Patent Publication Number: US-2017350874-A1

Title: Optical interrogation and control of dynamic biological functions

Description:
This invention was made with US government support under grant number HL111649 awarded by the National Institute of Health. The US government has certain rights in the invention. 
    
    
     FIELD OF THE INVENTION 
     The present invention relates to methods, apparatus and software for optical imaging of dynamic processes in live biological systems, and to optical interrogation and imaging of such systems. 
     BACKGROUND TO THE INVENTION 
     Researchers have been using in vitro multicellular preparations of cardiac myocytes for over 40 years to study critical tissue-level properties of the heart. In the last  15  years, these have included monolayers of cultured cardiomyocytes, derived from the native heart or differentiated from stem cells, e.g. embryonic stem cells (ESC), induced pluripotent stem cells (iPSC). When imaged at macroscopic space scales (mm and cm scales), such multicellular preparations have allowed the investigation of complex dynamic phenomena, such as wave propagation and pattern formation, and therefore are often used as a surrogate to analyze heart tissue behavior. The ability of macroscopic cardiac preparations to support spiral waves (synonymous with tachycardia) has validated their use as a model of arrhythmogenesis. High-resolution optical mapping of these preparations has given an insight into important arrhythmogenic mechanisms, including unidirectional conduction block, junctional coupling, electrical remodelling etc. Recent implementation of optogenetic means of stimulation further allows the space- and time-resolved study of dynamic processes in such multicellular systems. 
     Imaging of dynamic processes in live biological systems, for example as carried out on confluent myocyte monocultures or other small tissue samples, is typically dye-based (fluorescent synthetic dyes or genetically-encoded fluorescent dyes). This has many limitations, including: 1) the imaging is terminal when fluorescent dye labelling is applied due to phototoxicity, thus precluding long-term monitoring; 2) prior genetic modification is required when genetically-encoded dyes are used; 3) most current dye indicators/sensors require expensive high-sensitivity photodetectors and special focusing optics; and 4) such systems are not amenable to miniaturization, high-throughput applications and incubator long-term use. 
     An optical imaging method has been described by Hwang, Yea et al, 2004, in which white (non-coherent) light trans-illumination was used in conjunction with a pinhole on the axis of the imaging camera. This system required focusing optics, and only after image processing, it was possible to detect propagating waves in cardiac monolayers. As implemented, 1) this system is not easily miniaturizable; 2) it is not easily combinable with optogenetic means of actuation (due to the white light used); 3) it worked strictly in trans-illumination regime (the illuminator and the photodetector were on opposite sides of the sample); 4) it was not possible to observe propagation of waves directly (without processing); and 5) the spatial resolution was unclear. 
     SUMMARY OF THE INVENTION 
     The present invention provides an imaging system for imaging dynamic and static processes in live biological systems. According to one aspect of the invention, there is provided an imaging system which comprises a detector array (for example, a camera) having an optical axis and arranged to detect light and to output detector signals (usable single-pixel traces), a support arranged to support a biological system on the optical axis, and an illuminating light source that may be located off the optical axis and arranged to direct at least partially coherent light towards the biological system, and processing means arranged to receive the detector signals and generate image data. 
     Since the effective imaging volume of the system is the volume which can be imaged by the detector array and which is illuminated by the illuminating light source, the width of the beam of the illuminating light source needs to be large enough to define an imaging volume that can contain the sample to be imaged. The illuminating light source may be arranged to illuminate the whole of the sample simultaneously. For example it may produce an illuminating beam which is wide enough to illuminate the whole of the sample holder simultaneously. 
     The imaging system may have a field of view (FOV), which may encompass the imaging volume, and may be arranged to detect modulation due to optical path length (OPL) changes at spatial locations across the FOV. 
     The system may further comprise a display arranged to receive the image data and display an image based on the image data. The image may be a video image. 
     The system may comprise an all-optical interrogation system where the optical imaging is combined with optical stimulation means, which may comprise a stimulation light source, arranged to direct light at the imaging volume and therefore at the biological system thereby to stimulate activity in the biological system. For example the biological system may be treated to express light-sensitive ion channels and pumps (opsins), i.e. genetically modified so as to respond to optical stimulation using light at a stimulating wavelength or range of wavelengths (complementary to the wavelength(s) used for imaging). The stimulating light source may be arranged to generate a stimulating light pattern having a number of forms. The stimulating light source may be arranged to control and vary the position or positions on the sample at which light is directed, and the time for which each position is stimulated. For example the stimulating light pattern may comprise a single pulse directed at a small area, or point, of the biological system, or sample, and lasting only few milliseconds, or it may be directed at several areas, or larger areas of the sample, and over longer periods. The stimulating light source may also generate light which is intended to suppress rather than stimulate activity in the biological system. For example it may be arranged to direct light at a large part, or substantially the whole of the biological system, or a sample holder arranged to hold the system, or an imaging volume which can be imaged by the system. That light intensity level can be set so that it simultaneously depolarizes the cells, thereby suppressing activity in the system; or it may be arranged to hyperpolarize the cells and suppress activity (with expression of proper opsins). The control system may be arranged to control the stimulating light source to generate a suppressing light pattern prior to generating a stimulating light pattern, so that the sample is inactive when the stimulating light pattern is directed at it. 
