US20110131690A1 - Scanning Ion Conductance Microscopy - Google Patents

Scanning Ion Conductance Microscopy Download PDF

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Publication number
US20110131690A1
US20110131690A1 US12/864,302 US86430209A US2011131690A1 US 20110131690 A1 US20110131690 A1 US 20110131690A1 US 86430209 A US86430209 A US 86430209A US 2011131690 A1 US2011131690 A1 US 2011131690A1
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Prior art keywords
probe
scanning
region
measurement
sicm
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Inventor
Pavel Novak
Chao Li
Andrew Shevchuk
Victor Ostanin
David Klenerman
Yuri Korchev
Gregory Frolenkov
Richard Clarke
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Ip2ipo Innovations Ltd
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Imperial Innovations Ltd
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01Q—SCANNING-PROBE TECHNIQUES OR APPARATUS; APPLICATIONS OF SCANNING-PROBE TECHNIQUES, e.g. SCANNING PROBE MICROSCOPY [SPM]
    • G01Q60/00—Particular types of SPM [Scanning Probe Microscopy] or microscopes; Essential components thereof
    • G01Q60/44—SICM [Scanning Ion-Conductance Microscopy] or apparatus therefor, e.g. SICM probes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y35/00—Methods or apparatus for measurement or analysis of nanostructures
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01Q—SCANNING-PROBE TECHNIQUES OR APPARATUS; APPLICATIONS OF SCANNING-PROBE TECHNIQUES, e.g. SCANNING PROBE MICROSCOPY [SPM]
    • G01Q10/00—Scanning or positioning arrangements, i.e. arrangements for actively controlling the movement or position of the probe
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01Q—SCANNING-PROBE TECHNIQUES OR APPARATUS; APPLICATIONS OF SCANNING-PROBE TECHNIQUES, e.g. SCANNING PROBE MICROSCOPY [SPM]
    • G01Q10/00—Scanning or positioning arrangements, i.e. arrangements for actively controlling the movement or position of the probe
    • G01Q10/02—Coarse scanning or positioning
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01Q—SCANNING-PROBE TECHNIQUES OR APPARATUS; APPLICATIONS OF SCANNING-PROBE TECHNIQUES, e.g. SCANNING PROBE MICROSCOPY [SPM]
    • G01Q10/00—Scanning or positioning arrangements, i.e. arrangements for actively controlling the movement or position of the probe
    • G01Q10/04—Fine scanning or positioning
    • G01Q10/06—Circuits or algorithms therefor
    • G01Q10/065—Feedback mechanisms, i.e. wherein the signal for driving the probe is modified by a signal coming from the probe itself

Definitions

  • This invention relates to scanning ion conductance microscopy, and its use in the study of soft surfaces and interfaces, including those of cells and convoluted matrix structures.
  • Soft surfaces are a feature of many natural phenomena, particularly when immersed in liquid, including cell membranes and immiscible liquid droplets.
  • Many imaging and measurement techniques used for the study of such surfaces employ a probing method that applies forces which may induce errors by disturbing the surface under observation or which require modification of the surface before such observation can be carried out.
  • the cell is the most fundamental unit of living organisms, whether animal or plant.
  • the study of its structure and composition, and how its various constituents function, lends valuable insight into the complex processes that occur in integrated biological systems. This requires techniques that allow investigation of cell samples to be conducted in real-time, non-invasively, and in solutions that mimic physiological conditions so that cell functionality is retained.
  • Optical microscopy (using visible light) has been applied widely to study live cells.
  • the resolution is limited by diffraction to about 200-250 nm.
  • one commonly used method is electron microscopy, where it is possible to obtain images with 10 nm resolution, but the sample needs to be fixed prior to imaging. Hence, it is not possible to use an electron microscope to study living cells.
  • SPM scanning probe microscopy
  • AFM atomic force microscopy
  • SICM scanning ion-conductance microscopy
  • SNOM scanning near-field optical microscopy
  • Atomic force microscopy is commonly used to study the response of a surface to mechanical force or pressure.
  • AFM Atomic force microscopy
  • the tip cantilever spring constant affects how much the surface under study will be displaced by the measurement or detection process and sets a limit to the softness of a surface which can be studied.
  • An additional difficulty with AFM when used in contact or tapping mode is the likelihood of the surface adhering to the probe tip, altering the measurements during retraction and leading to contamination of the tip and mechanical damage to the surface.
  • the environment required by the probing method requires modification of the surface before imaging, as with electron microscopy where the need for a vacuum or low pressure gas may require stabilization of the surface and removal of liquid before imaging may be carried out.
  • SICM Scanning ion conductance microscopy
  • SPM scanning probe microscopy
  • an electrolyte-filled, glass micropipette is scanned over the surface of a sample bathed in an electrolytic solution; see Hansma et al (1989) Science 243:641-3.
  • a quartz pipette may also be used.
