) about the second axis x results in changing the width W at every relative position between the front face <NUM> and the knife edge <NUM> along the cutting direction.

It is noted that this constant width W during relative movement in the cutting direction c is an example for a geometric feature of the detected light gap <NUM>, which can be used to align the front face <NUM> to be parallel with the cutting direction c. Another possible geometric feature might be a variability of the width W; such variability should then be zero, i.e., the width should not vary after final alignment.

While in an embodiment, such aligning can be performed automatically, in another embodiment, indications might be generated from the geometric feature and provided to the user, for example, on the display shown in <FIG>. If a value of the width W was smaller, for example, in the situation shown on the left side of <FIG> than in the situation shown on the right side, such indication might include the instruction for the user to operate the second actor such that the specimen holder <NUM> (and, thus, the specimen <NUM> and its front face <NUM>) is rotated about the second axis x in a certain direction (clockwise, for example). In addition, such instruction could include a measure of how much or how far the specimen holder has to be rotated about the second axis x.

It is noted that, typically, it does not matter where along the light gap length L (see <FIG>) the values for the width W for different relative positions between the front face <NUM> and the knife edge <NUM> are acquired. In particular, if the previous aligning step, described with respect to <FIG>, the rotation about the first axis z', has been made, the values for the width W for a certain relative position are equal along the length L anyway.

In <FIG>, the light gap <NUM> is illustrated in a side view like along axis x. There are two different relative positions between the upper edge <NUM> of the front face <NUM> and the knife edge <NUM> shown, one on the left side and one on the right side.

On the left side, the relative position between the specimen <NUM> and the knife edge <NUM> is such that the upper edge <NUM> is located above the knife edge <NUM>, viewed in the cutting direction c. On the right side, the relative position between the specimen <NUM> and the knife edge <NUM> is such that the upper edge <NUM> is located approximately at or slightly below the knife edge <NUM>, viewed in the cutting direction c.

The light gap as detected by the detector is visible as such (with the form of a slit or rectangle with sharp edges) only if the entire upper edge <NUM> of the front face <NUM> is located sufficiently above the knife edge <NUM>, viewed in cutting direction c. This situation is illustrated in <FIG>. This means that, with an upper edge <NUM> being parallel to the knife edge <NUM> and the specimen <NUM> moving down in the cutting direction c, the light gap will become narrower and will disappear, when the upper edge <NUM> has moved sufficiently below the knife edge <NUM>. This is similar with the lower edge <NUM> of the front face <NUM> being or moving up sufficiently close to or above the knife edge <NUM>, viewed in cutting direction c.

If the upper edge <NUM> is not parallel to the knife edge <NUM>, a situation occurs, in which the relative position on the left side and the relative position on the right side of <FIG> are present at the same time. For example, the relative position on the left side can correspond to a view along A-A as indicated in <FIG>, and the relative position on the right side can correspond to a view along B-B as indicated in <FIG>. In other words, the upper edge <NUM> (and, thus, the specimen <NUM>) is rotated about the third axis y.

With the situation illustrated in <FIG>, when the specimen <NUM> is moved down in the cutting direction c, the light gap, will become narrower (with respect to width W) only where the upper edge <NUM> reaches or moves below the knife edge <NUM>. The narrowing of the light gap starts at the right side according to <FIG>, moving on to the left side. This results in the actual, light gap becoming smaller and smaller until it disappears. The light gap might be look like wedge shaped during such movement. This is illustrated in <FIG> with the knife edge <NUM> and the front face <NUM> on the lower side, viewed along axis y, and the wedge shaped light gap <NUM> on the upper side (the light gap as viewed along the cutting direction c).

In other words, the width W of the light gap changes (decreases) along the length L with moving the specimen <NUM> down in the cutting direction. The further the specimen is moved down, the further the decreased width moves towards the end of the length L. This change occurs over a certain distance in the cutting direction, where this distance depends on how far the upper edge <NUM> is rotated out of the position where it is parallel to the knife edge. Afterwards, the light gap becomes wedge shaped, becoming smaller and finally disappears.