     The illuminating light source may be monochromatic, such as a monochromatic LED or a laser diode, or it may be another form of light source, such as a white LED or incandescent light which is band-pass filtered so as to produce a partially-coherent light source. The coherence of light sources decreases with the spectral bandwidth and with the physical size of the source. In general, the narrower the spectral bandwidth, and the smaller the illuminating light source, the more coherent the illuminating light beam will be. The spectral bandwidth can be determined by the bandwidth of the LED or other emitting element, or by a bandpass filter. This may be less than  100 nm FWHM, or less than  50 nm FWHM, or less than  20 nm FWHM. The size of the source can be defined by the size of the LED or other emitting element itself, where essentially all of the light from the emitting element forms the illuminating beam, or by the size of aperture used to form the illuminating light beam, where some of the light from the emitting element is blocked out by an aperture to form the beam. In either case it is the size (specifically the cross sectional area) of the illuminating light beam at its narrowest point, i.e. the point where it is emitted or transmitted towards the sample. The size of the light source may be less than 10 mm 2  or less than 5 mm 2  or less than 2 mm 2  or less than 1 mm 2 . 
     The illuminating lights source may be arranged for trans-illumination, i.e. arranged on the opposite side of the sample, or sample holder, from the detector array. This means that light received at the detector array is light from the source that has been transmitted through the sample. 
     The processing means may be arranged to analyze the image data to determine one or more parameters of the image data, or one or more parameters of the biological system. The parameters may comprise the presence or absence of wavefronts if the biological system comprises cardiac tissue or cells, or they may include the speed, or direction, or frequency of the wavefronts, or a measure of the shape of the wavefronts, such as radius of curvature. The processing means may be arranged to compare one or more of these parameters with one or more reference values to determine whether the biological system meets one or more criteria, and may generate an output on the basis of that determination. Real-time feedback control may be achieved as the imaging output is compared to desired reference values and the stimulation pattern is applied to bring or maintain the biological system closer to the set target, including but not limited to prevention of arrhythmia events. For high-throughput systems, this enables the system to test large numbers of biological systems and record the results for analysis. 
     The support means may comprise a plurality of sample holders each arranged to hold a respective sample. It may further comprise a support arranged to support each of the sample holders. The support may have a plurality of apertures through it, and may be arranged to support each of the sample holders in a respective one of the apertures. If the sample holders are transparent to the illuminating light, then the illuminating light may be directed onto the samples through the sample holders, for example from the underside. 
     The system may further comprise drive means arranged to move the support so that each of the sample holders can be moved into an imaging volume. The imaging volume may be the volume which can be imaged by the detector array. 
     The system may provide a combination of dye-free imaging of excitation waves with optogenetic stimulation in a way that directly allows scalability, high-throughput, portability, long-term noninvasive probing and observation of electrical function. It may in particular be directly applicable for high-throughput drug screening and cardiotoxicity (arrhythmia) testing, among other things. It also may be used for cell phenotyping, for monitoring and optimization of electromechanical function in patient-specific stem-cell derived cardiomyocytes, for example. 
     The imaging technique is understood to be based on the idea that changes in the optical path length (OPL), in the z-direction, i.e. along the optical axis of the detector array, occur upon cell excitation. Such OPL changes may be captured across millions of cells in parallel and with a sub-cellular resolution by fast imaging for example using an interferometric or phase technique. This enables, for example, image propagation of fast electromechanical waves in cardiomyocytes, that otherwise are not visible and have commonly been imaged by fluorescent techniques. 
     The system may be a transmitted-light optical imaging system. Some embodiments of the invention can: 1) be extremely simple and affordable, not requiring special optics and light sources, lens-free or using low-NA lenses and coherent, partially coherent, or non-coherent light sources; 2) be completely non-invasive, non-toxic, dye free imaging, allowing for repeated monitoring over days; 3) be spectrally flexible (wavelength-independent), hence easily combinable with various optogenetic actuators for truly simultaneous imaging; 4) provide fast wide-field (non-scanning) imaging, suitable for tracking intricate fast excitation waves; 5) provide ultra-high spatiotemporal resolution, revealing subcellular events at centimeter field of view; 6) enable monitoring of multiple preparations and samples simultaneously in a very time efficient manner. 
     The system may not require focusing (moving the preparation to a particular position on the optical axis). This omission of focusing optics may allow for straightforward miniaturization and is a significant departure from conventional imaging systems which would have to focus on different preparations individually prior to data capture. The spectral flexibility of the imaging method (practically any wavelength can be used to illuminate, unlike standard fluorescent imaging), can allow for easy combination with optogenetic stimulation, and this can allow for real time, all-optical, stimulation and monitoring of biological systems. 
     The biological sample may be genetically modified with optogenetic tools (light-sensitive ion channels and pumps) to become light-responsive. Space- and time-resolved optical signals of particular wavelength may be delivered dynamically by the stimulating light source to stimulate, suppress or alter activity at desired locations. One possible implementation of this is by the use of digital micromirror device to direct the stimulating light. 
     The system may have immediate application to the pharmaceutical industry, where the most advanced current system for high-throughput cardiotoxicity testing (FLIPR from Molecular Devices) is limited in throughput because a KCl depolarizing solution needs to be added to each well to stimulate, which is irreversible, slow, and imprecise. In embodiments of the present invention, stimulation can be done at millions of locations in parallel without contact, by light, while the biological response is instantly imaged optically. 