  • WO-A-00/63736 discloses that SICM can be used effectively, e.g. to scan the surface of a live cell by controlling the position of such a probe.
  • the pipette-sample separation is maintained at a constant value by monitoring the ion-current that flows via the pipette aperture.
  • the flow is between two electrodes: one inside the pipette and another outside in the electrolyte solution.
  • the ion-current signal depends on a combination of the micropipette's resistance (R P ) and the access resistance (R AC ) which is the resistance along the convergent paths from the bath to the micropipette opening.
  • R P depends on the tip diameter and cone angle of the micropipette, whereas R AC displays complicated dependence on the sample's electrochemical properties of the bath and the sample, geometry and separation from the probe. It is R AC that lends ion-current sensitivity to the pipette-sample separation and allows its exploitation in maintaining the distance such that contact does not occur.
  • the optimum tip-sample separation that has allowed SICM to be established as a non-contact profiling method for elaborated surfaces, is approximately one-half of the tip diameter; see Korchev et al (1997), J. Microsc. 188:17-23, and also Biophys. J. 73:653-8.
  • the outputs of the system controlling the position of the tip are used to generate images of topographic features on the sample surface.
  • the spatial resolution achievable using SICM is dependent on the size of the tip aperture, and is typically between 50 nm and 1.5 ⁇ m. This produces a corresponding resolution.
  • the sensitivity of the micropipette used in SICM is highest to surfaces directly below the micropipette tip and is less so to surface structures that lie at the sides of the tip. If the micropipette is scanned across a surface whose features are of a similar scale to the diameter of the micropipette tip, the SICM system is able to keep the tip out of contact with the surface. However, if the surface contains features and structures of a height much larger than the tip diameter, and which include steep edges or walls, then the scanning speed on the SICM system must be reduced in order to avoid collision, resulting in a longer time spent at each point on the surface.
  • the target surface is a convoluted structure such as a cluster of interwoven neurons, or a matrix or scaffold within which cells are growing.
  • WO-A-00/63736 discloses a method by which the probe is scanned across the surface at a fixed speed or rate.
  • Other methods are known in which the time spent by the probe at any point is varied to allow the probe ion current and vertical position to stabilise within a given range.
  • the resolution of the scan or density of points measured during the scan is constant throughout that scan.
  • an increase in the time spent at each point leads to a proportionate increase in the total scan time.
  • the time to generate a high resolution image of a convoluted surface may become so long as to be prohibitive.
  • Happel et al, J. Microscopy, 2003; 212: 144-151 discloses the use of a pulse-mode scanning ion conductance microscopy to observe volume changes and cell membrane movements during the locomotion of cultured cells.
  • the microscope apparatus uses current pulses to control the difference between the cell surface and the electrode tip as well as a back-step to prevent contact of the tip with the cell membrane during lateral movements of the probe.
  • the apparatus is used with a constant resolution to determine areas having high surface structures. Lateral scans can then be performed at different heights depending on the expected height of the surface structures. Although this method has advantages, it still results in low scan speeds.
  • a method for interrogating a surface using scanning ion-conductance microscopy comprising the steps of:
  • the method includes sampling the surface to be scanned by SICM to ascertain which areas are of most relevance to the investigator.
  • the SICM micropipette is cycled in height above the surface, with amplitude which is greater than the maximum hill valley distance, at discrete points across the surface.
  • the micropipette is moved laterally only while distant from the surface. No lateral movement of the micropipette which could damage the surface or tip takes place while the tip is close to the surface.
  • the sampling takes place at four boundary corner points for each square region of the surface.
  • an estimate of surface roughness for the region can be determined.
  • the scanning probe e.g. SICM micropipette
  • the scanning probe is then cycled in height above the surface at a number of points within the square, the number of points being selected based upon e.g. the estimated surface roughness. This analysis would be ongoing for subsequent points to provide for a final scan over only the region or regions with structures of interest, and within that region or regions to produce an image whose resolution is adapted locally to the surface complexity.
  • surface roughness is described as the criterion for the adaptive scanning, to determine the number of pixels imaged in each square on the surface, other criteria could be used depending on the biological question of interest.
  • the presence of a fluorescence signal could be used as a surface characteristic, to increase imaging resolution.
  • Apparatus for enacting the method of the present invention comprises a SICM apparatus, including a scanning probe (micropipette), means for measuring and/or controlling the distance of the probe tip from a surface to be scanned, and means for moving the probe laterally relative to the surface.
  • a scanning probe micropipette
  • means for measuring and/or controlling the distance of the probe tip from a surface to be scanned and means for moving the probe laterally relative to the surface.
  • the method includes the following steps:—
  • the height of the probe retraction in any particular region is determined taking into account an estimate of the height range of structures in that region from observation of the variation in heights of the precursor points, with the addition of a safety margin.
  • the motion of the probe may be halted after the current falls below a preset threshold for the first time, for a given time or for a given number of measurement samples.
