GB2462605A

GB2462605A - Apparatus and method for measuring an encoded carrier

Info

Publication number: GB2462605A
Application number: GB0814660A
Authority: GB
Inventors: Carl Edward Norman; Katja Franziska Kastl
Original assignee: Toshiba Research Europe Ltd
Current assignee: Toshiba Europe Ltd
Priority date: 2008-08-11
Filing date: 2008-08-11
Publication date: 2010-02-17
Anticipated expiration: 2028-08-11
Also published as: GB2462605B; GB0814660D0

Abstract

An apparatus for performing an optical measurement on a carrier 109 comprises means such as a lens 115 to direct radiation onto a surface of said carrier and a detector for determining the position or configuration of the surface using a feature 123 present in the optical path of the radiation which irradiates the surface. The feature may be a reference mark placed on the lens and configured to cast a shadow on the surface of the carrier. Alternatively, the feature may be the size and shape of the area irradiated by the radiation, the lens for example directing radiation onto the surface in a frusto-conical beam. Variations in the position or configuration of the surface may cause changes in the location of the shadow or in the size and shape of the irradiated area as viewed at the detector. The optical measurement may be a surface plasmon resonance measurement, the detector being configured to determine the angle of incident radiation for which reflection is suppressed.

Description

A System and Method for Measuring an Encoded Carner The present invention relates to the field of reading apparatus for reading encoded carriers and for a method for reading a signal from an encoded carrier.

There has always been a need to be able to quickly and efficiently monitor reactions between different chemicals in order to both identify molecules and to study the reactions of both known and unknown molecules. This need is now all the more acute with the substantial and numerous discoveries being made in the biotechnology field.

Currently, there are a number of methods known for performing this analysis. One particular method is taught in GB 2 404 918. In this patent, encoded carriers are formed.

The encoded carriers have a first region which is a reaction region and a second region which is a code region. The reaction region has a variation in its refractive index so that a surface plasmon resonance measurement may be made.

In a surface plasmon resonance measurement, if radiation of a certain wavelength, polarisation angle and incident angle irradiates a structure which has a periodic variation in its refractive index, the radiation will couple to the surface plasmon mode causing a decrease in the amplitude of the reflected light. The periodic variation in the refractive index serves to couple radiation with a correct incident angle and properties to the surface plasrnon mode.

The incident angle at which surface plasmon resonance occurs will be dependent on any chemical species on the surface. In GB 2 404 918, probe molecules are attached to the surface of the reaction region. If the probe molecules then react with a further chemical species, the incident angle of the radiation necessary to excite surface plasmon resonance will vary. Therefore, it is possible to determine if a reaction has taken place.

In GB 2 404 918, encoded carriers are provided with a code corresponding to the different types of probe molecules used in the reaction region.

In the types of apparatus described in GB 2 404 918, the carriers are provided in a flow cell and axe measured when they come to rest in the flow cell. This results in the position of the surface of the carriers within the optical path varying from carrier to carrier. Also some of the carriers may be tilted by differing amounts and some of the carriers may not be completely planar. All of these factors affect the measurement of the angle at which surface plasmon resonance occurs. Therefore there is a need to calibrate the apparatus for each measurement.

Therefore, in a first aspect, the present invention provides an apparatus for performing an optical measurement on a carrier, the apparatus comprising means to direct radiation onto a surface of said carrier, the apparatus further comprising a detector for determining the position or configuration of the surface using a feature present in the optical path of the radiation which irradiates the surface.

The above apparatus can be used to determine the tilt of the surface of carrier, the curvature of the surface of carrier or the distance of the surface along the optical path.

Generally, the detector determines the position or configuration of the surface using an artefact which occurs in an image of the carrier due to the presence of the feature in the optical path. The measurements may then be calibrated for each carrier.

The detector for determining the position or configuration of the surface is preferably also used for perfonning the optical measurement of the carrier. In an embodiment, the detector is configured to image the carrier.