     In some embodiments, both the optical imaging and the optical actuation can be realized by simple mobile device technology, i.e. direct macroscopic imaging of excitation is possible using a cell phone camera without further optics; similarly, color videos projected from the cell phone display can be used to optically stimulate desired locations at desired times. Under certain conditions, such low irradiance can be sufficient to elicit response. The importance of this aspect is that, unlike any other technology for the study of cardiac arrhythmias, this high-throughput stimulation and imaging can be done over long periods repeatedly, remotely, in a standard incubator or custom-designed environmental chamber, without special requirements for bulky optics. This is relevant to testing of maturity and phenotype of stem cell derived cardiomyocytes over extended periods, for example. 
     The system may further comprise a sample holding means arranged to hold a plurality of samples and movable to move each of the samples into the field of view, or imaging volume, of the detector array in turn. The sample holding means may comprise, or be arranged to support, a plurality of sample holders. The sample holders may be transparent. The sample holding means may comprise a sample table arranged to support the sample holders. The sample holding means may be arranged to leave the undersides of the sample holders exposed. The source of illuminating light may be arranged to direct light onto the undersides of the sample holders. 
     The processing means may comprise a controller and may be arranged to control the sample holding means so as to move each of the sample holders into the imaging volume. The processing means may be arranged to acquire image data during each of a plurality of imaging periods, during each of which a respective one of the sample holders is arranged to be located in the imaging volume. 
     The invention further provides a method of imaging a biological system, the method comprising providing an imaging system having an optical axis, placing the biological system on the optical axis, illuminating the biological system with at least partially coherent light from a direction that may be inclined to the optical axis, and imaging the biological system. 
     The biological system may be a monolayer or thin layer of cells, for example less than lmm thick, or less than 100 μm thick. The layer may be sufficiently thin for a detectable proportion of the light to pass through it. for example cardiac cells, in particular optogenetically modified cardiomyocytes or myocytes mixed with other cell types, where cell-specific optical stimulation may be possible by genetically modifying different cell types to respond to different wavelengths. 
     The method may comprise optically stimulating the biological system, for example using a pulse of stimulating light, at one or more points. The stimulation may be done prior to or during the imaging. 
     The method may further comprise optically suppressing activity of the biological system, for example prior to, during or after the stimulation. 
     The method may further comprise generating image data from the imaging system or a part thereof, and analyzing the image data, for example to determine whether the image data, or the biological system, meets one or more criteria. 
     According to a further aspect of the invention there is provided an imaging and control system for imaging and controlling live biological systems, the system comprising a detector array arranged to detect light from a field of view and output detector signals, a support arranged so support a biological system in the field of view, an illuminating light source arranged to direct light towards the biological system, processing means arranged to receive the detector signals and generate image data; and optical stimulation means arranged to direct light at the biological system thereby to stimulate activity in the biological system. 
     The processing means may be arranged to control the optical stimulation means, and to vary its optical output in response to the analysis of the image data. The processing means may be arranged to vary said optical output while the imaging system is imaging the biological system. The system may thereby provide real-time control of activity of the biological system. 
     According to a further aspect of the invention there is provided a method of imaging and controlling an optogenetic biological system, the method comprising providing an imaging system, placing the biological system in the field of view of the imaging system, optically stimulating or suppressing activity in the biological system using a first light source, illuminating the biological system using a second light source, and imaging the biological system. The optical stimulation or suppression of activity in the biological system, the illumination of the biological system and the imaging of the biological system may be performed simultaneously. For example the imaging of the biological system may be performed over an imaging period, and the stimulation or suppression may be varied during the imaging period to provide real-time control of the activity. 
     Some areas of applicability of the present invention include:
         High-throughput drug screening—since it can offer massive parallelization at low cost and with new functionality (the ability to stimulate and image optically at millions of locations);   Phenotype screening of stem-cell derived cardiomyocytes (CMs), arrhythmogenicity index;   Active control of phenotype in (stem-cell derived) cardiomyocytes or other cell types;   Patient-specific drug testing using stem-cell derived CMs;   Automation and remote control of laboratory experiments.       

