U.S. patent application number 10/910562 was filed with the patent office on 2005-03-31 for method and system for automated focus-distance determination for molecular array scanners.
Invention is credited to Corson, John F., Curry, Bo U., Parker, Russell A., Woods, Stanley P., Zhou, Xiangyang.
Application Number | 20050067583 10/910562 |
Document ID | / |
Family ID | 27753852 |
Filed Date | 2005-03-31 |
United States Patent
Application |
20050067583 |
Kind Code |
A1 |
Corson, John F. ; et
al. |
March 31, 2005 |
Method and system for automated focus-distance determination for
molecular array scanners
Abstract
An automated method and system for determining an optimal focus
distance for scanning a molecular array by a molecular array
scanner. Blocks of rows of a reference array are automatically
scanned at successively greater distances of the stage from a light
gathering medium, such as an optical fiber, or z-positions, to
produce data providing a functional relationship between z-position
and measured signal intensities. The data is then processed by a
peak-height-based, or window-based, focus-finding routine that
selects an optimal focus-distance for data scans.
Inventors: |
Corson, John F.; (Mountain
View, CA) ; Woods, Stanley P.; (Cupertino, CA)
; Parker, Russell A.; (San Jose, CA) ; Zhou,
Xiangyang; (Mountain View, OH) ; Curry, Bo U.;
(Redwood City, CA) |
Correspondence
Address: |
AGILENT TECHNOLOGIES, INC.
Legal Department, DL429
Intellectual Property Administration
P.O. Box 7599
Loveland
CO
80537-0599
US
|
Family ID: |
27753852 |
Appl. No.: |
10/910562 |
Filed: |
August 2, 2004 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10910562 |
Aug 2, 2004 |
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10086743 |
Feb 28, 2002 |
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6770892 |
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Current U.S.
Class: |
250/458.1 |
Current CPC
Class: |
G01N 21/6458 20130101;
G01N 21/6452 20130101; G01N 2021/6463 20130101 |
Class at
Publication: |
250/458.1 |
International
Class: |
G01N 021/64 |
Claims
1. A method for determining an optimal focus distance of a
molecular scanner, the method comprising: scanning portions of a
reference array over a range of positions, each position
representing a different distance between an illuminated region of
the reference array and an emitted-light detection component of the
molecular array, each portion scanned at a different position;
assembling data collected from scanning the reference array into a
representation of an intensity/position function; and employing a
focus-distance determination method to determine an optimal focus
distance or range of focus distances.
2. The method of claim 1 wherein scanning portions of a reference
array over a range of positions relative to an emitted-light
detection component further includes: for each position, scanning a
set of rows, filtering the intensity values scanned for each row,
and averaging the intensity values for the set of rows into an
average intensity value for the position.
3. The method of claim 1 wherein assembling data collected from
scanning the reference array into a representation of an
intensity/position function further includes associating each
position with an average intensity value.
4. The method of claim 1 wherein employing a focus-distance
determination method to determine an optimal focus distance or
range of focus distances further includes employing a
peak-intensity-focus-distance determination method.
5. The method of claim 4 wherein the peak-intensity-focus-distance
determination method comprises: using an intensity/position
function for each channel of the molecular array scanner,
determining the position of the peak intensity in the
intensity/position function, and starting from the peak-intensity
position, moving right and left in position in order to identify a
left plateau position and a right plateau position at which the
corresponding intensity falls below a threshold value, and
selecting the positions between the left plateau position and the
right plateau position as the plateau interval for the channel;
determining an overlap position interval corresponding to the
overlap in position of the plateau intervals of each channel; and
when the overlap position interval and plateau for each channel
meet acceptance criteria, returning a position within a plateau
interval as the focus distance.
6. The method of claim 5 wherein the acceptance criteria comprise
the overlap position interval having a size greater than an overlap
position interval threshold size and the plateau for each channel
having a size greater than a plateau threshold size.
7. The method of claim 1 wherein employing a focus-distance
determination method to determine an optimal focus distance or
range of focus distances further includes employing a
window-focus-distance determination method.
8. The method of claim 7 wherein the focus-distance determination
method comprises: using an intensity/position function for each
channel of the molecular array scanner, determining the position of
the peak intensity in the intensity/position function for each
channel, and returning an error when the positions of peak
intensity for each channel do not all fall within a central portion
of the range of position; finding, for each channel, a plateau
interval in the intensity/position function for the channel;
finding an overlap position interval that represents overlap in
positions from the plateau intervals for each channel; when the
overlap position interval meets a set of acceptance criteria,
finding a focus-distance within the overlap position interval.
9. The method of claim 8 wherein finding, for each channel, a
plateau interval in the intensity/position function for the channel
further includes: for decreasing window intervals sizes, searching
window intervals in the position range of the intensity/position
function for the channel for a window interval in which intensities
differ by less than a threshold value, when a single window
interval contains intensities that differ by less than the
threshold value, returning the single window interval, when more
than one window interval contains intensities that differ by less
than a threshold value, selecting a window interval having the
least difference in intensities and returning the selected window
interval, and when the current window interval size is less than a
minimum window interval size, returning a default window
interval.