  • a preset threshold for the first time, for a given time or for a given number of measurement samples.
  • Such additional measurements provide information about the relationship between ion current and distance from the probe to the surface in the region close to that surface.
  • the graphical representation of this relationship is commonly called an “approach curve”.
  • this relationship may indicate characteristics of the surface, including its roughness, its conductivity relative to the surrounding solution, or the degree to which it is normal to the probe axis.
  • the threshold current may be set differently, taking into account the recent level of current while the probe is distant from the surface. This current may be measured immediately prior to the advancement, may be an average of a number of such measurements, or may be an average including such measurements over a number of cycles of retraction. Such adaptation of the threshold may be necessary to take into account factors unrelated to surface distance which might change the current.
  • the reduction in ion current as the pipette (probe) approaches the surface is used to determine information about the surface curvature and mechanical properties of the sample at this point.
  • the shape of the reduction in current contains information about both these additional properties of the surface, as well as topography. If the surface is soft the pipette needs to move further down to get the same reduction in ion current since the surface moves away as the pipette approaches, due to forces exerted when the pipette is closer to the surface. The pipette also needs to move further down if the surface is more curved.
  • the present invention therefore makes it possible to map other surface properties as well as the sample topography. This may provide more contrast in the obtained image making certain features of interest easier to detect, e.g. the underlying cell cytoskeleton under the cell membrane.
  • an apparatus for carrying out scanning probe microscopy comprising:
  • the first piezo actuator has a travel range of at least 100 ⁇ m and the second piezo actuator has a travel range less than 50 ⁇ m, preferably no more than 25 ⁇ m.
  • FIG. 1 shows the configuration of a hopping mode SICM system used to investigate a cell surface
  • FIG. 2 illustrates the problem with conventional SICM
  • (b) illustrates the hopping mode SICM to overcome the problem
  • (c) and (d) show scans of hippocampal neurons with conventional raster scan (c) and hopping mode SICM (d)
  • (e) illustrates the principles of hopping mode SICM
  • FIG. 3 shows different scan resolutions for different regions of a surface
  • FIG. 4 shows different compression levels for a region
  • FIG. 5 shows the number of pixels in an exemplary prescan (A) and final scan (B);
  • FIG. 6 shows images vertically protruding mechanosensitive stereoclia of auditory hair cells, produced with hopping mode SICM;
  • FIG. 7 shows images of live hippocampal neurons
  • FIG. 8 shows the configuration of a SICM system having primary and secondary feedback systems
  • FIG. 9 shows different compression levels utilised in the invention.
  • FIG. 10 illustrates probe movement during fluorescence mapping
  • FIG. 11 shows images taken of live hippocampus neuron cells during fluorescence mapping, where (A,D) are excited fluorescence SCIM images of neurons, (B,E) are differential fluorescence images between the excited and reference fluorescence images of the neurons and (C,F) are topographical SICM images of neurons; and
  • FIG. 12 is a simultaneous fluorescence signal recorded while scanning on live hippocampus neurons, the arrow showing a burst in the signal while the pipette was held close to the cell membrane, which depolarised the cell membrane.
  • a typical SICM apparatus of the invention comprises a scanning probe, piezo-actuator scanning elements, control electronics and a computer. These components may be built in and around an inverted microscope, e.g. Diaphot 200 (Nikon Corporation, Tokyo, Japan).
  • the piezo-actuator can be used to measure and/or control the distance of the probe tip from the surface to be interrogated and to move the probe laterally relative to the surface.
  • the term ‘interrogate’ is intended to refer to the ability to monitor changes at the surface of a structure, e.g. to detect structural changes on or at the surface at a single position or as the probe scans the surface, or to measure the height of a structure.
  • the surface may be pliable, and allow imaging of structures underneath the surface, e.g. cytoskeleton underneath a cell surface. This is included in the term. It is not intended that the term be restricted to detecting structural changes, and the monitoring of, for example, electrophysiological or chemical changes is also included.
  • SLM scanning ion-conductance microscopy
  • the software of an existing SICM unit is modified so as to drive the z-piezo (vertical) stage to implement the sequences outlined above.
  • the estimate of the amplitude of the preliminary “hopping” interrogation of the surface would be input by the user, and is used by the software to govern the maximum z span of the pipette tip in approaching the initial points on the surface.
  • the height information derived from these probes is fed into the software to calculate the positions of the next set of readings and so on until the region of maximum roughness has been defined, when a normal scan is performed in that region at the required resolution.
  • the “hopping amplitude” is usually greater than 1 ⁇ m, typically of the order 1 ⁇ m-8 ⁇ m, more preferably 2 ⁇ m-6 ⁇ m, more preferably 3 ⁇ m-6 ⁇ m, e.g. 5 ⁇ m
  • the SICM the pipette (probe) may be adapted such that, when located in proximity to the surface under study, a localised and controlled pressure or force can be applied to the measurement surface by means of a regulated flow of liquid through the probe.