     The system may further comprise any one or more features, in any workable combination, of the embodiments of the invention which will now be described by way of example only with reference to the accompanying drawings. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  is a schematic view of an imaging and control system according to a first embodiment of the invention; 
         FIG. 2  is a schematic side view of an imaging and control system according to a second embodiment of the invention; and 
         FIG. 3  is a plan view of the system of  FIG. 2 ; 
         FIG. 4  is a schematic side view of an imaging and control system according to a further embodiment of the invention; 
         FIG. 5  is a top view of part of the system of  FIG. 4 ; 
         FIG. 6  is a schematic side view of a system comprising several of the systems of  FIG. 4  housed in a single incubator; 
         FIGS. 7 and 8  show two successive image frames showing the presence of a re-entrant spiral wave of activity in a monolayer culture captured using a system similar to that of  FIG. 1 ; 
         FIGS. 9 a  to 9 c    show intensity vs time plots for the central  5 x 5  pixels for the data set of  FIGS. 7 and 8 :  FIG. 9 a    shows intensity from unprocessed images and  FIGS. 9 b  and 9 c    show the improved s/n after processing, with  FIG. 9 c    showing the intensity vs time plot from  1  pixel, or a  6 . 5  p.m area on the monolayer; 
         FIG. 10  is a schematic diagram of the optical arrangement of some embodiments of the invention; 
         FIG. 11  is a schematic diagram of an imaging system forming part of a further embodiment of the invention; 
         FIG. 12  is a schematic diagram of an imaging system forming part of a still further embodiment of the invention; 
         FIG. 13  is a schematic view of an optical stimulation and imaging system according to a further embodiment of the invention; 
         FIG. 14  is an image generated by the system of  FIG. 13 ; 
         FIG. 15  is a further image generated by the system of  FIG. 13 ; 
         FIG. 16  is a plot of intensity at one pixel of the images of  FIGS. 14 and 15  as a function of time during pulsed optical stimulation of the sample; 
         FIGS. 17 and 18  are activation maps obtained from the system of  FIG. 13 ; 
         FIG. 19  is a plot of intensity as a function of time for two pixels in the images of  FIGS. 14 and 15  showing transient activity; 
         FIG. 20  is an image generated using the system of  FIG. 13 ; 
         FIG. 21  is an enlargement of part of the image of  FIG. 20 ; 
         FIG. 22  is a plot of intensity as a function of time for a responsive pixel and a non-responsive pixel in the image of  FIG. 21 ; 
         FIG. 23  shows various steps in an image processing method used to analyse data from the system of  FIG. 13 ; 
         FIG. 24  shows plots of intensity as a function of time for one pixel of an image generated using the system of  FIG. 13 , for different light sources and different distances from the focal plane; and 
         FIG. 25  is a plot showing variations in signal to noise ratio as a function of defocus for the plots of  FIG. 24 . 
     
    
    
     DESCRIPTION OF THE PREFERRED EMBODIMENTS 
     Referring to  FIG. 1 , an imaging system according to an embodiment of the invention comprises a sample holder  10 , and a camera  12  arranged above the sample holder  10  with its axis X-X, extending, in this case, vertically downwards, through the centre of the sample holder  10 . The camera comprises a detector array  12   a  and a lens system  12   b.  The axis X-X of the camera extends through the centre point of the detector array and perpendicular to the plane of the detector array. The lens system can be very simple and may be non-adjustable so that the imaging system cannot be focussed. The focal plane of the imaging system, for example if it comprises a simple objective lens, may be above or below the sample holder  10 . A stimulating light source  14 , for example in the form of a light projector, is arranged to project images or light patterns onto a dichroic mirror  20  arranged obliquely on the optical axis of the camera  12 , between the camera  12  and the sample holder  10 , so that the images are reflected down onto the sample holder  10 . The mirror  20  is arranged to transmit light of an illuminating wavelength, different from the wavelength of the stimulating light, from the sample holder  10  to the camera  12  so that the camera can image the sample while the projector is projecting light onto the sample. The system further comprises an illuminating light source, in this case in the form of a source of at least a semi-coherent light  16 , such as a monochromatic LED light source, which is located, in this case, below the sample holder  10 , and is arranged to direct light onto the sample holder from an illumination direction which is off the axis X-X of the camera  12  so that light from the light source  16  illuminates the whole, or at least a substantial part of, the sample holder, but does not saturate the camera  12 . Other partially or fully coherent light sources, such as lasers, can be used as the illuminating light source. 
     A control system  18  is connected to the projector  14  and is arranged to control it so as to control the projection of light onto samples in the sample holder  10 . The dichromic mirror  20 , which is located on the optical axis X-X of the camera between the camera and the sample holder, is arranged to direct light from the projector onto the sample. The projector  14  is arranged to transmit light from any combination of one or more points or light sources, which can be individually activated or de-activated, so that light can be projected simultaneously onto any combination of points on the sample holder, and consequently onto any combination of points on a sample that is held in the sample holder. The control system  18  can therefore control the projector so as to illuminate any area or combination of areas of the sample on the sample holder. 
     The control system  18  is also connected to the camera  12  and is arranged to receive and process detector signals from the detector array  12   a  of the camera and to generate image data from the signals. It is further arranged to process the image data using image processing algorithms to improve the image data. The control system  18  is also connected to a display  22  and arranged to use the image data to control the display  22  to display images of the sample. The images may be real time video images. The control system may be arranged to analyse the image data, for example as described below with reference to the second embodiment. 
     It has been found that if multicellular preparations of optogenetically modified cardiomyocytes, produced for example using channelrhodopsins, are placed on the sample holder  10 , and stimulated with light, for example at a point or line, or series of points or lines, the activation wavefronts that travel through the sample can be seen in real time in the images with only basic background subtraction image processing algorithms. The images are therefore not simple transmission images, but involve a degree of refraction and/or interference of the illuminating light. 
     It has been found that good contrast and signal-to-noise ratio are achieved when the illuminating light source is arranged to direct the illuminating light onto the sample from an illumination direction at an angle θ of at least 5°, and typically at least 10° off the camera axis X-X, and preferably no more than 80° off axis, where an angle of zero corresponds to the light being along the axis towards the camera. This angle depends on the detector optics or lack thereof, i.e. wider angle may be needed for imaging optics with higher numerical aperture. Illumination at small angles, including zero, is possible when combined with other imaging methods, for example as described below with reference to  FIGS. 11 and 12 . However, with the particular implementation of trans-illumination off-axis of the embodiments described above, there is no need for a pinhole or a reference beam since all light needed to produce the image comes from the illuminating light source, and any interference is produced by that light interacting with the biological system components. Other system solutions are also applicable to achieve such dynamic macroscopic imaging, as will be described in more detail below. 