10. The method of claim 9 wherein finding a focus-distance within
the overlap position interval further includes: starting from a
center position within the overlap position interval, searching
outward from the center position to find a small window interval
closest to the center position with intensity differences less than
a small-window-final-intens- ity-difference threshold.
11. Signal intensity data scanned from the surface of a molecular
array at a focus distance determined by the method of claim 1
encoded by: storing representations of the signal intensity data in
a machine readable medium; transmitting representations of the
signal intensity data over an electronic communications medium;
displaying the signal intensity data on display device; and
printing representations of the signal intensity data in a human
readable medium.
12. A set of computer instructions for carrying out the method of
claim 1 encoded by one of: storing the computer instructions in a
machine readable medium; transmitting the computer instructions
over an electronic communications medium; and printing the computer
instructions in a human readable medium.
13. A molecular array scanner comprising: a probe-molecule
excitation system; an emitted-light photodetection system that
produces a signal representative of the emitted-light intensity; a
molecular-array-holding stage that holds a molecular array for
scanning and that can be moved through a range of positions that
place an illuminated region of the surface of the molecular array
at different distances from the emitted-light photodetection
system; and an automated focus-distance-determination
subsystem.
14. The molecular array scanner of claim 13 wherein the automated
focus-distance determination subsystem: scans portions of a
reference array over a range of positions, each position
representing a different distance between an illuminated region of
the reference array and the emitted-light photodetection system,
each portion scanned at a different position; assembles data
collected from scanning the reference array into a representation
of an intensity/position function; and employs a focus-distance
determination method to determine an optimal focus distance or
range of focus distances.
15. The molecular array scanner of claim 14 wherein the automated
focus-distance-determination subsystem scans portions of a
reference array over a range of positions by: for each position,
scanning a set of rows, filtering the intensity values scanned for
each row, and averaging the intensity values for the set of rows
into an average intensity value for the position.
16. The molecular array scanner of claim 15 wherein the automated
focus-distance-determination subsystem assembles data collected
from scanning the reference array into a representation of an
intensity/position function by associating each position with an
average intensity value.
17. The molecular array scanner of claim 15 wherein the automated
focus-distance-determination subsystem employs a focus-distance
determination method to determine an optimal focus distance or
range of focus distances by employing a
peak-intensity-focus-distance determination method.
18. The molecular array scanner of claim 15 wherein the automated
focus-distance-determination subsystem employs a focus-distance
determination method to determine an optimal focus distance or
range of focus distances by employing a window-focus-distance
determination method.
19. Signal intensity data scanned from the surface of a molecular
array at a focus distance determined by the molecular array scanner
of claim 13 encoded by: storing representations of the signal
intensity data in a machine readable medium; transmitting
representations of the signal intensity data over an electronic
communications medium; displaying the signal intensity data on
display device; and printing representations of the signal
intensity data in a human readable medium.
20. A set computer instructions that implement the
molecular-array-scanner automated focus-distance-determination
subsystem of claim 1 encoded by one of: storing the computer
instructions in a machine readable medium; transmitting the
computer instructions over an electronic communications medium; and
printing the computer instructions in a human readable medium.
Description
[0001] This application claims priority to copending application
Ser. No.10/086,743, filed Feb. 28, 2002, under 35 U.S.C. 120, the
entirety of which is incorporated herein by reference.
TECHNICAL FIELD
[0002] The present invention relates to the molecular array
scanners and, in particular, to automated adjustment of the focal
distance at which a sample molecular array is positioned with
respect to laser light sources and photodetectors to produce
optimal data acquisition.
BACKGROUND OF THE INVENTION
[0003] The present invention is related to acquisition of
molecular-array data and other types of genetic, biochemical, and
chemical data from molecular arrays by molecular array scanners. A
general background of molecular-array technology is first provided,
in this section, to facilitate discussion of the scanning
techniques described in following sections.
[0004] Array technologies have gained prominence in biological
research and are likely to become important and widely used
diagnostic tools in the healthcare industry. Currently,
molecular-array techniques are most often used to determine the
concentrations of particular nucleic-acid polymers in complex
sample solutions. Molecular-array-based analytical techniques are
not, however, restricted to analysis of nucleic acid solutions, but
may be employed to analyze complex solutions of any type of
molecule that can be optically or radiometrically scanned and that
can bind with high specificity to complementary molecules
synthesized within, or bound to, discrete features on the surface
of an array. Because arrays are widely used for analysis of nucleic
acid samples, the following background information on arrays is
introduced in the context of analysis of nucleic acid solutions
following a brief background of nucleic acid chemistry.