In a preferred embodiment, the feature is configured to cast a shadow on the said surface. For example, the feature may be a reference mark provided on a focussing element. The feature may also be provided on a further optical element such as a mirror or on an optical element which has no function other than to provide the feature into the path of the radiation.

The reference mark may be positioned along the central axis of the optical path. Such a reference mark may be used to easily determine tilt of the carrier. The reference mark may also be positioned off the central axis of the optical path. Such a mark can also be used to determine the distance of the surface along the optical path. In some embodiments both reference marks along the axis and off the central axis are used.

The feature does not have to be a mark. In a further embodiment, the size of the lens itself may be used as the feature by measuring the diameter or other size indication of the final image produced. The lens may be bounded by a collar to sharpen the boundary of the image. The lens may also be configured such that it illuminates an area of a certain shape and the shape of this area or distortion thereof can be used as the feature.

The means to direct radiation is preferably configured to direct radiation having a plurality of incident angles to said surface. Preferably, the radiation irradiates the surface with a frusto-conical beam, the narrowest part of said beam being located at the surface.

The present invention may be used to determine the position of a carrier for a variety of different optical measurements. However, in a preferred embodiment the measurement is a surface plasmon resonance measurement and said detector is configured to determine the angle of incident radiation for which reflection is suppressed.

The apparatus may be configured to automatically correct the measurement of the angle of incident radiation dependent on the measured position or profile of the surface. In an embodiment, means are provided to apply a correctional transformation to the result of the optical measurement. In a further embodiment correction of the measurement may be performed manually or by a different apparatus, such as tilting the entire sample stage. The apparatus may be configured to discard results where the position or profile of the carrier is not within specified limits.

The apparatus may be configured to irradiate the carrier with radiation with its polarisation oriented in a first direction where the transverse magnetic mode excites a surface plasmon mode within the carrier and in a second direction where the transverse electric mode does not excite a surface plasmon mode within the carrier, the apparatus further comprising means to combine the measurements from the first and second directions.

The apparatus according to any preceding claim, wherein the apparatus preferably further comprises means to move the carrier into the path of the beam of radiation and this apparatus is preferably a flow cell.

The present invention will generally be arranged such that radiation is reflected from the carrier. However, it may also operate in transmission mode.

In a second aspect, the present invention provides a method for performing an optical measurement on a carrier, the method comprising: directing radiation onto a surface of said carrier; and determining the position or configuration of the surface using a feature present in the optical path of the radiation which irradiates the surface.

The method may further comprise the step of correcting for the position or configuration of the surface or discarding measurements where the position or configuration of the surface is not flat or level.

The present invention will now be described with reference to the following non-limiting embodiments, in which: Figure 1 a is a schematic of an encoded carrier undergoing a surface plasmon resonance measurement prior to reaction of the encoded carrier with a target species, Figure lb is a plot of reflected amplitude against the angle of incidence indicating the resonance angle; Figure 2a is a schematic of the encoded carrier of Figure la undergoing a surface plasmon resonance measurement after reaction of the encoded carrier with a target species, Figure 2b is a plot of the reflected amplitude against the angle of incidence indicated in the resonance angle; Figure 3 is schematic of a surface plasmon resonance measurement apparatus in

accordance with the prior art;

