text: referring to fig1 and 2 , the alignment tool 2 a comprises a generally planar rigid member carrying on its face a detailed pattern of optical features suitable for calibration of the instrument . the rigid member is typically of the same dimensions as the microscope slide , microarray chip or other object to be examined , to fit in the same position on the instrument . the optical features of the alignment tool include lines and circular dots of various dimensions to emulate the various sizes of dots and linear features of biological or other material to be examined . the finest features have dimensions of the order of 1 micron or less to suitably calibrate for detection of features of a few micron dimensions or less . the calibration tool shown in fig1 and 2 includes regions t - 1 , t - 2 , t - 3 , t - 4 , and t - 5 . region t - 1 includes a set of “ barcode ” lines having thickness 2 micron , 4 micron , 6 micron , 8 micron , 10 micron , and 12 micron , separated by twice their size . region t - 2 include a long 5 micron and 10 micron line across . region t - 3 includes a solid layer of the fluorescing material . region t - 4 includes three arrays of circular features having diameters from 300 micron to 25 micron , and squares having sizes from 300 micron to 25 micron . region t - 5 is a solid metallic area . referring to fig3 , in one preferred embodiment the first step in manufacture of the calibration tool is to provide a rigid support plate having effective fluorophores confined to a solid surface layer 4 of only an incremental thickness , see fig2 . typically this depth , delta t , is negligible such that fluorescent emission occurs essentially as a surface phenomenon . upon this layer , step two , a nickel or other suitable very thin and opaque metal film is applied that is etchable to form a reference pattern . sputter coating , vacuum metal deposition or other known techniques may be employed . a photo - resist is then applied in general to the metal layer , the photoresist on the tool preform is exposed through a precision mask defining the alignment features and then the surface is chemically etched to form the resulting reference pattern . the resultant tool is used to calibrate fluorescence measurements as well as the conventional image components of fluorescent microscopes . referring to fig4 , an oscillating arm 19 , rotating about axis a , carries an on - axis micro objective lens 18 for on - axis scanning over the alignment tool 2 a which is positioned in the place ordinarily occupied by specimens to be examined . mirrors 15 and 17 are effective to introduce excitation light from a stationary laser source , along axis of rotation a , thence out along the arm to lens 18 , thence to the specimen ( or in this case , to the calibration tool ). light reaching the surface layer 4 of the tool excites effective fluorophores , which emanate in all directions at a different wavelength . a significant feature is that this radiation is captured by micro lens 18 ( whose axis is always perpendicular to the object plane ), and directed back through the optical path and through a restriction such as a pin hole 103 , to detector d , 95 , typically a photo multiplier tube ( pmt ). in the case of fig4 , the surface layer 4 is a separately applied layer of uniform minimum thickness applied to a solid , optically flat , opaque support plate . preferably surface layer 4 is also opaque such that excited light does not substantially penetrate even the surface layer ; but even if it does penetrate to a degree , because of the great uniformity of the layer , and the non - emitting character of its support , any incidental fluorescence from below the surface layerδ t is uniform throughout , hence its disturbing effect can in many instances be tolerated . depending upon the particular instrument and application , in some cases , in which the solid surface layer is extremely thin and sufficiently uniform in thickness and distribution of fluorophore , the surface layer need not be opaque and will still function appropriately to produce essentially only surface emissions . the alternative processes of fig5 and 5 b are self explanatory , both producing calibration tools which , in use , are illuminated by light passing through the transparent pattern support . the tool of fig5 a is produced by the steps of fig5 while the tools of fig5 d and 6 are produced employing the steps of fig5 b . the tools of fig5 d and 6 differ from each other in the same respect that tools of fig4 and 4a differ , described above . the resultant tools are effective to enable standardization of wide field of view fluorescent scanning microscopes such as the microscope depicted in fig8 and 9 . this microscope is described in detail in pct application pct / us99 / 06097 , published as wo99 / 47964 , entitled “ wide field of view and high speed scanning microscopy ,” which is hereby incorporated by reference as if fully set forth herein . it is sufficient to say that the micro objective lens 18 , mounted on a rotary arm 19 for