[0005] Deoxyribonucleic acid ("DNA") and ribonucleic acid ("RNA")
are linear polymers, each synthesized from four different types of
subunit molecules. The subunit molecules for DNA include: (1)
deoxy-adenosine, abbreviated "A," a purine nucleoside; (2)
deoxy-thymidine, abbreviated "T," a pyrimidine nucleoside; (3)
deoxy-cytosine, abbreviated "C," a pyrimidine nucleoside; and (4)
deoxy-guanosine, abbreviated "G," a purine nucleoside. The subunit
molecules for RNA include: (1) adenosine, abbreviated "A," a purine
nucleoside; (2) uracil, abbreviated "U," a pyrimidine nucleoside;
(3) cytosine, abbreviated "C," a pyrimidine nucleoside; and (4)
guanosine, abbreviated "G," a purine nucleoside. FIG. 1 illustrates
a short DNA polymer 100, called an oligomer, composed of the
following subunits: (1) deoxy-adenosine 102; (2) deoxy-thymidine
104; (3) deoxy-cytosine 106; and (4) deoxy-guanosine 108. When
phosphorylated, subunits of DNA and RNA molecules are called
"nucleotides" and are linked together through phosphodiester bonds
110-115 to form DNA and RNA polymers. A linear DNA molecule, such
as the oligomer shown in FIG. 1, has a 5' end 118 and a 3' end 120.
A DNA polymer can be chemically characterized by writing, in
sequence from the 5' end to the 3' end, the single letter
abbreviations for the nucleotide subunits that together compose the
DNA polymer. For example, the oligomer 100 shown in FIG. 1 can be
chemically represented as "ATCG." A DNA nucleotide comprises a
purine or pyrimidine base (e.g. adenine 122 of the deoxy-adenylate
nucleotide 102), a deoxy-ribose sugar (e.g. deoxy-ribose 124 of the
deoxy-adenylate nucleotide 102), and a phosphate group (e.g.
phosphate 126) that links one nucleotide to another nucleotide in
the DNA polymer. In RNA polymers, the nucleotides contain ribose
sugars rather than deoxy-ribose sugars. In ribose, a hydroxyl group
takes the place of the 2' hydrogen 128 in a DNA nucleotide. RNA
polymers contain uridine nucleosides rather than the
deoxy-thymidine nucleosides contained in DNA. The pyrimidine base
uracil lacks a methyl group (130 in FIG. 1) contained in the
pyrimidine base thymine of deoxy-thymidine.
[0006] The DNA polymers that contain the organization information
for living organisms occur in the nuclei of cells in pairs, forming
double-stranded DNA helixes. One polymer of the pair is laid out in
a 5' to 3' direction, and the other polymer of the pair is laid out
in a 3'to 5' direction. The two DNA polymers in a double-stranded
DNA helix are therefore described as being anti-parallel. The two
DNA polymers, or strands, within a double-stranded DNA helix are
bound to each other through attractive forces including hydrophobic
interactions between stacked purine and pyrimidine bases and
hydrogen bonding between purine and pyrimidine bases, the
attractive forces emphasized by conformational constraints of DNA
polymers. Because of a number of chemical and topographic
constraints, double-stranded DNA helices are most stable when
deoxy-adenylate subunits of one strand hydrogen bond to
deoxy-thymidylate subunits of the other strand, and deoxy-guanylate
subunits of one strand hydrogen bond to corresponding
deoxy-cytidilate subunits of the other strand.
[0007] FIGS. 2A-B illustrate the hydrogen bonding between the
purine and pyrimidine bases of two anti-parallel DNA strands. FIG.
2A shows hydrogen bonding between adenine and thymine bases of
corresponding adenosine and thymidine subunits, and FIG. 2B shows
hydrogen bonding between guanine and cytosine bases of
corresponding guanosine and cytosine subunits. Note that there are
two hydrogen bonds 202 and 203 in the adenine/thymine base pair,
and three hydrogen bonds 204-206 in the guanosine/cytosine base
pair, as a result of which GC base pairs contribute greater
thermodynamic stability to DNA duplexes than AT base pairs. AT and
GC base pairs, illustrated in FIGS. 2A-B, are known as Watson-Crick
("WC") base pairs.
[0008] Two DNA strands linked together by hydrogen bonds forms the
familiar helix structure of a double-stranded DNA helix. FIG. 3
illustrates a short section of a DNA double helix 300 comprising a
first strand 302 and a second, anti-parallel strand 304. The
ribbon-like strands in FIG. 3 represent the deoxyribose and
phosphate backbones of the two anti-parallel strands, with
hydrogen-bonding purine and pyrimidine base pairs, such as base
pair 306, interconnecting the two strands. Deoxy-guanylate subunits
of one strand are generally paired with deoxy-cytidilate subunits
from the other strand, and deoxy-thymidilate subunits in one strand
are generally paired with deoxy-adenylate subunits from the other
strand. However, non-WC base pairings may occur within
double-stranded DNA.
[0009] Double-stranded DNA may be denatured, or converted into
single stranded DNA, by changing the ionic strength of the solution
containing the double-stranded DNA or by raising the temperature of
the solution. Single-stranded DNA polymers may be renatured, or
converted back into DNA duplexes, by reversing the denaturing
conditions, for example by lowering the temperature of the solution
containing complementary single-stranded DNA polymers. During
renaturing or hybridization, complementary bases of anti-parallel
DNA strands form WC base pairs in a cooperative fashion, leading to
reannealing of the DNA duplex. Strictly A-T and G-C complementarity
between anti-parallel polymers leads to the greatest thermodynamic
stability, but partial complementarity including non-WC base
pairing may also occur to produce relatively stable associations
between partially-complementary polymers. In general, the longer
the regions of consecutive WC base pairing between two nucleic acid
polymers, the greater the stability of hybridization between the
two polymers under renaturing conditions.