Figure 4 is an encoded carrier having a planar strip diffraction grating and a barcode; Figure 5 is a schematic of an apparatus in accordance with an embodiment of the present invention; Figure 6a is a schematic of a lens to be used in accordance with an embodiment of the present invention and the optical path affected by the lens, figure 6b is a plan view of the lens of figure 6a, figure 6c is a schematic of an image of a carrier taken by the arrangement of figure 6a when the carrier is planar, figure 6d is a schematic of an image of a carrier taken by the apparatus of figure 6a when the carrier is tilted, figure 6e is a schematic of the optical paths of the arrangement of figure 6a showing how two reflections are produced from a single spot with the carrier in a first position and figure 6f is a schematic of the optical paths followed by radiation in the system of figure 6a with a carrier in the second position; Figure 7a is a schematic of a lens of figure 6a and the optical paths when the carrier is provided at three different vertical positions, figure 7b is a schematic of a lens of figure 7a and the optical paths when the carrier is planar and tilted, figure 7c is a variation on the lens shown in figure 7a and the optical paths followed when the carrier is planar or tilted, figure 7d shows the lens of figure 7a and the resulting optical paths when the carrier is planar or curved and figure 7e is a further arrangement of the lens where it is bounded by a collar and the carrier is shown at three different positions; Figure 8a is a schematic of a fan angled imaging arrangement in the TM mode, figure 8b is an image of a carrier performed using the apparatus of figure 5 in the TM mode, figure 8c is the corresponding image in the TE mode, figure 8d is the image produced by combining the TE and TM imaging modes, figure 8e is a plot of the intensity taken across the central line of figure 8d and figure 8f is a plot of the intensity taken along the vertical central line of the TE image of figure 8c; and Figure 9a is a TM image of a carrier taken at a first vertical position, figure 9b is a TM image of a carrier taken at a second vertical position and figure 9c is a TE image with overlaid computer graphics indicating the range over which the beam diameter is measured, figure 9d shows results from an experiment where the carrier is position at two different vertical positions and figure 9e shows the results of figure 9d as real angles corrected for the position of the carrier.

Figure la is a schematic cross-section of an encoded carrier 1 of the type intended to be measured using apparatus in accordance with an embodiment of the invention. The encoded carrier 1 comprises a first metallic layer 5 of Au and second dielectric layer 7 of Si02.

Region 3 is the reaction region of the encoded carrier 1, in this region, the first metal layer 5 and second dielectric layer 7 are corrugated to form a diffraction grating.

A beam of radiation 10 is incident on said carrier 1 at angle 0. Radiation 10 enters the dielectric medium 15. Dielectric medium 15 may be provided by the gas or liquid within which the carrier sits. When the radiation has the appropriate wavelength, polarisation and angle of incidence, the energy from the incident radiation couples to the electrons of the metal layer 5 to excite surface plasmons at the interface 17 between dielectric medium 15 and metal layer 5. At this "resonance" condition, there is a steep fall in radiation reflected from the reaction region since this radiation is now absorbed by coupling to the surface plasmon mode.

The surface plasmon mode travels along the plane of the interface and extends for approximately 200nm from the interface 17 into the dielectric 15. The characteristics of the surface plasmon mode can thus be governed by physical properties of layers which are within the range of the surface plasmon. Thus chemical species 11 adhering to the surface of the reaction region may affect the surface plasmon characteristics.

The carrier is primarily intended for determining if molecules of a first type or "probes" 11, react with molecules of a second type or "targets" 13.

In figure 2a, the probes 11 have adhered to the targets 13 and thus both chemical species are attached to metal layer 5. The presence of the targets 13 will further affect the angle at which incident radiation couples to the surface plasmons, or the "resonance angle".

In figure Ia, where just the probes 11 adhere to the surface of the reaction region, the resonance angle is 0 to the surface normal. In figure 2b, where both the probes 11 and targets 13 adhere to the surface of the reaction region, the resonance angle is 0' to the surface normal. This is illustrated in figures lb and 2b respectively which show a plot of the reflected amplitude of radiation against the incident angle of radiation.

Thus, since the reaction between the probes 11 with the targets 13 causes a variation in resonance angle, measurement of the resonance angle, can be used to determine if the second type of molecules 13 has reacted with the first type of molecules 11.

The SPR measurement is generally performed using so-called fan angle arrangement of the type shown in figure 3.

In figure 3, a carrier 21 of the type described with reference to figures 1 and 2 is provided on a reading bed 23.

Radiation is provided to the carrier in the form of a cone 25. The cone comprises a plurality of beams of radiation with incident angles to the normal between 00 and 80°, but preferably 0° to 200 of the surface of the carrier 21.

In the figure the solid lines 26 schematically illustrate the optical path for various radiation beams present in the cone and the dotted lines correspond to the reflections arising from the incident beams impinging on the surface of the carrier 21.