     It has been found that the imaging system is capable of very high resolution and may be diffraction-limited. In macroscopic imaging, with FOV in the centimetre range, the spatial resolution of the detector may be the limiting factor, i.e. single pixel (6.7 μm) in 1× imaging was found to give informative signals without the need for binning. 
     It has also been found that, with this imaging system, good images can be obtained even if the optical system  12   b  of the imaging system is not focussed on the sample. For example the optical system  12   b  may be arranged to focus an image of the sample either in front of or behind the detector array  12   a.  This also means that the image which is focused on the detector array is of a region above or below the sample holder  10 . This means that a very simple focusing optics, or indeed no focusing optics, can be used and the activity in the sample can still be imaged and observed clearly in real time. 
     A possible explanation for the imaging of the system is that the detector array is arranged to detect interfering light that has travelled along different paths having been refracted at different parts of the sample, with the difference in optical path length dependent on the activity in the sample. A further possible explanation is that the contracting cells are optically more dense, and therefore scatter light more effectively, and this gives rise to a brighter signal above contracted cells (since all the zero-order light is pointed away from the camera), so the detector will detect the wavefront which is then visible in the image. A further possible explanation is that the cells act as optical elements, and when they contract they refract light toward the sensor. In this case the relaxed cells would be acting like a flat piece of glass and simply transmit light, and the contracted cells would act as a lens and refract it. A still further possible explanation is that the internal structure of the myocytes acts as a diffraction grating, producing lines of constructive and destructive interference forming a diffraction pattern, so that when the cells are relaxed the lines in the diffraction pattern are far apart, and when they contract they are close together. Since the illuminating light source is off axis, then more light is directed to the camera when the lines are far apart (during contraction). 
     Using this system, like in other imaging modalities, in particular holographic modalities, it is possible, with knowledge of the optical system and optical paths and inclusion of a reference beam, to reconstruct information about simultaneous activity from multiple planes within the biological system (to achieve  4 D imaging in three spatial dimensions and over time) using post-processing on single recording (without moving through different planes). 
     Therefore the control system  18  may be arranged to control the stimulation and imaging of the sample. For example the control system may be arranged to generate a stimulating pulse of light directed at one point on the sample holder (and hence the sample) for a short stimulation period, and the camera  12  may then be arranged to capture a video image over an imaging period immediately following the stimulation period or concurrent with the stimulation or after the stimulation, for a period that may last for example from 5 to 20 seconds. 
     The control system  18  may also be arranged to control the projector  14  to generate a light pattern intended to suppress rather than stimulate activity in the biological system. For example it may be arranged to direct light at a large part, or substantially the whole of the sample holder  10 . That light can be stronger, i.e. of a higher intensity, that the light needed for stimulation (when the biological systems is modified by depolarizing channelrhodopsins) or it may be of a wavelength suitable for suppressing activity in the system (when the biological system is modified by hyperpolarizing opsins, including but not limited to eNpHR3.0 (chloride pumps) or iC1C2 (chloride channel) or ArchT (H+ pump) or Jaws, which may be different from that of the stimulating light pattern. Bi-directional control (stimulation and suppression) may be applied with the combined expression of depolarizing and hyperpolarizing opsins and two different wavelengths. 
     The control system  18  may be arranged to provide real time control of the activity in the biological system. For example, during the imaging period the control system may be arranged to identify, from the image data, one or more features of the imaged biological system, and to monitor how the one or more features varies over time. For example the control system may be arranged to determine the location of activity within the biological system, or the speed or direction of movement, or the shape, of patterns of activity in the biological system. The patterns of activity may be wave fronts in cardiac tissue. The control system may then be arranged to monitor those parameters and to determine whether they are within predetermined values or limits, which may be stored in memory in the control system. If the control system determines that the parameters are outside those values or limits, it may be arranged to vary the stimulating light source, so as to vary the stimulating and/or suppressing light patterns it generates, thereby to maintain the activity in the desired parameter ranges, for example in the desired location. 
     Referring to  FIGS. 2 and 3 , a system according to a second embodiment of the invention comprise an incubator  100  having a sample table  110  arranged to carry a number of samples in a number of sample holders  111 , for example petri dishes. The sample table  110  has a number of holes through it each with a lip around the bottom so that a sample holder can be place in each hole, supported on the lip, with its underside exposed by the hole. The sample table  110  is rotatably mounted on a rotary drive mechanism  113  which in turn can be moved horizontally by a lateral drive mechanism  113   a.  A camera  112  is arranged in a window  115  in the top of the incubator  100 , above the sample table  110  with its axis extending vertically downwards. The camera comprises a detector array  112   a  and a lens system  112   b.  The lens system is in this case simply adjustable to provide a degree of focusing, but could be completely fixed. The system further comprises a source of at least semi-coherent light,  116  such as an LED light source, which is located, in this case, below the sample table  110 , and arranged to direct light onto, and thereby illuminate, an imaging volume  117  which is on the axis of the camera  112  and in the plane level with the sample holders  111 . As the illuminating light source  116  is below the sample table  110  it is arranged to direct light upwards though the hole in the sample table  110  into whichever sample is located in the imaging volume. The sample holders  111  are transparent so that the illuminating light can pass through them into the samples. The rotational and horizontal adjustment of the sample table  110  allows each of the sample holders  111  to be moved into the imaging volume  117  so that it can be illuminated by the light source  116  and imaged by the camera  112 . The illuminating light source  116  can again be arranged off the camera axis so as to direct light onto the samples from an illumination direction which is off the axis X-X of the camera  112 . A stimulating light source in this system comprises a fibre optic cable  114  arranged to direct semi-coherent light upwards towards the underside of the sample table at a point on the axis of the camera  112  and therefore within the imaging volume  117 . 