[0010] The ability to denature and renature double-stranded DNA has
led to the development of many extremely powerful and
discriminating assay technologies for identifying the presence of
DNA and RNA polymers having particular base sequences or containing
particular base subsequences within complex mixtures of different
nucleic acid polymers, other biopolymers, and inorganic and organic
chemical compounds. One such methodology is the array-based
hybridization assay. FIGS. 4-7 illustrate the principle of the
array-based hybridization assay. An array (402 in FIG. 4) comprises
a substrate upon which a regular pattern of features are prepared
by various manufacturing processes. The array 402 in FIG. 4, and in
subsequent FIGS. 5-7, has a grid-like two-dimensional pattern of
square features, such as feature 404 shown in the upper left-hand
corner of the array. It should be noted that many molecular arrays
contain disk-shaped features, rather than round features. Each
feature of the array contains a large number of identical
oligonucleotides covalently bound to the surface of the feature.
These bound oligonucleotides are known as probes. In general,
chemically distinct probes are bound to the different features of
an array, so that each feature corresponds to a particular
nucleotide sequence. In FIGS. 4-6, the principle of array-based
hybridization assays is illustrated with respect to the single
feature 404 to which a number of identical probes 405-409 are
bound. In practice, each feature of the array contains a high
density of such probes but, for the sake of clarity, only a subset
of these are shown in FIGS. 4-6.
[0011] Once an array has been prepared, the array may be exposed to
a sample solution of target DNA or RNA molecules (410-413 in FIG.
4) labeled with fluorophores, chemiluminescent compounds, or
radioactive atoms 415-418. Labeled target DNA or RNA hybridizes
through base pairing interactions to the complementary probe DNA,
synthesized on the surface of the array. FIG. 5 shows a number of
such target molecules 502-504 hybridized to complementary probes
505-507, which are in turn bound to the surface of the array 402.
Targets, such as labeled DNA molecules 508 and 509, that do not
contains nucleotide sequences complementary to any of the probes
bound to array surface, do not hybridize to generate stable
duplexes and, as a result, tend to remain in solution. The sample
solution is then rinsed from the surface of the array, washing away
any unbound labeled DNA molecules. Finally, the bound labeled DNA
molecules are detected via optical or radiometric scanning. FIG. 6
shows labeled target molecules emitting detectable fluorescence,
radiation, or other detectable signal. Optical scanning involves
exciting labels of bound labeled DNA molecules with electromagnetic
radiation of appropriate frequency and detecting fluorescent
emissions from the labels, or detecting light emitted from
chemiluminescent labels. When radioisotope labels are employed,
radiometric scanning can be used to detect the signal emitted from
the hybridized features. Additional types of signals are also
possible, including electrical signals generated by electrical
properties of bound target molecules, magnetic properties of bound
target molecules, and other such physical properties of bound
target molecules that can produce a detectable signal. Optical,
radiometric, or other types of scanning produce an analog or
digital representation of the array as shown in FIG. 7, with
features to which labeled target molecules are hybridized similar
to 706 optically or digitally differentiated from those features to
which no labeled DNA molecules are bound. In other words, the
analog or digital representation of a scanned array displays
positive signals for features to which labeled DNA molecules are
hybridized and displays negative features to which no, or an
undetectably small number of, labeled DNA molecules are bound.
Features displaying positive signals in the analog or digital
representation indicate the presence of DNA molecules with
complementary nucleotide sequences in the original sample solution.
Moreover, the signal intensity produced by a feature is generally
related to the amount of labeled DNA bound to the feature, in turn
related to the concentration, in the sample to which the array was
exposed, of labeled DNA complementary to the oligonucleotide within
the feature.
[0012] Array-based hybridization techniques allow extremely complex
solutions of DNA molecules to be analyzed in a single experiment.
An array may contain from hundreds to tens of thousands of
different oligonucleotide probes, allowing for the detection of a
subset of complementary sequences from a complex pool of different
target DNA or RNA polymers. In order to perform different sets of
hybridization analyses, arrays containing different sets of bound
oligonucleotides are manufactured by any of a number of complex
manufacturing techniques. These techniques generally involve
synthesizing the oligonucleotides within corresponding features of
the array through a series of complex iterative synthetic steps, or
depositing oligonucleotides isolated from biological material.