  • the application of this pressure can be used to measure the flexibility or elasticity of the surface by monitoring the relationship between the applied pressure and the resulting movement of the surface. It can also be used to stimulate cell surface components, e.g. mechanosensitive ion channels, with subsequent measurement of this stimulation carried out by monitoring consequent changes in electrophysiological or chemical signals.
  • the pressure applied to the surface will, if the surface is sufficiently pliable, cause the surface to move.
  • Positive pressure i.e. flow through the probe towards the surface, has the effect of pushing the surface away from the probe, increasing the separation between the surface and probe tip.
  • a negative pressure draws the surface towards the probe tip, decreasing the separation.
  • the relationship between the applied pressure and the resulting movement of the surface can therefore provide information on the elasticity of the surface structure.
  • the probe may be used to scan the surface while simultaneously applying pressure to it.
  • the invention can be used to build up a detailed picture of the surface as it responds to the applied pressure, to reveal surface and sub-surface structures.
  • SICM probe images a surface without contact, and it can be operated in a mode that exerts negligible force on the surface.
  • the electric field at the tip of such a micropipette is strong enough that forces due to electrotension in the surrounding media are no longer negligible and are recognised to be strong enough to actuate the constriction of cell membranes (C. Bae, P. Butler Biomech. Model Mechanobiol. 7; 379: 2008).
  • this electrotension has the additional effect of exerting a small repulsive force on media of lower static dielectric constant, repelling them from the region of high electric field around the micropipette tip.
  • This correction is realised technically by measuring at each point the relative displacements between two set percentages of decrease in ion current, first at low voltage where deviation from the expected difference can only be due to curvature in the surface, and then at higher applied electrode bias, where the deviation may be expected to increase because of the electrotensive force pushing the surface away slightly. Moreover, this force can be exploited to constrain the superficial surface against elements underlying it so that these can also be imaged by the micropipette.
  • the invention can be used to make a simultaneous measurement of a structure when the pipette is far from the surface and when it is close in the “hopping mode” so a differential map of the surface can be obtained by subtracting these two measurements taken shortly after one another.
  • a differential map of the surface can be obtained by subtracting these two measurements taken shortly after one another.
  • the pipette When the pipette is close to the surface it will locally deliver an agonist or ions efficiently to the surface and give a larger response, measured by fluorescence detecting intracellular calcium or whole cell recording of increased calcium channels, the delivery is negligible when it is far away.
  • the pipette can be stopped at the bottom of the hop and apply a voltage pulse (e.g. a short 500 mx-2V pulse) for efficient local delivery—this differential mode can be used to map receptors or mechanosensitive ion channels as outlined below.
  • FIG. 10 illustrates the fluorescence mapping embodiment.
  • the SCIM probe first measures the background fluorescence signal while the probe is distant to the surface waiting for lateral movement. Next, it approaches the surface and measures the surface topography.
  • the control software may drive the probe (pipette) to jump up a small distance in order to prevent ant further piezo movement.
  • the feedback control is on hold and the software measures increased fluorescence signal.
  • the apparatus can be adopted for simultaneous measurement of cell topography and detection of a fluorescence signal that is excited by a laser beam focused at the tip of the pipette.
  • this “surface confocal imaging” can be done by using the SICM in a “hopping mode”.
  • the level of background fluorescence will be recorded first when the pipette is far from the surface and no force is exerted on the cell.
  • the pipette is then brought to a pre-defined distance from the surface of the cell and both position of the pipette and fluorescence signal will be simultaneously recorded.
  • a pressure stimulus is applied to the pipette, it may activate mechanotransducer channels that are generally permeable to calcium.
  • This signal can be subtracted from the fluorescence signal when the pipette is far away from the cell surface. Subtracting the background fluorescence will reveal the local changes in fluorescence on application of pressure.
  • This technique will be used to map the position of, for example, MS ion channels in DRG neurons and auditory hair cells.
  • the “hopping mode” combined with simultaneous fluorescence or whole cell recording or any other simultaneous measurement of the sample can be used to obtain differential maps, map receptors and mechanosensitive ion channels and other properties e.g. local mechanical properties or local chemical groups.
  • Multi-dimensional imaging of surface topography can be achieved and local surface properties or function probed by any agent or stimulus delivered from the pipette. Measuring the response of the surface from this local change with the baseline level of the parameter of interest measured just before or after the bottom of the hop, provides a difference image.
  • This technique could be used in a method to determine how drug candidates affect a receptor or mechanosensitive ion channel response or any agent which alters the response.
  • the hollow micropipette or nanopipette can be fabricated by pulling borosiliate glass capilliaries with, for example, outer and inner diameters of 1.00 mm and 0.58 mm respectively, using a laser-based micropipette puller (for example model P-2000, Sutter Instrument Co., San Rafael, Calif., USA). Probes with conical taper lengths and apex diameters of 200 nm, 400 nm and 1.0 ⁇ M, can be achieved.