Beam 29 which has an angle 0 to the normal impinges on the carrier 21 at the exact angle which gives rise to surface plasmon resonance for the particular carrier 21.

Therefore, the magnitude of the reflected radiation 31 for beam 29 is reduced compared to the other reflections from carrier 21. Therefore, it is possible to determine the surface plasmon resonance angle from the fan angle arrangement of figure 3. However, it can be seen from this figure that any variation in the tilt of the surface of the carrier 21, the curvature of the surface or the height of the surface will affect the measured resonance angle.

The whole system will now be described, first starting with a description of an actual carrier. Figure 4 is a schematic of a carrier of the type described with reference to figures 1 and 2.

Figure 4 illustrates an encoded carrier. The encoded carrier has a reaction region 43 and a coding region 45 comprising a code 47.

The reaction region 43 comprises a diffraction grating 49. In this embodiment, the diffraction grating comprises elongate rectangular holes 51 which are oriented parallel to one another and extend through the whole of the encoded carrier 41. Thus, the diffraction grating 49 comprises a plurality of stripes. Although in this particular embodiment, the holes 51 extend through the whole of the encoded carrier, they may also extend just part of the way into the reaction region, such that the diffraction grating 49 comprises alternating stripes of different thickness in the direction into the plane of the encoded carrier 41. Alternatively, the carrier may be corrugated (as shown in figures 1 and 2), possessing a series of ridges in the upper surface, each of which correspond exactly to a groove in the lower surface, and vice-versa. Thus the overall thickness of the carrier may be approximately constant, with corresponding undulations in the two larger surfaces of the carrier providing the diffraction grating.

The code 47 is a bar code provided at the edge of the encoded carrier 41 and extends over the edge of the carrier 41. The code has been designed so that if the encoded carrier 41 is read from the opposite side, i.e. from underneath the plain of paper, each numeral can still be uniquely identified.

Corner 53 of encoded carrier 41 has been removed so that the orientation of the carrier can be determined. Confirmation of the orientation of the carrier 41 is necessary in order to correctly measure the reaction area since the orientation of the diffraction grating 49 with respect to the laser should be the same for all encoded carriers 41. The orientation of the carrier 41 may also be useful for reading the code 47.

Typically, the encoded carrier 41 will be 50 to 100 j.Lm square. Each of the characters of the bar code will typically have a length between 5 and 10.im.

In use, probes will be attached to reaction region 43 as shown in figure 1. The molecules may be attached using a number of methods, but will preferably be attached by placing the encoded carriers in a solution of probes.

The encoded carriers 41 will then be introduced to molecules of a different type, "target molecules". Typically, this will again be performed by placing the encoded carriers with the probes in a solution or suspension of the target molecules.

If the probes attached to reaction area 43 react with the targets, the surface plasmon resonance characteristics of the reaction area will change as described with reference to Figures ito 3.

In practice, a plurality of encoded carriers 41 will be prepared, by attaching a first type of probes to a first plurality of encoded carriers having the same "first" code, a second type of probes (different to the first type of probes) to a second plurality of encoded carriers having the same "second" code. The second code is different to the first code.

Further encoded carriers with third, fourth, fifth etc codes and types of probes will be prepared. The reaction region 43 for each different type of encoded carrier having a different probe will be analysed as explained with reference to Figure 3 to determine the resonance angle prior to reaction. The different types of encoded carriers 41 will then be introduced into a solution containing the target molecules. The encoded carriers may then be removed from the solution and measured, Alternatively, the carriers may be read while in the solution.

Each type of encoded carrier may be determined from its code. An SPR measurement can then be performed to determine if the probes on the carrier have reacted with the target molecule.

The encoded carriers 41 may also be used to monitor the progress of a reaction between a molecule attached to the carrier and a target molecule. At the start of the reaction, only a few of the probes attached to the encoded carrier will react with target molecules.

Figure 5 is a schematic of the apparatus used for measuring a carrier in accordance with an embodiment of the present invention.