on - axis scanning , is driven in rapid rotary oscillation movement by galvanometer or oscillating motor 3 , whose position is detected by position sensor 43 for the purpose of relating data acquisition to position on the specimen . by employing a pin hole or other restriction 103 in front of the light sensor 95 , the resulting confocal microscope has a significantly limited depth of field , which could not be calibrated well by prior techniques but which can be readily calibrated to high accuracy using calibration tools featuring broad band surface emission by fluorescence as has been described here . fig9 depicts employing a calibration tool as described above with a flying objective microscope , whereas fig1 depicts the subsequent scanning of a microarray using the same instrument , now calibrated , to achieve quantified fluorescence microscopy that can readily be compared to the results produced by other microscopes that have been calibrated in the same way . a rudimentary analysis of the amount of fluorescence required to stimulate an actual specimen is presented in the following appendix with respect to a commercial confocal fluorescence scanning microscope , based on a microlens carried on a rapidly oscillating arm , the 418 array scanner ™, available from genetic microsystems , inc . by following a similar analysis for other instruments one can arrive at suitable fluorescent levels for those instruments ; by considering the sets of data for all instruments a standard calibration tool is obtainable . flying objective microscope with on - axis scanning ( 418 array scanner available from genetic microsystems , inc .) in this table , illumination power represents the amount of power that is typically delivered to the microscope slide for exciting fluorescent emission . the delivery efficiency ( 2 ) is defined by three values . the first is the geometric collection efficiency of the lens , based upon the size of the confocal pinhole and the distance to the microscope slide . for the instrument of the example , 13 % of the fluorescing light emitted is collected , i . e . the fluorescence light is emitted at the target with spherical distribution , and the instrument collects 13 % of that light . that light passes through a dichroic mirror , necessarily involving a loss factor , so that 90 % of the light is passed and 10 % is reflected elsewhere in the system and is wasted . finally , in front of the photomultiplyer tube an emission filter passes about 60 % of the fluorescent light . the emission filter is a multi - layer optical filter which rejects the excitation light that accompanies the fluorescent energy which is generally centered about 25 – 30 nanometers away from the wavelength of the excitation laser energy . the model 418 array scanner instrument operates at 532 and 637 nanometer . another useful wavelength is 473 nanometer . at these wavelengths , for this instrument , the surface layer of fluorescing material in the calibration tool must produce fluorescence power leaving its surface of the order of at least 1 millionth the illumination power reaching a specimen . the product of the three numbers discussed , 0 . 13 × 0 . 9 × 0 . 6 , shows that the delivery efficiency is approximately 0 . 070 . referring further to the table , line 3 relates to the gain of the photomultiplyer tube modules employed in the 418 array scanner . the modules with the least gain have a gain of 5 volts per nanowatt , meaning typically around 637 nm σ , the pmt produces a 5 volt signal for every nanowatt of light reaching it . at line 4 , the 418 array scanner system is such that when a full strength signal is obtained , the instrument produces ½ a volt at the photomultiplyer tube . thus by assuming that a desired test material will saturate the weakest photomultiplyer tube , an equation is produced that shows the desired performance of the material . the response of the photomultiplyer tube is equal to the gain times the signal ( amount of light falling on the photomultiplyer tube ). this gives a signal equal to ½ volt divided by 5 volts per nanowatt , or 0 . 1 nanowatts of light are obtained at the photomultiplyer tube . by taking the 0 . 1 nanowatt and dividing it by the efficiency of 0 . 07 , one determines that at the microscope slide 1 . 4 nanowatts of fluorescent light are produced , or a little higher . thus , the fluorescence production rate is approximately 1 . 4 or 1 . 5 × 10 − 9 which is the nanowatts divided by 3 × 10 − 3 , which is equal to 3 milliwatts . this results in a value of about ½ × 10 − 6 or a factor of 1 million , meaning that for each fluorescing photon reaching the pmt , approximately 1 million photons are required to impinge on the surface layer of fluorescent material . this shows that the fluorescent efficiency of the fluorophore needs to be approximately 1 × 10 − 6 or higher . it needs to receive 10 6 photons for every photon it emits . accordingly , the conversion efficiency of a suitable fluorescent reference material needs to be of the order of 1 × 10 − 6 or higher .