     A processor  118  is connected to the camera  112  and arranged to receive and process the raw detector signals from the camera. The processing may be as described above with reference to  FIG. 1 , or may take other forms as described in more detail below. In particular it may be arranged to analyse the image data and determine one or more parameters of the image data, or of the sample. It may then be arranged to determine whether it meets one or more criteria, for example by comparing the parameters with reference values stored in memory. It may then be arranged to generate an output indicative of whether each of samples, or each of the images of a respective one of the samples, meets those criteria. Alternatively it may simply store the parameters for later analysis. 
     The parameters that processor  118  is arranged to determine may comprise the presence or absence of wavefronts if the biological system comprises cardiac tissue or cells, or they may include the speed, or direction, or frequency of the wavefronts, or a measure of the shape of the wavefronts, such as radius of curvature. The processor  118  may be arranged to compare one or more of these parameters with one or more reference values to determine whether the biological system meets one or more criteria, and may generate an output on the basis of that determination. Real-time feedback control may be achieved as the imaging output is compared to desired reference values and the stimulation pattern is applied to bring or maintain the biological system closer to the set target, for example to prevent of arrhythmia events. For high-throughput systems, this enables the system to test large numbers of biological systems and record the results for analysis. 
     The system also comprises a microscopic imaging system  120  arranged to form microscopic images of the samples in a separate imaging volume  122 , and a macroscopic imaging system  124  also arranged to image samples in the imaging volume  122 . 
     The controller  118  is connected to the rotary and lateral drive mechanisms  113 ,  133   a  for the sample table  110  and is arranged to move the table so that each of the position above each of the sample apertures in turn is located in the imaging volume  117 , and held there for a predetermined imaging period, before the table is moved again and the position above the next aperture is located in the imaging volume. This moves each of the samples into the imaging volume in turn. During each imaging period, the controller  118  is arranged to stimulate the sample in the imaging volume by activating the stimulating illumination from the fibre optic cable  114 , and then to acquire video image data from the camera  112  over the course of the imaging period. It is then arranged to store the image data for analysis and display. 
     Referring to  FIGS. 4 and 5 , in a third embodiment of the invention, a group of four camera devices  212 , which in this case are mobile phones with cameras, are arranged over a standard  96  well plate  210 , so that each camera device  212  images a respective group of  24  of the wells  211  each of which holds a respective sample. Two illuminating light sources  216 , which again can be LEDs or laser diodes, are arranged to direct illuminating light simultaneously at the undersides of all of the wells  211 . A further LED light source  214 , of a different wavelength from the illuminating light source, is provided for optogenetic stimulation of samples located in the wells  211 . These may be preparations with opsins. In this embodiment the stimulating LED  214  provides uniform illumination to stimulate all samples in the wells  211 . The camera devices  212  are each connected to a central control unit  218 , which may be in the form of a suitably programmed PC, and the illuminating light sources  216  and stimulating light source  214  are also connected to the control unit  218 . The control unit  218  is arranged to control the stimulating light source  214  so as to control the timing and intensity of the illuminating light that it generates. This may be in the form of pulses, in which case the start times, duration, and intensity of each of the pulses may each be controlled. The control unit  218  is also arranged to receive image data from the camera devices  212 , either streamed during acquisition or as image data files after image acquisition is complete. 
     The system of  FIGS. 4 and 5  is very compact and simple, and, referring to  FIG. 6 , a number of such systems  201  are, in one embodiment, mounted within a standard incubator  200  on shelves  203 . In this case each of the systems  201  can be connected to the same control unit. This provides a simple high throughput system that can be used for controlling and imaging a variety of different types of biological system under controlled conditions. 
     Referring to  FIGS. 7 and 8 , a system based on  FIG. 1 , in which the illuminating light source was a green light emitting diode (Cairn Research OptoLED light source), the camera was an Andor Neo 5.5 sCMOS, was used to produce images of a monolayer culture of neonatal rat cardiomyocytes.  FIG. 9 a    shows intensity from unprocessed images and  FIGS. 9 b  and 9 c    show the improved s/n ratio after processing, with  FIG. 9 c    showing the enhanced intensity vs time plot from  1  pixel, or a 6.5 μm area on the monolayer. 