<FIG> illustrates how the width W of the light becomes narrower with the upper edge <NUM> moving down to and then below the knife edge <NUM>. The situation illustrated in <FIG> is similar to that of <FIG>, however, with the upper edge <NUM> located approximately at or slightly below the knife edge <NUM>, viewed in the cutting direction c (see also right side of <FIG>). The light ray <NUM> shown in <FIG> that is reflected at the top end of side surface <NUM>, is not reflected at the front face <NUM> anymore, because the upper edge <NUM> is too low. Thus, this light ray cannot contribute to the light gap anymore, resulting in a narrower light gap.

In order to cut sections or slices from the specimen <NUM> with cutting starting at the entire edge of the front face <NUM> at the same time, the knife edge <NUM> shall be aligned with the front face <NUM> such that the upper edge <NUM> and/or the lower edge <NUM> of the front face <NUM> is arranged parallel to the knife edge <NUM>. It is noted that the upper edge <NUM> and the lower edge <NUM> of the front face <NUM> are, typically, parallel to each other. In other words, the situation illustrated in <FIG> shall not occur after alignment.

This can be achieved by controlling the third actor <NUM> that causes the specimen holder <NUM> and, thus, also the upper edge <NUM> and/or the lower edge <NUM> of the front face <NUM>, to rotate about the third axis y. When, during relative movement in the cutting direction c between the knife edge <NUM> and the specimen <NUM>, the width W remains constant along the length L of the light gap <NUM> over a predetermined upper region up to the upper edge <NUM> of the front face <NUM> and then - for example, when a certain distance ΔH between the knife edge <NUM> and the upper edge <NUM> is reached - decreases evenly along the length L of the light gap <NUM> the upper edge <NUM> and/or the lower edge <NUM> of the front face <NUM> is at least almost parallel to the knife edge <NUM>. Such distance ΔH is illustrated in <FIG>: when the upper edge <NUM>, with the specimen <NUM> moving down, is only ΔH away from the knife edge <NUM>, the leftmost light ray will not anymore be reflected at the front face <NUM> - thus, the width W becomes narrower. For the upper region up to the upper edge, until the distance ΔH away from the upper edge <NUM> is reached, the width W is constant.

It is noted the three alignment procedures - i) knife edge <NUM> to be parallel with the front face <NUM> of the specimen <NUM>, ii) front face <NUM> of the specimen <NUM> parallel to the cutting direction c, iii) upper edge <NUM>. ) and/or lower edge <NUM> of the front face <NUM> of the specimen <NUM> parallel to the knife edge <NUM> - using the respective first, second and third actor can also be performed individually, in an arbitrary sequence and also only one or two of them can be used. For example, if one or two of such alignment procedures are not able to done or are not necessary for any reason.

<FIG> illustrates images of an upper edge of a light gap, acquired by the detector <NUM> or the camera thereof. A detector, typically, has multiple pixels arranged in a matrix array. This results in each pixel of the detector being exposed to high or low light intensity when acquiring an image of the light gap. A typical size of such pixels rated with the magnification of the camera (or detector) optics is in the range of <NUM>. This means that dimensions of the light gap can be determined, from a single image acquired with such detector, only with a precision of down to <NUM>.

A typical thickness of sections or slices to be cut off the specimen by means of the microtome system, however, often shall be less than <NUM>. Thus, the precision with which the knife edge <NUM> and the front face <NUM> have to be aligned, should be better than <NUM>. For example, an angle between knife edge <NUM> and the front face <NUM> should be less than <NUM>° (what can be considered sufficiently parallel). This can be achieved with a typical detector as mentioned above by acquiring multiple images at the same relative positions between the knife holder <NUM> and the sample holder <NUM>.