The apparatus comprises a motorised stage 101 which is capable of moving in the x, y and z directions. A flow cell 103 is provided overlying the motorised stage such that movement of the motorised stage causes movement of the flow cell. The flow cell has an inlet 105 and an outlet 107. Carriers 109 of the type described with reference to figures 1 to 4 are provided in the flow cell such that they distribute themselves within the flow cell so that they can be moved into the optical path by movement of the flow cell using the motorised stage.

The carriers 109 are introduced onto the flow cell via a liquid medium. Therefore, although the carriers rest on the base of the flow cell, some of the carriers may be tilted or slightly raised from the base. Also, since the carriers are small and thin, some carriers may be slightly curved.

The SPR is measured using collimated polarised light source 111. This is directed via mirror 113 through lens 115 to produce a cone of radiation of the type described with reference to figure 3 directed onto the central carrier 109 of the flow cell 103. The radiation which is reflected from the carrier is then directed via beamsplitter 117 into SPR detector 119.

The SPR technique requires the accurate measurement of angle. Therefore, variations in the profile of the carrier, for example if the carrier 109 is tilted or curved in some way will vary the angle measured in SPR detector 119. Also, if the distance of the carrier from the lens 115 varies for example due to the carrier not resting perfectly flat on the flow cell 103, the SPR measurement will also be affected.

Figure 6a is a schematic of the lens 115 used to produce the cone of radiation which illuminates carrier 109 in accordance with an embodiment of the present invention.

The lens 115 has two reference marks, a cross-hair 121 provided on the central optical axis and a spot 123 provided off the central optical axis. The carrier 109 is flat and not tilted. However, in this example, it is shown in one of three positions (i), (ii) or (iii).

Dependent on the position of the carrier 109, the shadow caused by spot marker 123 is shown in one of three different positions 125i, 125ii and l25iii. Therefore, by placing a marker on lens 115, it is possible to determine the distance of the carrier 109 from the lens 115 by measuring the position of the reflection due to the marker 123.

As the carrier 109 is flat and non-tilted, the shadow due to the cross hair reference which is provided along the central optical axis is not moved.

Figure 6b shows a plan view of lens 115 with cross-hairs 121 provided in the centre of the lens and spot 123.

Figure 6c is a schematic of the image produced by reflection from a carrier 109 shown in the arrangement of figure 6a where the carrier is flat. The reflection of the cross-hairs 121 is shown along the central axis. The spot 123 of figure 6a will produce two reflections 125 arid 127. The reason for the two reflections 125, 127 will be explained with reference to figure 6e and 6f.

Figure 6d shows the expected image if the surface is tilted. The reflections 125 and 127 due to the spot 123 are moved slightly from their position shown in figure 6c.

However, the shadow due to the cross hair 121 due to the tilt will be reflected off the central optical axis indicating tilt of the carrier 109.

Figures 6e and 6f schematically illustrate why a single spot 123 on the lens 115 gives rise to two spots 203, 205 in the final image.

In figure 6e, the carrier 109 is illuminated by a cone of radiation 201. The cone of radiation is created by lens 115 which has a single spot reference mark 123. The beam paths clearly show that there are two spots formed 203 and 205 in the final image due to the single mark on lens 123.

However, as shown in figure 6f, when the position of the upper surface is raised, the position of the reflected dots 203 and 205 changes considerably.

Figures 7a to 7e show further lenses which may be used in apparatus in accordance with embodiments of the present invention.

Figure 7a is similar to that of figure 6a which shows that the position of carrier 109 affects the position of the reflected spot 125.

Figure 7b shows the lens 115 with a single reference spot 123 provided off the central optical axis and the carrier 109 which is either in planar position (i) or in a tilted position (ii). In the planar position (i), the shadow of spot 123 is seen to be reflected back to point 131(i) and when the carrier is in tilted position to the spot is seen to be reflected back to point 131(u).

In figure 7c, the lens 115 is provided with a single cross-hair 121 provided along the central optical axis of the type described with reference to figure 6a. A single cross-hair will not allow the vertical position of the carrier 109 to affect the position of the reflection/shadow of the cross-hairs. However, if the carrier is tilted between planar position (i) and tilted position (ii) then the cross-hairs will either be reflected back to be coincident with the cross-hairs on the lens 121 or to position 133.