  • the pressure can be exerted by conventional means to control the flow of liquid through the probe.
  • a programmable pressure injector system for example model PM-4, Warner Instruments, Hamden, Conn., USA, is coupled to the shank of the SICM pipette holder by means of a flexible tube, and the injector programmed to generate the required pressure/time profile.
  • the amount of pressure required can be determined by the skilled person.
  • a positive pressure of at least 10 kPa e.g. from 10 to 50 kPa is applied. More typically a pressure of from 13 to 40 kPa is applied.
  • the apparatus may further include means to measure electrophysiological or chemical signals which may be generated by a cell or biological surface and stimulated by the applied pressure.
  • Such measurement means is conventional in SICM.
  • the SICM uses a patch-clamp nanopipette arranged perpendicularly to the sample as a scanning probe.
  • the pipette is mounted on a three-axis piezo translation stage.
  • the probe In a traditional line scanning mode the probe approaches the cell surface and scans over it while maintaining a constant tip-sample separation distance, using the SICM feedback control that keeps the ion current through the pipette constant.
  • the SICM controller produces a surface image of the cell, and makes possible a straightforward pipette approach precisely over an identified specific area or structure of the cell, to within approximately 100 nm from the cell membrane.
  • the apparatus used to carry out the method comprises a second piezo-actuator, to improve the stopping ability of the probe.
  • the hopping probe protocol requires immediate stoppage and withdrawal of the pipette when ion current is reduced to a specified set point. Delaying the stoppage and subsequent pipette withdrawal may result in pipette and/or sample damage due to collision.
  • FIG. 1 is a schematic diagram of the scanner where two piezo actuators are combined in order to serve as one long travel high speed actuator.
  • FIG. 1 Although the combined vertical actuator presented in FIG. 1 is intended to be operated in hopping probe mode it can be used for conventional DC or modulated scanning.
  • the fast piezo receives a pulse of driving signal that is generated by hopping probe control software immediately after the ion current reaches a specified set point.
  • a combined vertical actuator system is used in DC or modulated scanning, two separate feedback controls are used.
  • Primary feedback that has ion current as an input signal works as a SICM standard feedback and has its output connected to drive a fast short-travel piezo-actuator.
  • the secondary feedback uses a fast piezo-actuator position as an input signal and by adjusting the long travel actuator position brings the fast actuator to its middle range (see FIG. 8 ).
  • the present invention uses a scanning protocol developed to scan a subject surface with multiple resolutions. It scans interesting features with high resolution (slower scan) and low resolution (quicker scan) for un-interesting ones.
  • FIG. 3 shows an image generated according to the principles of the present invention in which the flat, un-interesting region in the lower portion of the image has been scanned at low resolution, whereas the rough, interesting region in the upper portion of the image has been scanned at high resolution.
  • a reduction in scan time of at least 50 percent can be achieved using the present invention. This therefore allows cells to be imaged at higher resolution than has previously been possible.
  • the entire surface to be imaged is divided into a number of individual squares. These squares can each be imaged at different resolutions and so the resultant image has multiple resolutions.
  • the square size is in pixels where each pixel is also used as an imaging point. The square sizes used were 4 ⁇ 4, 6 ⁇ 6, 8 ⁇ 8, 16 ⁇ 16 and 32 ⁇ 32 pixels. The image size is fixed to 512 ⁇ 512.
  • the entire surface to be imaged is scanned by imaging individual squares one by one. A 32 ⁇ 32 square forms 16 squares in a row and 16 lines to give 256 squares in the whole image. If a 4 ⁇ 4 square is used this yields 128 squares in a row and 128 lines, giving 16384 squares in the whole image.
  • Compression levels determine imaging resolutions. Higher compression levels give higher compression and therefore lower resolution. However, it takes less imaging points and less scanning time.
  • the compression levels used are: 1, 2, 4, 6, 8, 16 and 32. These levels are also in pixels; compression level 1 means image every pixel; level 4 means imaging 1 pixel for every 4 pixel.
  • a square cannot have compression level higher than its side length. A 32 ⁇ 32 square can use any compression levels up to 32, whereas a 4 ⁇ 4 square can only use compression levels up to 4. For instance, if a 4 ⁇ 4 square is used as shown in FIG.
  • An intermediate compression level d/ ⁇ square root over (2) ⁇ is created by overlaying two grids of measurement points corresponding to compression level d, displaced one from another by d/2 pixels in both x and y direction (see FIG. 9 ). Intermediate compression level d/ ⁇ square root over (2) ⁇ offers ⁇ square root over (2) ⁇ -times higher resolution than the closest higher standard resolution level at only 2-times slower scanning speed.
  • scanning consists of a prescan and a final scan.