By means of example, three images <NUM>, <NUM>, <NUM> are shown in <FIG>, each illustrating the edge of the light gap. For example, this might be the edge <NUM> illustrated in <FIG>. Individual pixels <NUM> are indicated, which were exposed with either high or low light intensity (dark shaded). Due to the low precision, individual pixel might exhibit different intensities for different images having been acquired. This is also due to noise. Note that, typically, also other grades of intensity, not only high and low, will appear. A straight line or edge (edge vector) can be determined from each image. Then, an average edge (or edge vector) can be determined from these multiple edges (or edge vectors). By averaging the edges over the number of images (three images in this example), a more precise value can be achieved. This results in that a very precise alignment of the knife edge <NUM> and the front face <NUM> can be achieved, even in a sub-pixel resolution.

It is noted that this way of improving accuracy can be used in every one of the steps for aligning mentioned above, i.e., for an alignment based on a rotation about the first, the second and the third axis. For example, every time or at least sometimes when a geometric feature or dimension of the light gap has to be detected or determined for a certain relative position, multiple images can be acquired instead of only one image.

<FIG> illustrate, in diagrams, values for the at least one geometric feature of the light gap for a plurality of different relative positions between the sample holder and knife holder.

In <FIG>, values φ1, φ2, φ3, φ4, φ5 for an angle φ between the two edges <NUM> and <NUM> of the light gap (see <FIG>), which is related to the width W along the length L are shown versus an angle α. The angle α corresponds to an angle of rotation of the knife holder about the first axis z'. Note that a reference value for the angle α can set appropriately. In the example shown, the five values φ1, φ2, φ3, φ4, φ5 for an angle φ are either below or above zero. As has been described with respect to <FIG>, however, the angle φ should be zero; this corresponds to the edges <NUM> and <NUM> of the light gap being parallel.

Due to detector resolution issues, for example, no further values between the ones shown can be achieved. By means of interpolation of the values <NUM>, <NUM>, <NUM>, <NUM>, <NUM> however, see the line in <FIG>, a value α' for the angle α can be determined, which corresponds to the angle φ being zero. Such value α' can then be set by the first actor such that the knife edge <NUM> is aligned with and, in particular, is parallel to the front face <NUM> of the specimen <NUM>. Accuracy can be improved in this way.

In <FIG>, values for the width W of the light gap (see <FIG>) are shown versus an angle β. The angle β corresponds to an angle of rotation of the specimen holder about the second axis x (tilt angle). As mentioned above with respect to <FIG>, a relative movement in the cutting direction c between the knife edge <NUM> and the specimen <NUM> can be performed in order to arrange the front face <NUM> of the specimen <NUM> parallel to the cutting direction c. Thus, during one move of the specimen along the knife edge <NUM>, several values for the width W can be acquired at different relative positions between the sample holder <NUM> and knife holder <NUM>. For example, a first value can be acquired at a relative position where the knife edge <NUM> is near the upper edge <NUM> of the front face <NUM> (see <FIG>, right side), and second value can be acquired at a relative position where the knife edge <NUM> is near the lower edge <NUM> of the front face <NUM> (see <FIG>, left side).

Such values can be acquired for different settings of the angle β. In <FIG>, by means of example, three of such first values W11, W12, W13, and three of such second values W21, W22, W23 obtained for three settings of β are shown. In addition, an interpolation line for the first and second values, respectively, is added. This shows that, for example, with increasing the value of angle β, the width W near the upper edge decreases while the width W near the lower edge increases. As mentioned above, the width W shall be equal for both relative positons. The appropriate value of angle β, where this is achieved, is where both lines are crossing, i.e., value β'. Such value β'can then be set by the second actor such that the knife edge <NUM> is aligned with the front face <NUM> of the specimen <NUM> such that the front face <NUM> is parallel to the cutting direction c. Accuracy can be improved in this way.

It is noted that each of both ways of improving accuracy, multiple images per relative position and a plurality of values for different relative positions, helps increasing accuracy. Also, both ways can be combined to even further increase accuracy.

<FIG> illustrates a method according to a further embodiment of the invention by means of a flow diagram. Such method can be performed, for example, using a microtome system <NUM>, <NUM> or <NUM> as illustrated in <FIG> and described above.