Figure 7d also shows a single lens 115 with an off axis reference mark 123 of the type described with reference figure 6a. However, here, the carrier is in the same position in all three situations. However, the carrier is either planar (i) or has a concave profile (ii) such that its ends are closer to the lens 115 than its middle or a convex profile (iii) such that its ends are further away from the lens 115 than the middle of the carrier 109. The curvature of the carrier 109 results in the position of the reflection of spot 123 varying between three positions 135.

Figure 7e shows a variation on the schemes previously described. Here, the lens 115 is not provided with any reference marks. However, there is collar 141 provided around lens 115. Therefore, there is a clear boundary to the end of the lens. The collar 141 defines the size of the area of the lens which passes light. However, the collar may also define the shape of the area which passes light. For example, the collar may define a square, rectangle, circle, ellipse or other shape.

The carrier 109 is provided in one of three positions (i), (ii), (iii). If it is provided in the uppermost position (i), the diameter of the cone of radiation irradiating the carrier 109 is larger than the diameter of the cone of radiation if the carrier 109 is in the lowermost position (iii). Therefore, by measuring the diameter of the image of the carrier 109, it is possible to determine the vertical position of the surface of the carrier.

In one embodiment, the apparatus is configured to discard measurements from carriers where the tilt is greater than a specified angle, for example, if the tilt is greater than 100.

Also results may be discarded if the radius of curvature of the carrier is below a specified limit.

The apparatus may be configured to automatically correct the measurement of the angle of incident radiation dependent on the measured position or profile of the surface. For instance, the tilt angle and tilt direction determined by the reflection of a reference mark along the central axis of the optical path could be used to calculate and apply a correctional transformation to the subsequent image of the SPR obtained at a detector.

Alternatively, correction of the measurement may be performed manually or by a different apparatus, such as tilting the entire sample stage.

The SPR effect will occur if the radiation is polarised such that the magnetic component of the radiation is parallel to the direction of the grating lines whilst the electric component of the radiation is perpendicular to the direction of the grating lines and hence parallel to the direction of the greatest periodic variation of the refractive index of the carrier surface. This imaging mode is generally referred to as the TM mode. An example of this arrangement is shown in figure 8a.

Figure 8b shows a typical result from a carrier measured in TM mode. The surface plasmon resonance effect is shown as fringes 151 where there is a decrease in the amplitude of the reflected radiation.

The position of the markers on the lens, 153 and 155 is also shown in the figure. The marker which produced shadows 153 and 155 is a spot on the lens provided off the central optical axis.

If the polarisation of the incident radiation is rotated by 900, a measurement in the so-called transverse electric (TE) mode is generated as shown in figure 8c. In this arrangement, since the transverse electric component is parallel to the grating lines, no strong SPR signal is seen and only the reflections due to the reference markers 153 and is observed in the image. Therefore, subtracting the two images as shown in figure 8d will provide a result with only the surface plasmon resonance fringes 151.

In order to obtain data concerrnng the surface plasmon resonance, an intensity measurement is taken across the box 161 of figure 8d. Figure 8e shows the SPR measurement obtained from this image.

For calibration purposes, the transverse electric image shown in figure 8c can be used which accurately shows the position of the reflected reference marks 153 and 155. This is shown in figure 8f.

Figures 9a and 9b show images obtained from carriers 109 which are at different heights with respect to the lens 115 as shown in figure 7e. The same carrier is imaged in both figure 9a and figure 9b. However, in figure 9a, the carrier is further away from the lens 115 than the carrier of figure 9b.

By comparing the two images in transverse electric mode as explained with reference to figure 8, it is possible to compare the images and obtain differences in the size of the illuminated area of the carrier and hence determine the distance of the carrier from the lens in figure 9c.