  • the prescan is used to determine the resolution of the square, and the subsequent final scan records the topographical data of the square.
  • the probe is driven by the SCIM controller and interrogates each of four corner pixels of the square in turn, as shown in FIG. 5A .
  • the computer is configured to process the probe signals and compare the subject surface height (z) values for each of the four corner points. The maximum difference between these four pixels is compared with a defined “roughness” z height threshold. If the difference is greater than the threshold then the square region bounded by the corner points is rough and so a high resolution final scan is to be used, otherwise low resolution is used.
  • the final scan records topographical data after the prescan.
  • the final scan images the same square region at a number of discrete positions.
  • the spacing between the final scan imaging positions is dependent on the compression level elected by the computer following the prescan.
  • the square imaged at the four boundary corners in FIG. 5A is imaged in a final scan at 16 positions.
  • the different compression levels used to scan the regions of the subject surface to collect the topographical data represent the image resolutions of the resultant image. It is also possible to use only a single compression level, such that the same resolution is used everywhere in the image.
  • the standard external solution used for scanning of hippocampal neurons contained (mM): NaCl 145; KCl 3; CaCl 2 2.5; MgCl 2 1.2; Glucose 10; HEPES 10.
  • the loading solution used for FM1-43 staining of synaptic boutons contained (mM): NaCl 103; KCl 45; CaCl 2 2.5; MgCl 2 1.2; Glucose 10; HEPES 10 and 10 ⁇ M FM1-43 (Molecular Probes).
  • PBS composition, in mM, NaCl 137, KCl 2.7, KH 2 PO 4 1.5, Na 2 HPO 4 4.3, pH 7.2
  • nanopipettes were filled with PBS in all experiments. Both the external and pipette solutions were filtered using sterile 0.2 ⁇ m Acrodisc Syringe Filters (Pall Corporation, USA) to minimize blockage of nanopipettes during imaging.
  • Organ of Corti explants were dissected from mice at postnatal days 2-4 (P2-4) and placed in glass-bottom Petri dishes (WillCo Wells, Netherlands). The explants were cultured in DMEM medium supplemented with 25 mM HEPES and 7% fetal bovine serum (Invitrogen, Carlsbad, Calif.) at 37° C. and 95% air/5% CO 2 . Cultured organs of Corti were used in experiments within 1-5 days. In some experiments, 10 ⁇ g/ml of ampicillin (Calbiochem, La Jolla, Calif.) was added to the medium. The organs of Corti from left and right cochleae of a mouse were processed simultaneously.
  • the cultured organs of Corti were immersed in 2.5% glutaraldehyde in 0.1M cacodylate buffer supplemented with 2 mM CaCl 2 for 1-2 hours at room temperature.
  • One cochlea was used for HPICM imaging while the other one was used for SEM imaging.
  • Hippocampal neurons were prepared as described in Shah et al, J. Neurophysiol. 2000; 83:2554-2561, and cultured on glass coverslips to allow confocal microscopy. Cells were kept in an incubator at 37° C. and 95% air/5% CO 2 for 1 to 2 weeks. Once out of the incubator, cells were washed with standard external solution and scanned within two hours, at room temperature. For combined topography/fluorescent measurements hippocampal neurons were first incubated for 90 seconds at room temperature in 1.5 ml of loading solution to stain synaptic boutons with FM1-43 and then washed three times with a total volume of at least 10 ml of standard external solution and left for 15 min in the dark before imaging.
  • Nanopipettes were pulled from borosilicate glass (O.D. 1 mm, I.D. 0.58, Intracell, UK) using a laser-based puller Model P-2000 (Sutter Instruments Co., USA). Two different pipettes were used: Standard pipettes, displayed resistances ranging from 100 M ⁇ to 150 M ⁇ (measured in a standard external solution) and inner diameter of ⁇ 100 nm. These pipettes were used for scanning hippocampal neurons (Example 2). High resolution images of stereocilia bundles in cochlear hair cells (Example 1) were recorded with sharp pipettes, with resistances of ⁇ 400 M ⁇ (range 300-500 M ⁇ ) and estimated inner diameter of ⁇ 30 nm. The pipette inner diameters are estimated from the pipette resistance using a half cone angle of 3°.
  • the hopping technique requires careful damping of mechanical vibrations that arise from the large, rapid vertical motions of the Z-piezo with the attached probe.
  • the apparatus has the nanopipette moving in the Z-direction while the sample is mounted on a separate piezo system moving it in the X-Y plane ( FIG. 1 ). This separation of Z-piezo from the X-Y piezos is required to prevent mechanical interference.
  • the circuit that drives the movement of the piezo along the Z-axis is then tuned to allow a non-oscillating step response as fast as 1 ms.