     Referring to  FIG. 10 , each of the embodiments described above includes, in general terms, an imaging device or system  312 , and an off-axis illuminating light source  316 , for imaging a sample in a sample holder  310 . However, the combined optical stimulation and imaging provided by those embodiments can also be provided using different types of imaging system. For example, referring to  FIG. 11 , in a further embodiment the illumination of the sample holder  410  is provided by a pinhole aperture  416   a,  illuminated by a light source  416   b,  which can be a simple white incandescent lamp, optionally with a lens  416   c  provided between the pinhole  416   a  and the sample. The imaging is performed by a camera device  412 , with the sample and the pinhole being located on the axis of the camera device  412 . The stimulating light source is not shown in  FIG. 11 , but can be a simple light source similar to that of  FIG. 4  with a control unit arranged to control the timing and intensity of the light, but not the position, or it can be a more complex projector light source similar to that of  FIG. 1  with a control unit arranged to control the position and timing and optionally also the intensity of the stimulating (or suppressing) light. 
     Referring to  FIG. 12 , a further embodiment of the invention comprises an imaging system having a Mach-Zehnder interferometric setup. This comprises a light source  516  with a lens  520  forming an illuminating beam, a beam splitter  522  arranged to split the beam into a main beam  524  and a reference beam  526 , mirrors  528 ,  530  arranged to reflect the main beam  524  and the reference beam  526  onto a further beam splitter  532 , and a photodetector array  534  arranged to detect the re-combined beams. A sample holder  510  is located in the path of the main beam, between the mirror  528  and the second beam splitter  532 . As with the embodiment of  FIG. 11 , a stimulating light source (not shown) is arranged to stimulate activity in a sample in the sample holder and can take any of the forms described above. 
     Each of the systems of  FIGS. 11 and 12  can provide all-optical stimulation/suppression and imaging of the sample providing real time control and interrogation in a similar way to the previous embodiments. 
     Referring to  FIG. 13  an optical control and imaging system according to a further embodiment of the invention comprises a sample holder  610 , a camera  612  mounted above the sample holder  610  and arranged to image samples on the holder  610 , a stimulating light source  614 , an illuminating light source  616  and a computer  618 . The camera  612  is a scientific complementary metal-oxide semiconductor (sCMOS) camera. An objective lens  613 , an imaging lens  615 , and a long-pass emission filter  617  are arranged between the sample holder  610  and the camera  612 , on a common axis with the centre of the camera  612  and the centre of the sample holder  610  which forms the optical axis of the imaging system, and a dichroic mirror  620  is located on the optical axis and inclined at 45° to it, between the objective and imaging lenses  613 ,  615 . The dichroic mirror is arranged to reflect light with wavelength less than a threshold wavelength, in this case 510 nm, and to transmit light of higher wavelengths. The stimulating light source  614  comprises a source of semi-coherent light in the form of a 10W LED  630  arranged to output light of wavelength 460 nm, a total-internal-reflection prism  632 , and a digital micromirror device (DMD)  634  which is controlled by the computer  618 . The LED  630  is arranged to direct light onto the prism  632  which is arranged to reflect it onto the DMD device  634 . The DMD device is arranged to reflect some of the light, in a pattern that is controlled by the computer  618 , as a patterned stimulating light beam  636 , back through the prism  632 , through a further pair of lenses  638  onto the dichroic mirror  620 , which reflects the stimulating light beam down onto the biological sample which is on the sample holder  610 . The illuminating light source  616  is located below the sample holder  610  and off the optical axis of the imaging system, and comprises a white LED, bandpass filtered at  580  ± 20  nm. It is arranged to generate an illuminating light beam  640  directed at the underside of the sample holder. The sample holder  610  is transparent to light at the wavelength of the illuminating light source  616 , which therefore provides oblique trans-illumination of any sample placed on the sample holder. 
     The system of  FIG. 13  was used to stimulate and image a genetically modified cardiac monolayer, which was placed on the sample holder  610 . The computer  618  was arranged to control the stimulating illumination to provide over a period P 1  a uniform stimulating pulse P 1  of about is in length, followed by a sequence, over period P 2 , of periodic line stimuli each of which illuminated a line across the centre of the sample, at pulse frequency of about  2  pulses per second. 
       FIGS. 14 and 15  are examples of minimally filtered images of the sample responding to the pulsed optical line stimulation, at the time of one of the pulses, and  80 ms after the pulse. 
       FIG. 16  is a trace of intensity (I) versus time (t) from a single pixel in the images of  FIGS. 14 and 15 , indicating the time of the high intensity pulse P 1  and the periodic linear pulses P 2 . 
       FIGS. 17 and 18  are activation maps showing ongoing spontaneous activity (a spiral) pre-stimulus, and, following termination of the spiral activity by a high intensity light pulse applied over the entire field, generation of a planar wave by application of a linearly patterned light pulse. 
     In some cases, excitation waves are visible without image processing. Visibility of excitation waves was enhanced during live recording by applying a running background subtraction followed by an absolute value operation on each pixel: 
         P   t ( i,j )=| p   t ( i,j )− p   t−n ( i,j )|  (1)
 
     Where p t (i, j) is the value of pixel p at location i,j at time t, and p t−n (t,j) is the value of the same pixel at an earlier time point (typically 120 ms, or 6 frames apart, where n is the number of frames). The low computational overhead of this filter operation allowed assessment of activity in real time. An example of the output of this operation is the two frames in  FIGS. 14 and 15 . Plotting the filtered intensity vs. time curves for the data yields a doubled humped curve, where the first spike corresponds to activation and the second hump corresponds to relaxation as shown in  FIG. 19 , which shows curves for two pixels located at different points in the path of a travelling wave front. Data filtered in this fashion can be directly used for analysing simple wave dynamics (e.g. calculation of conduction velocity for planar waves). However, interpretation of complex spiral and wavelet patterns were hindered by the presence of the second hump, as it was often difficult to distinguish excitation from relaxation waves. A different method was therefore used to measure the shape of excitation waves for generating the activation maps of  FIGS. 17 and 18 . 