[0013] As pointed out above, array-based assays can involve other
types of biopolymers, synthetic polymers, and other types of
chemical entities. For example, one might attach protein antibodies
to features of the array that would bind to soluble labeled
antigens in a sample solution. Many other types of chemical assays
may be facilitated by array technologies. For example,
polysaccharides, glycoproteins, synthetic copolymers, including
block copolymers, biopolymer-like polymers with synthetic or
derivitized monomers or monomer linkages, and many other types of
chemical or biochemical entities may serve as probe and target
molecules for array-based analysis. A fundamental principle upon
which arrays are based is that of specific recognition, by probe
molecules affixed to the array, of target molecules, whether by
sequence-mediated binding affinities, binding affinities based on
conformational or topological properties of probe and target
molecules, or binding affinities based on spatial distribution of
electrical charge on the surfaces of target and probe
molecules.
[0014] An "array", unless a contrary intention appears, includes
any one, two or three dimensional arrangement of addressable
regions bearing a particular chemical moiety to moieties (for
example, biopolymers such as polynucleotide sequences) associated
with that region. An array is "addressable" in that it has multiple
regions of different moieties (for example, different
polynucleotide sequences) such that a region (a "feature" or "spot"
of the array) at a particular predetermined location (an "address")
on the array will detect a particular target or class of targets
(although a feature may incidentally detect non-targets of that
feature). Array features are typically, but need not be, separated
by intervening spaces. In the case of an array, the "target" will
be referenced as a moiety in a mobile phase (typically fluid), to
be detected by probes ("target probes") which are bound to the
substrate at the various regions. However, either of the "target"
or "target probes" may be the one which is to be evaluated by the
other (thus, either one could be an unknown mixture of
polynucleotides to be evaluated by binding with the other). An
"array layout" refers collectively to one or more characteristics
of the features, such as feature positioning, one or more feature
dimensions, and the chemical moiety or mixture of moieties at a
given feature. "Hybridizing" and "binding", with respect to
polynucleotides, are used interchangeably.
[0015] Any given substrate may carry one, two, four or more or more
arrays disposed on a front surface of the substrate. Depending upon
the use, any or all of the arrays may be the same or different from
one another and each may contain multiple spots or features. A
typical array may contain more than ten, more than one hundred,
more than one thousand more ten thousand features, or even more
than one hundred thousand features, in an area of less than 20
cm.sup.2 or even less than 10 cm.sup.2. For example, features may
have widths (that is, diameter, for a round spot) in the range from
a 10 .mu.m to 1.0 cm. In other embodiments each feature may have a
width in the range of 1.0 .mu.m to 1.0 mm, usually 5.0 .mu.m to 500
.mu.m, and more usually 10 .mu.m to 200 .mu.m. Non-round features
may have area ranges equivalent to that of circular features with
the foregoing width (diameter) ranges. At least some, or all, of
the features may be of different compositions (for example, when
any repeats of each feature composition are excluded the remaining
features may account for at least 5%, 10%, or 20% of the total
number of features). Interfeature areas will typically (but not
essentially) be present which do not carry any polynucleotide (or
other biopolymer of a type of which the features are composed).
Such interfeature areas typically will be present where the arrays
are formed by processes involving drop deposition of reagents but
may not be present when, for example, photolithographic array
fabrication processes are used. It will be appreciated though, that
the interfeature areas, when present, could be of various sizes and
configurations.
[0016] The array features can have widths (that is, diameter, for a
round spot) in the range from a minimum of about 10 .mu.m to a
maximum of about 1.0 cm. In embodiments where very small spot sizes
or feature sizes are desired, material can be deposited according
to the invention in small spots whose width is in the range about
1.0 .mu.m to 1.0 mm, usually about 5.0 .mu.m to 500 .mu.m, and more
usually about 10 .mu.m to 200 .mu.m. Features which are not round
may have areas equivalent to the area ranges of round features 16
resulting from the foregoing diameter ranges.
[0017] Each array may cover an area of less than 100 cm, or even
less than 50, 10 or 1 cm.sup.2. In many embodiments, the substrate
carrying the one or more arrays will be shaped generally as a
rectangular solid (although other shapes are possible), having a
length of more than 4 mm and less than 1 m, usually more than 4 mm
and less than 600 mm, more usually less than 400 mm; a width of
more than 4 mm and less than 1 m, usually less than 500 mm and more
usually less than 400 mm; and a thickness of more than 0.01 mm and
less than 5.0 mm, usually more than 0.1 mm and less than 2 mm and
more usually more than 0.2 and less than 1 mm. With arrays that are
read by detecting fluorescence, the substrate may be of a material
that emits low fluorescence upon illumination with the excitation
light. Additionally in this situation, the substrate may be
relatively transparent to reduce the absorption of the incident
illuminating laser light and subsequent heating if the focused
laser beam travels too slowly over a region. For example, substrate
10 may transmit at least 20%, or 50% (or even at least 70%, 90%, or
95%), of the illuminating light incident on the front as may be
measured across the entire integrated spectrum of such illuminating
light or alternatively at 532 nm or 633 nm.
[0018] Once the labeled target molecule has been hybridized to the
probe on the surface, the array may be scanned by an appropriate
technique, such as by optical scanning in cases where the labeling
molecule is a fluorophore or by radiometric scanning in cases where
the signal is generated through a radioactive decay of labeled
target. In the case of optical scanning, more than one fluorophore
can be excited, with each different wavelength at which an array is
scanned producing a different signal. In optical scanning, it is
common to describe the signals produced by scanning in terms of the
colors of the wavelengths of light employed for the scan. For
example, a red signal is produced by scanning the array with light
having a wavelength corresponding to that of visible red light.