  • Scan head #1 consisted of a PIHera P-621.2 XY Nanopositioning Stage (Physik Instrumente (PI), Germany) with 100 ⁇ 100 ⁇ m travel range that moved the sample and a LISA piezo actuator P-753.21C (PI, Germany) with travel range 25 ⁇ m for pipette positioning along the Z-axis. Coarse positioning was achieved with translation stages M-111.2DG (XY directions) and M-112.1DG (Z-axis) (PI, Germany).
  • the Z piezo actuator was driven by a 200 W peak power low voltage PZT amplifier E-505 (PI, Germany), while the XY nanopositioning stage was driven by 3 ⁇ 14 W amplifier E-503 (PI, Germany).
  • Scan head #2 consisted of a P-733.2DD Ultra-High-Speed, XY Scanning Microscopy Stage (PI, Germany) customized for 10 ⁇ 10 ⁇ m travel range (XY movement of the sample) and a LISA piezo actuator P-753.21C customized for 5 ⁇ m travel range (PI, Germany) that moved the nanopipette along Z-axis.
  • a translation stage M-112.1DG with a travel range of 25 mm (PI, Germany) was used for coarse positioning of the pipette in the Z-axis. All piezos were driven by 200 W peak power low voltage PZT amplifiers E-505 (PI, Germany).
  • Scan head #2 was used for high resolution scanning of the cochlear hair bundles. All other experiments were performed using scan head #1.
  • the LCS-DTL-364 laser diode (473 nm wavelength, Laser Compact, Moscow, Russia) was used to provide the excitation light source during confocal microscopy measurements.
  • the fluorescence signal was collected using oil-immersion objective 100 ⁇ 1.3 NA, an epifluorescent filter block and a photomultiplier with a pinhole (D-104-814, Photon Technology International, Surbiton, England).
  • the vertical Z positioning of the hopping probe and the movement of the sample in the XY plane were controlled by a SICM controller (Ionscope, UK) utilising a SBC6711 DSP board (Innovative Integration, USA) at a sampling frequency of 20 kHz.
  • the measurement of height at each imaging point consisted of three phases. First, the probe was withdrawn from its existing position either by a specified distance or to a specified absolute height level. Second, the vertical position of the probe was maintained for 10 ms, while the XY Nanopositioning Stage completed the sample's movement to a new point in the XY plane. During this time a reference current I REF was measured as an average of the DC current through the HPICM probe.
  • the probe was lowered at constant fall rate of 100 nm/ms (for a standard pipette) or 30 nm/ms (for a sharp pipette) while monitoring the difference in current, ⁇ I, between I REF and the instantaneous value of current through the probe I MV .
  • ⁇ I exceeded the specified value of the setpoint, I S , during at least four consecutive sample periods (that is 200 ⁇ s)
  • the vertical position of the probe was saved into the corresponding image pixel and the probe was quickly withdrawn by a specified hop amplitude to start a new measurement cycle.
  • I S values ranged from 0.25 to 1% of I REF .
  • the final topography of a “512 ⁇ 512” pixels image was actually acquired in squares of different sampling/resolution depending on the roughness observed within each square.
  • the sizes of the squares were 4 ⁇ 4, 8 ⁇ 8, 16 ⁇ 16, and 32 ⁇ 32 pixels, while the resolution levels were equivalent to 512 ⁇ 512, 256 ⁇ 256, 128 ⁇ 128, 64 ⁇ 64, 32 ⁇ 32, 16 ⁇ 16 pixels per whole image.
  • Example 2 Large area images of hippocampal neural network at a high resolution (Example 2) were typically taken with a pre-scan hop amplitude of 5 ⁇ m, square size of 4 ⁇ 4 pixels, two resolution levels of 256 ⁇ 256 and 128 ⁇ 128 pixels and R T value of 100 nm.
  • the pre-scan hop amplitude was reduced to 3 ⁇ m and the R T value to 25 nm for the high resolution scans of hair bundles (Example 1).
  • the square size was typically increased to 8 ⁇ 8 pixels and the resolution levels of 128 ⁇ 128 and 64 ⁇ 64 were used.
  • the overall time required to image the specimen varied significantly depending on the proportion of the sample area exhibiting high roughness.
  • imaging duration increased with slower probe fall rates (i.e. with sharper probes), smaller size of scan squares, higher pre-scan hop amplitude and higher resolution level.
  • High resolution images of elaborate samples took between 30 and 40 min. The images of less elaborated areas took 5 to 12 min. Note that at each imaging square the upward hopping typically starts at the different initial heights. Therefore, the algorithm allows us to “climb” up a tall sample without an excessive increase of the amplitude of the hops in each imaging square.
  • the HPICM pipette was positioned over the region of interest and lowered down to a safe distance of about 200 ⁇ m from the sample surface. Then the 100 ⁇ oil-immersion objective was chosen and an automated approach algorithm brought the HPICM probe to a distance of about one pipette radius from the sample surface. The XY position of the whole microscope platform was then adjusted to align the tip of the pipette with the confocal laser beam. To minimise photo-bleaching, fluorescence images of the selected area were recorded within 3 min separately from topography. The HPICM probe was retracted by ⁇ 24 ⁇ m to prevent pipette-sample collisions during rapid fluorescence acquisition. Topography imaging of the same area was performed immediately after obtaining a fluorescent image.