     Measurement of activation wave patterns as shown in  FIGS. 17 and 18  was achieved as follows. After acquisition, a running background subtraction (where each pixel at frame t is replaced by its value minus the average value of that pixel over 2n+1 frames between t−n and t+n), where n can be selected as appropriate, gives a clear image of wave dynamics. The dichroic mirror and band pass filters pass a small amount of excitation light so that the imposed illumination patterns may be directly visible in this record. Referring to  FIGS. 20 and 21  raw data consists of high contrast regions distributed throughout the sample.  FIG. 20  is a full field of view single frame. The edge of the  35 mm petri dish is clearly visible.  FIG. 21  is a full resolution zoom showing bright and dark regions.  FIG. 22  shows intensity vs. time plots from two pixels in  FIG. 21 , as indicated by the arrows, which show markedly different transients. Bright regions in the image, as shown in the upper plot, are more likely to show activity related to contraction of the monolayer than dark regions, as shown in the lower plot. 
     Quantification of wavefront location was performed in several steps. Off-axis illumination results in localised regions of high contrast as can be seen in  FIGS. 20 and 21 . These regions typically display an increase in intensity that corresponds to contraction, as shown in the upper plot in  FIG. 22 , while darker regions do not display transients that can be distinguished from noise, as shown in the lower plot of  FIG. 22 . The data sets generated from this imaging technique yield a sparse set of points that can be used to track the continuous contraction waves in the underlying tissue. 
     One method of data analysis which can be used to obtain the wavefront patterns will now be described. Images are first spatially binned by a factor of 8 prior to processing in order to reduce computation time, the data from one binning being shown in  FIG. 23 b   . The data is then scaled between 0 and 1, and all pixels with average value less than 0.1 are classified as nonresponsive and all pixels with average value equal or greater than 0.1 are classified as responsive. These are shown as black and white pixels in  FIG. 23 c   . Nonresponsive pixels are replaced by the average of those responsive pixels within a radius of 8 (binned) pixels for each frame. After this operation, responsive pixels are also spatially averaged (radius  8 ) the result of which is shown in  FIG. 23 d   . Intensity as a function of time traces for each pixel are then cross correlated against a single transient from a representative active pixel. The value of the cross correlation is then used to generate a data set that is used to locate wavefronts as shown in  FIG. 23 e   . Isochronal maps, which show the location of the wave front over several frames as in  FIG. 23 h    are generated by performing a threshold operation (pixel intensity&gt;50% maximum) on the cross correlation data sets, as shown in  FIG. 23 f   , and replacing the active pixels with a time stamp. Sequential frames are collapsed into one frame so that time of activation values overwrite existing values if the difference between them is greater than 50 ms (the minimum refractory period), as shown in  FIG. 23 h   . Isochronal lines are found using a marching squares algorithm, and colour coded using the ‘rainbow smooth.lut’ lookup table. 
     It will be appreciated that the image of  FIG. 23 h    shows the progress of the wave fronts over time, and that parameters of the shape of the wave fronts, such as radius of curvature, can be extracted from this type of image, and that the speed and direction of the wave fronts can also be determined from the relative positions of the boundaries of the different areas in the image. 
     Referring to  FIGS. 24 and 25 , the performance of the imaging system were experimentally characterised using three light sources which differed in their spatial and temporal coherence: a white LED, a blue LED (Cairn Research), and a red laser (Thorlabs CPS186), imaging spontaneously active samples. The three light sources were held within the same optical mount, and a series of images were captured at different focal planes (every 1.25 mm) using a mechanical focus motor (Prior Scientific H22) to move the objective to ensure that the image series can be directly compared. The image contrast was assessed for the three light sources by measuring the signal to noise ratio (Matlab ‘snr’ function) of time-varying intensity (raw image data was first filtered using Eq. 1 above), extracted from  64  equidistant regions of interest within 200 frame image sequences. Light sources were adjusted so that waves were visible at the focal plane. When in perfect focus, all three sources can image wave activity and show strong spikes in the intensity vs time plots (SNR&gt;5 decibels). When defocused, the white LED loses signal rapidly, while the more coherent blue LED maintains signal over several millimetres. The difference in signal quality is significant for the LED sources (P&lt;0.01, t-test and Wilcoxon ranksum) for all defocus values over 0. The laser, with the highest coherence, maintains a high SNR over the entire defocus range. This dependence of image quality on the spectral bandwidth (coherence) of the light source is indicative of likely interference contribution to the image formation. 
     Many of the described applications are for fast excitation waves in excitable tissue, e.g. cardiac tissue, but the invention is applicable to other dynamic processes, which can be optically manipulated (including but not limited to molecule signalling, pH changes, optically-controlled gene expression changes etc.) and can result in OPL changes to be imaged with the described dye-free system. 
     Indeed, while specific embodiments of the invention have been described, the skilled man will readily appreciate that modifications to any one or more features of these embodiments can be made as appropriate to make the system suitable for a variety of applications.