[0019] Scanning of a feature by an optical scanning device or
radiometric scanning device generally produces a scanned image
comprising a rectilinear grid of pixels, with each pixel having a
corresponding signal intensity. These signal intensities are
processed by an array-data-processing program that analyzes data
scanned from an array to produce experimental or diagnostic results
which are stored in a computer-readable medium, transferred to an
intercommunicating entity via electronic signals, printed in a
human-readable format, or otherwise made available for further use.
Molecular array experiments can indicate precise gene-expression
responses of organisms to drugs, other chemical and biological
substances, environmental factors, and other effects. Molecular
array experiments can also be used to diagnose disease, for gene
sequencing, and for analytical chemistry. Processing of molecular
array data can produce detailed chemical and biological analyses,
disease diagnoses, and other information that can be stored in a
computer-readable medium, transferred to an intercommunicating
entity via electronic signals, printed in a human-readable format,
or otherwise made available for further use.
[0020] FIG. 8 illustrates components of a molecular array scanner.
Lasers 800a-b emit coherent light that passes through electro-optic
modulators ("EOMs") 810a-b with attached polarizers 820a-b. Each
EOM and corresponding polarizer together act as a variable optical
attenuator. A control signal in the form of a variable voltage is
applied to each EOM 810a-b by controller 880. The controller 880
may include a suitably programmed processor, logic circuit,
firmware, or a combination of software programs, logic circuits,
and firmware. The control signal changes the polarization of the
laser light, which alters the intensity of the light that passes
through the EOM. In general, laser 800a provides coherent light of
a different wavelength than that provided by laser 810b. For
example, one laser may provide red light and the other laser may
provide green light. The beams may be combined along a path toward
a stage 800 by the use of full mirror 851 and dichroic mirror 853.
The light from the lasers 800a-b is then transmitted through a
dichroic beam splitter 854, reflected off fully reflecting mirror
856, and then focused, using optical components in beam focuser
860, onto a molecular array mounted on a holder 800. Fluorescent
light, emitted at two different wavelengths (for example, green
light and red light) from features of the molecular array in
response to illumination by the laser light, is imaged using the
optics in the focuser/scanner 860, and is reflected off mirrors 856
and 854. The two different wavelengths are further separated by a
dichroic mirror 858 and are passed to photodetectors 850a-b. More
optical components (not shown in FIG. 8) may be used between the
dichroic mirror and the photodetectors 850a-b, such as lenses,
pinholes, filters, and fibers. The photodetectors 850a-b may be of
various different types, including photo-multiplier tubes,
charge-coupled devices, and avalanche photodiodes.
[0021] A scan system causes a light spot from each laser 800a-b to
be moved in a regular pattern about the surface of the molecular
array. The molecular array is mounted to a stage that can be moved
in horizontal and vertical directions to position light from the
lasers onto a particular region at the surface of the molecular
array, from which region fluorescent emission is passed back to the
photodetectors via the optical path described above. An autofocus
detector 870 is provided to sense and correct any offset between
different regions of the molecular array and the focal plane of the
system during scanning. An autofocus system includes detector 870,
processor 880, and a motorized adjuster to move the stage in the
direction of arrow 896.
[0022] The controller 880 receives signals from photodetectors
850a-b, called "channels," corresponding to the intensity of the
green and red fluorescent light emitted by probe labels excited by
the laser light. The controller 880 also receives a signal from
autofocus offset detector 870 in order to control stage adjustment,
provides the control signal to the EOMs 810a-b, and controls the
scan system. Controller 880 may also analyze, store, and output
data relating to emitted signals received from detectors
850a-b.
[0023] The dynamic autofocus mechanism, described above, provides a
means for maintaining a constant focus distance during scanning of
a molecular array. However, any of various different focus
distances may be selected to be held constant during a scan. In
general, the focus distance must correspond to the depth of focus
of the molecular array optics, but, in general, there is one or a
small range of optimal focus distances for a particular molecular
array scanner. Designers, manufacturers, and users of molecular
arrays have recognized a need for an automated focus-distance
optimization method.
SUMMARY OF THE INVENTION
[0024] One embodiment of the present invention provides an
automated method for determining an optimal focus distance for
scanning a molecular array by a molecular array scanner. Blocks of
rows of a reference array are automatically scanned over a range of
focus distances, or z-positions, to produce data providing a
functional relationship between focus distance, or z-position, and
measured signal intensities. The data is then processed by a
peak-height-based, or local variation-based, focus-finding routine
that selects an optimal focus distance for data scans.
[0025] The present invention further provides a computer program
product for use with an apparatus such as described herein. The
program product includes a computer readable storage medium having
a computer program stored thereon and which, when loaded into a
programmable processor, provides instructions to the processor of
that apparatus such that it will execute the procedures required of
it to perform a method of the present invention.