Figure 9d shows experimental results. Tn the first experiment, a carrier of the type described with reference to figures 1, 2 and 4 is provided in the flow cell 103 of figure 5. At a time of approximately 300 seconds, the water flowing in the flow cell is replaced by 10% glycerol solution which causes surface plasmon resonance fringes to adopt a wider separation. The change in separation between the two single Plasmon fringes shown in figure 9b is approximately 80 pixels due to the addition of 10% glycerol.

In the second experiment, glycerol solution is added to the flow cell at a time of approximately 600 seconds. However, here, the change in separation between the surface plasmon resonance fringes shown in figure 9a is seen to be approximately 60 pixels due to the addition of 10% glycerol.

This dramatic difference in the change of separation of the single Plasmon resonance fringes occurs due to the fact that the carrier in experiment 2 is further away from the lens than the carrier in experiment 1, the carrier being in both cases above the focal point of the illuminating cone of light.

Figure 9e shows results from the same measurement but here the fringe separation has been corrected by the measured size of the image. It can be seen that the corrected signals both correspond to a change in separation between the two fringes of approximately 1.750.

Claims

CLAIMS: 1. An apparatus for performing an optical measurement on a carrier, the apparatus comprising means to direct radiation onto a surface of said carrier, the apparatus further comprising a detector for determining the position or configuration of the surface using a feature present in the optical path of the radiation which irradiates the surface.
2. An apparatus according to claim 1, wherein the tilt of the surface, the curvature of the surface or the distance of the surface along the optical path of the radiation is determined using said feature.
3. An apparatus according to either of claims 1 or 2, wherein said feature is configured to cast a shadow on the said surface.
4. An apparatus according to claim 3, wherein said feature is a reference mark provided on a focussing element.
5. An apparatus according to claim 4, wherein said reference mark is positioned along the central axis of the optical path.
6. An apparatus according to claim 4, wherein reference mark is positioned off the central axis of the optical path.
7. An apparatus according to any preceding claim, where the feature is the size and shape of the area irradiated by said radiation.
8. An apparatus according to any preceding claim, wherein said means to direct radiation is configured to direct radiation having a plurality of incident angles to said surface.
9. An apparatus according to any preceding claim, wherein the radiation irradiates the surface with a frusto-conical beam, the narrowest part of said beam being located at the surface.
10. An apparatus according to any preceding claim, wherein the measurement is a surface plasmon resonance measurement and said detector is configured to determine the angle of incident radiation for which reflection is suppressed.
11. An apparatus according to claim 10, wherein the apparatus is further configured to correct the measurement of the angle of incident radiation dependent on the measured position or profile of the surface.
12. An apparatus according to any preceding claim, configured to irradiate the carrier with radiation with its polarisation oriented in a first direction where the transverse magnetic mode excites a surface plasmon mode within the carrier arid in a second direction where the transverse magnetic mode does not excite a surface plasmon mode within the carrier, the apparatus further comprising means to combine the measurements from the first and second directions.
13. An apparatus according to any preceding claim, wherein the apparatus further comprises means to move the carrier into the path of the beam of radiation.
14. An apparatus according to claim 13, the apparatus further comprising a flow cell configured to move a carrier into the path of the beam of radiation.
15. An apparatus according to any preceding claim, wherein the detector determines the position or configuration of the surface using an artefact which occurs in an image of the carrier due to the presence of the feature in the optical path.
16. An apparatus according to any preceding claim, wherein the detector is configured to detect radiation which has been reflected from said carrier.
17. A method for performing an optical measurement on a carrier, the method comprising: directing radiation onto a surface of said carrier; and determining the position or configuration of the surface using a feature present in the optical path of the radiation which irradiates the surface.
18. A method according to claim 17, further configured to perform a surface plasmon resonance measurement by using said detector to determine the angle of incident radiation for which reflection is suppressed.
19. A method according to claim 17, further comprising: correcting the measurement of the angle of incident radiation dependent on the measured position or profile of the surface.
20. A method according to any of claims 17 to 19, wherein the position or configuration of the surface is determined using an artefact which occurs in an image of the carrier due to the presence of the feature in the optical path.