In a step <NUM>, the knife <NUM> can be arranged at or in the knife holder <NUM> and the specimen <NUM> can be arranged at or in the specimen holder <NUM>. In a step <NUM>, a light gap is generated between the front face <NUM> of the specimen <NUM> and the knife edge <NUM>. This can be performed using and/or controlling the illumination <NUM>. In a step <NUM>, at least one geometric feature of the light gap <NUM> is detected by means of the detector <NUM> (or its camera). Such geometric features can be, for example, the width W or the angle φ mentioned above.

In a step <NUM>, the knife edge <NUM> is aligned automatically with the front face <NUM> of the specimen <NUM> by controlling, with the controller <NUM>, the first actor <NUM> depending on the detected at least one geometric feature of the light gap. This can comprise controlling the first actor <NUM> such that the knife edge <NUM> is arranged parallel to the front face <NUM> as explained above, in particular, with respect to <FIG>.

In an embodiment, in a step <NUM>, the front face <NUM> of the specimen <NUM> is arranged parallel to the cutting direction c by controlling, with the controller <NUM>, the second actor <NUM>. This can comprise controlling the second actor <NUM> such that the width W remains constant during relative movement in the cutting direction c between the knife edge <NUM> and the specimen <NUM> as explained above, in particular, with respect to <FIG>.

In an embodiment, in a step <NUM>, the upper edge and/or the lower edge of the front face <NUM> of the specimen is arranged parallel to the knife edge <NUM> by controlling, with the controller <NUM>, the third actor <NUM>. This can comprise controlling the third actor <NUM> such that during relative movement in the cutting direction c between the knife edge <NUM> and the specimen <NUM> when held by the specimen holder <NUM>, the at least one geometric feature of the detected light gap <NUM> comprises a dimension, e.g., width W, that remains constant along the length L of the light gap <NUM> over a predetermined upper region up to the upper edge of the front face <NUM> of the specimen <NUM> and then decreases evenly along the length L of the light gap <NUM>. Alternatively, or additionally, the dimension, e.g., the width W, remains constant along the length L of the light gap <NUM> over a predetermined lower region down to the lower edge of the front face <NUM> of the specimen <NUM> and then decreases evenly along the length L of the light gap <NUM>.

In an embodiment, a step <NUM> can be performed in addition to or alternatively to step <NUM>. In step <NUM>, indications are provided to a user depending on the detected at least one geometric feature of the light gap <NUM> on how to manually control the first actor in order to align the knife edge <NUM> with the front face <NUM> of the specimen <NUM>. Such indications might be instructions in text form and/or graphics like assistances lines on a display. Based on such indications, the user can then operate the first actor (it might be motorized but does not need to be in this embodiment) in order to achieve that the knife edge <NUM> is aligned with the front face <NUM> of the specimen <NUM>.

Similar to step <NUM>, in a step <NUM>, indications might be provided to the user, depending on the detected at least one geometric feature of the light gap, on how to manually control the second actor in order to arrange the front face <NUM> of the specimen <NUM> parallel to the cutting direction c.

Similar to step <NUM>, in a step <NUM>, indications might be provided to the user, depending on the detected at least one geometric feature of the light gap, on how to manually control the third actor in order to arrange the upper edge and/or the lower edge of the front face <NUM> of the specimen parallel to the knife edge <NUM>.

Some embodiments relate to a microtome system comprising a controller as described in connection with one or more of the <FIG>. Alternatively, a microscope may be part of or connected to a system as described in connection with one or more of the <FIG>. <FIG> shows a schematic illustration of a microtome system <NUM> configured to perform a method described herein. The microtome system <NUM> comprises a detector <NUM> and a computer system or controller <NUM>. The detector <NUM> is configured to take images and is connected to the computer system <NUM>. The computer system <NUM> is configured to execute at least a part of a method described herein. The computer system <NUM> may be configured to execute a machine learning algorithm. The computer system <NUM> and detector <NUM> may be separate entities but can also be integrated together in one common housing. The computer system <NUM> may be part of a central processing system of the detector <NUM> and/or the computer system <NUM> may be part of a subcomponent of the detector <NUM>, such as a sensor, an actor, a camera or an illumination unit, etc. of the detector <NUM>.