BRIEF DESCRIPTION OF THE DRAWINGS
[0026] FIG. 1 illustrates a short DNA polymer 100, called an
oligomer, composed of the following subunits: (1) deoxy-adenosine
102; (2) deoxy-thymidine 104; (3) deoxy-cytosine 106; and (4)
deoxy-guanosine 108.
[0027] FIGS. 2A-B illustrate the hydrogen bonding between the
purine and pyrimidine bases of two anti-parallel DNA strands.
[0028] FIG. 3 illustrates a short section of a DNA double helix 300
comprising a first strand 302 and a second, anti-parallel strand
304.
[0029] FIGS. 4-7 illustrate the principle of the array-based
hybridization assay.
[0030] FIG. 8 is a block diagram of major optical and electronic
components of a molecular array scanner.
[0031] FIG. 9 abstractly illustrates the scanner components related
to the automated focus-distance-determination method that
represents one embodiment of the present invention.
[0032] FIG. 10 illustrates the effect of small changes in the
z-position of an illuminated spot on the surface of a molecular
array with respect to the image of the emitted light from the
illuminated spot of the surface of the molecular array focused on
the surface of an optical fiber.
[0033] FIG. 11 shows a representation of the function of the signal
intensity I measured by the photodetector of a molecular array
scanner as a function of the z-position of an illuminated region of
the molecular array that generates the signal.
[0034] FIG. 12 illustrates the variation in signal intensity I with
z-position z in the vicinity of the peak of the I.sub.z curve.
[0035] FIG. 13 illustrates selection of an optimal focus distance
Z.sub.p.
[0036] FIG. 14 illustrates the signal intensity variation over a
z-position variation centered about the peak of the I/z curve.
[0037] FIG. 15 illustrates the scan pattern employed in a preferred
embodiment of the present invention.
[0038] FIG. 16 is a flow-control diagram for the optimal
focus-distance determination method "focus_distance" that
represents one embodiment of the present invention.
[0039] FIGS. 17-21 illustrate operation of the routine
"peak_intensity_focus" with reference to I/z functional curves.
[0040] FIG. 22 is a flow-control diagram for the routine
"peak_intensity_focus."
[0041] FIGS. 23-29 illustrate operation of window_focus using
graphical representations of I/z curves.
[0042] FIGS. 30-31 show flow-control diagrams that describe
operation of window_focus.
DETAILED DESCRIPTION OF THE INVENTION
[0043] One embodiment of the present invention is a method for
determining an optimal focus distance at which to scan the surface
of a molecular array during data collection from the molecular
array by an automated molecular array scanner. The molecular array
scanner includes dynamic autofocus functionality for maintaining
the focus distance at a constant value during scanning of a
molecular array. However, current scanners lack an automated
focus-distance optimizing feature, and instead require a tedious
and error-prone manual optimal focus-distance determination. The
method for automated focus-distance determination that represents
one embodiment of the present invention may be incorporated into
logic circuits, firmware, or software, or a combination of logic
circuits, firmware, and software, within the control logic of a
molecular scanner.
[0044] FIG. 9 abstractly illustrates the scanner components related
to the automated focus-distance determination method that
represents one embodiment of the present invention. A molecular
array 902 is mounted to the stage 904 of a molecular array scanner.
The stage 904 can be translated vertically and horizontally in a
plane coincident with the plane of the surface of the stage by X
and Y translation mechanisms not shown in FIG. 9. In addition, the
distance of the stage 904 from the optical fiber or other
light-gathering medium can be controlled by a distance-control
mechanism that moves the stage and stage support 906 in a direction
perpendicular to the plane of the scanner.
[0045] Light from a laser 908, focused and filtered via various
optic components 910, illuminates a small region of the array 912
from which light of a generally longer wavelength is emitted by
fluorescent or chemiluminescent compounds incorporated into target
molecules. The emitted light is filtered and focused by various
optical components 914 and 916 into a roughly disk-shaped spot 918
that impinges on the surface of an optical fiber 920 or another
light-collection medium that inputs emitted light from the surface
of the molecular array into a photodetector 922.
[0046] An orthogonal x, y, z coordinate system 924 is shown near
the left, lower corner of the molecular array-scanner stage 904 to
indicate the directions in which the stage can be moved relative to
the surface of the optical fiber 920 on which emitted light is
focused. The exact functional relationship between variations in
the distance from the emitted-light source to the surface of the
optical fiber 920, closely related to the distance of the stage
from the optical fiber 920, referred to as the z-position of the
stage, depends on the geometry of the laser, molecular array, and
optical fiber geometries. However, the focus-distance is a
continuous function of z-position. If the plane of the surface of
the molecular array 902 is not parallel to the plane of the surface
of the stage 904, then horizontal translations in the x, y plane of
the stage may also affect the distance between light-emitting probe
molecules on the surface of the molecular array and the optical
fiber 920. The dynamic autofocus feedback-control mechanism within
this scanner can dynamically adjust the z-position of the stage as
the stage is translated in the x, y plane in order to correct for
the small focus-distance variation during a scan due to
molecular-array-surface irregularities and positioning and
orientation problems that cause the plane of the surface of the
molecular array to be inclined with respect to the plane of the
surface of the stage. Thus, when an optimal focus-distance is
determined, a molecular array can be scanned at this focus distance
by the autofocus mechanisms within the scanner. Because the focus
distance is a continuous function of the z-coordinate of the
spatial location of the illuminated spot 912 of the molecular-array
surface, which is, in turn, a continuous function of the z-position
of the stage, the following discussion is related to optimizing the
z-position of the stage 904. It should be noted that the following
discussion and Figures could also be cast in terms of z-coordinate
of the laser-illuminated region of a molecular array, or the
distance of either the stage or the laser-illuminated region of a
molecular array from the emitted-light-collection medium.