  • the fixed organs of Corti were dissected in ultra-pure distilled water, dehydrated in a graded series of acetone, and critical-point dried from liquid CO 2 . Then, the specimens were sputter-coated (EMS 575X Sputter Coater, Electron Microscopy Sciences, USA) with 5.0 nm of platinum under control with a film thickness monitor (EMS 150). The coated specimens were observed with a field-emission SEM (S-4800, Hitachi Technologies, Japan) at low accelerating voltage (1-5 kV).
  • Raw height data obtained with varying resolution were interpolated using bilinear interpolation to produce a final image of 512 ⁇ 512 pixels.
  • the images were corrected to remove stripes caused by small displacement of XY nanopositioning stages in Z-axis and further corrected for the slope present in the preparations to aid visualisation of fine details.
  • the experimental approach curve demonstrates that the minimum reliably detectable current drop, expressed as a percentage of the reference current recorded far from surface (I REF ), ranges from 0.25% (for a standard pipette of 100 nm inner diameter) to 0.75% (for a sharp pipette of 30 nm inner diameter). Because of the high signal-to-noise ratio of the current measurements in our experimental setup, the estimated vertical resolution at a 1% setpoint is 9 nm for a standard pipette and 6 nm for a sharp pipette. The real vertical resolution depends on the lateral dimension of the feature. The vertical sensitivity of the 30 nm pipette can be further improved to ⁇ 3 nm using a 1 kHz low-pass filter instead of a standard 5 kHz. However, this would reduce the response time of the feedback control.
  • links fine extracellular filaments (links) that interconnect stereocilia and are crucial for their mechanosensory function, were imaged. These links could be as small as ⁇ 8-10 nm in diameter. In wild type hair cells, most of the links are inaccessible to the HPICM probe, because it approaches vertically to the bundle. Therefore, we used abnormally short, but still mechanosensitive, stereocilia of Shaker 2 mice ( FIG. 6 d - f ).
  • HPICM uses the same sensor as SICM and, therefore, shares the same physical principles that determine lateral and vertical resolution.
  • the HPICM and SEM observations are therefore in excellent agreement, demonstrating the high resolution that is attainable.
  • FIG. 7 a live hippocampal neurons were examined ( FIG. 7 a ), which represent an unmet challenge for any scanning probe microscopy because of the complex three dimensional shapes that are formed by axons and dendrites.
  • HPICM revealed structures that resembled synaptic boutons ( FIG. 7 b, c ) as well as very fine (down to 50-60 nm in diameter) processes, tentatively identified as axons ( FIG. 7 b,c ).
  • This specimen was labelled with FM1-43, an activity-dependent marker that is accumulated in synaptic vesicles during cycles of endo- and exocytosis, and recorded the topography and the FM1-43 fluorescence of the same sample. Whenever a fluorescent signal was observed, it was also possible to identify varicosities in the images ( FIG. 7 d - g ). The size and shape of these varicosities is consistent with the geometry expected of synaptic boutons.
  • Mapping ion channels on cell membrane has been a great interest in biology.
  • live neurons were stimulated to open their ion channels by depolarisation of the cell membrane.
  • the response of neurons was measured using fluorescence detection with simultaneous scanning.
  • the cells were loaded with fluo4 dye which is sensitive to high calcium concentration and the pipette was filled with solution that contained potassium.
  • Potassium ions released from the pipette tip depolarised the cell membrane, while the pipette close to the surface, causing the cell membrane to open its calcium channels. Calcium ions entered the cell through these channels and combined with fluo4, causing the dye to become fluorescent.
  • a negative voltage potential in the pipette was used to keep potassium inside the tip prior to the scan.
  • a positive voltage was used for dosing potassium out of the pipette during scan.
  • the hopping setpoint used was between 0.5%-0.7% drop of the reference ion current and the hopping amplitude was between 5 ⁇ 7 ⁇ m.
  • the pipette was positioned 80 nm above the cell membrane for 80 ms. In this period, potassium ions released from the pipette locally depolarised the cell membrane and the excited fluorescence signal, due to influx of calcium, was collected as shown in FIGS. 11 A&D.
  • FIGS. 11 B&E a reference signal measured when the pipette was far away from the membrane at each pixel, was subtracted from the excited fluorescence signal to produce a differential signal. From these images, it can be clearly seen that part of neuron cell body and dendrites were depolarised by the pipette's stimulation, and the ion channels were mapped as a result. The excited fluorescence signal was recorded and burst was observed while the pipette was close to the cell membrane, which is indicated of the opening of ion channels, as shown in FIG. 12 .

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