The computer system <NUM> may be a local computer device (e.g. personal computer, laptop, tablet computer or mobile phone) with one or more processors and one or more storage devices or may be a distributed computer system (e.g. a cloud computing system with one or more processors and one or more storage devices distributed at various locations, for example, at a local client and/or one or more remote server farms and/or data centers). The computer system <NUM> may comprise any circuit or combination of circuits. In one embodiment, the computer system <NUM> may include one or more processors which can be of any type. As used herein, processor may mean any type of computational circuit, such as but not limited to a microprocessor, a microcontroller, a complex instruction set computing (CISC) microprocessor, a reduced instruction set computing (RISC) microprocessor, a very long instruction word (VLIW) microprocessor, a graphics processor, a digital signal processor (DSP), multiple core processor, a field programmable gate array (FPGA), for example, of a microscope or a microscope component (e.g. camera) or any other type of processor or processing circuit. Other types of circuits that may be included in the computer system <NUM> may be a custom circuit, an application-specific integrated circuit (ASIC), or the like, such as, for example, one or more circuits (such as a communication circuit) for use in wireless devices like mobile telephones, tablet computers, laptop computers, two-way radios, and similar electronic systems. The computer system <NUM> may include one or more storage devices, which may include one or more memory elements suitable to the particular application, such as a main memory in the form of random access memory (RAM), one or more hard drives, and/or one or more drives that handle removable media such as compact disks (CD), flash memory cards, digital video disk (DVD), and the like. The computer system <NUM> may also include a display device, one or more speakers, and a keyboard and/or controller, which can include a mouse, trackball, touch screen, voice-recognition device, or any other device that permits a system user to input information into and receive information from the computer system <NUM>.

Claim 1:
Microtome system (<NUM>, <NUM>, <NUM>) for cutting sections from a specimen (<NUM>), the microtome system (<NUM>, <NUM>, <NUM>) comprising:
- a knife (<NUM>) having a knife edge (<NUM>) configured to cut a section from the specimen (<NUM>),
- a knife holder (<NUM>) holding said knife (<NUM>),
- a specimen holder (<NUM>) configured to hold the specimen (<NUM>),
- a light source (<NUM>),
- a first actor (<NUM>),
- a detector (<NUM>), and
- a controller (<NUM>);
wherein the knife holder (<NUM>) and the specimen holder (<NUM>) are configured to be moveable relative to one another in a cutting direction (c);
wherein the knife holder (<NUM>) or the specimen holder (<NUM>) is mounted rotatably about a first axis (z, z');
wherein the first actor (<NUM>) is configured to cause a rotation of the knife holder (<NUM>) or specimen holder (<NUM>) about the first axis (z');
wherein the light source (<NUM>) is configured to illuminate a gap (<NUM>) between a front face (<NUM>) of the specimen (<NUM>) when held by the specimen holder (<NUM>) and the knife edge (<NUM>), in order to generate a light gap (<NUM>),
wherein the detector (<NUM>) is configured to detect at least one geometric feature (W, φ) of the light gap (<NUM>), and
wherein the controller (<NUM>) is configured to
a) automatically align the knife edge (<NUM>) with the front face (<NUM>) of the specimen (<NUM>) by controlling the first actor (<NUM>) depending on the detected at least one geometric feature (W, φ) of the light gap (<NUM>), and/or
b) provide instructions (<NUM>) to a user depending on the detected at least one geometric feature (W, φ) of the light gap (<NUM>) on how to manually control the first actor (<NUM>) in order to align the knife edge (<NUM>) with the front face (<NUM>) of the specimen (<NUM>),
characterised in that
the controller (<NUM>) is configured to control the first actor (<NUM>) for arranging the knife edge (<NUM>) parallel to the front face (<NUM>) of the specimen (<NUM>) such that the at least one geometric feature of the detected light gap comprises a constant width (W) along a light gap length (L).