[0047] FIG. 10 illustrates the effect of small changes in the
z-position of the stage, or z-coordinate of an illuminated spot on
the surface of a molecular array, with respect to the position of
the image of the emitted light from the illuminated spot of the
surface of the molecular array focused onto the surface of an
optical fiber. This is one example of how the measured intensity of
the emitted light can vary with changes in the focal distance.
Another example is the loss of emission-intensity due to the lack
of correct focus of the illuminated spot on the surface of the
molecular array.
[0048] In FIG. 10, the circular cross section of the surface of an
optical fiber (920 in FIG. 9) is represented by circles 1002-1007.
The image of an illuminated spot on the surface of the molecular
array is shown in FIG. 10 by various differently sized,
cross-hatch-filled circles 1008-1013. In FIG. 10, representations
1014-1019 of the focusing of the emitted light onto the plane of
the circular cross section of the surface of the optical fiber are
shown at the left. In each representation, a lens-like optic, e.g.
lens-like optic 1020, focuses light to a point, e.g. point 1021,
above, on, or below the plane, e.g. plane 1022, of the surface of
the optical fiber. As the illuminated spot on the surface of the
molecular array is moved in the z direction, the image of the
illuminated spot focused onto the surface of the optical fiber,
first defocused as illuminated spot 1008, focuses and decreases in
diameter relative to the diameter of the cross section of the
optical fiber. Illuminated spot 1010 represents a focused spot,
corresponding to the optics representation 1016. As the illuminated
spot on the surface of the molecular array is moved further in the
z direction, the illuminated spot gradually defocuses and grows in
diameter relative to the diameter of the cross section of the
optical fiber. At either extreme of the z-position range, as
indicated by optics representations 1014 and 1019, the image of the
illuminated spot is sufficiently defocused that the image of the
illuminated spot is larger than the cross section of the optical
fiber, and emission photons representing a portion of the
emitted-light are lost, resulting in a decrease in the intensity of
the resulting measured signal. In FIG. 10, the z-positions that
result in the corresponding respective sizes of the image of the
illuminated spot and the cross section of the optical fiber plotted
along a coordinate axis 1024 corresponding to the z-position of the
stage of the molecular scanner. The z-positions range from a lowest
value, Z.sub.max.sup.- to a highest z value, Z.sub.max.sup.+. In
FIG. 10, for example, the z-position of the stage resulting in a
centered, focused image of the illuminated spot on the surface of
the optical fiber 1026 is shown with z coordinate 1028. In FIG. 10,
a vertical coordinate axis 1030 is shown orthogonal to the
z-position coordinate axis 1024. This orthogonal coordinate axis
corresponds to the intensity of the emitted light detected by a
photodetector (922 in FIG. 9) of the molecular array scanner. In
FIG. 10, the horizontal lines, such as horizontal line 1032,
plotted along the vertical z-position axis represent the signal
intensities measured for a particular region of the surface of the
molecular array corresponding to the z-positions of the stage of
the molecular array. Again, as the image of the illuminated region
of the molecular array defocuses past the edges of the fiber, not
all of the emitted light is captured by the fiber and, as a result,
the intensities 1034-1036 of the signal level decreases
proportionally to the fraction of light that is missing the
fiber.
[0049] The graph of signal intensity to z-position, as shown in
FIG. 10, can be rotated 90 degrees and plotted as a continuous,
rather than a discrete, function. FIG. 11 shows a representation of
the function of the signal intensity I measured by the
photodetector of a molecular array scanner as a function of the
z-position of an illuminated region of the molecular array that
generates the signal. The function illustrated in FIG. 11 1102 is
exaggerated in order to clearly illustrate the general features of
a typical signal-intensity-to-z-position ("I/z") relationship for
one class of molecular array scanners. As in FIG. 10, the
functional relationship is plotted from a Z.sub.max.sup.- position
to a Z.sub.max.sup.+ position along the z-position axis 1104, with
the height of the curve representing the measured signal intensity
with respect to the signal-intensity axis 1106. Proceeding
rightward from the Z.sub.max.sup.- position 1108 towards to the
Z.sub.max.sup.+position 1110, the signal intensity sharply rises to
a signal intensity peak 1112 and then falls gradually to the edge
1114 of a steeply descending curve that falls back to nearly 0
intensity at Z.sub.max.sup.+. In one class of molecular array
scanners, the I/z function appears as a mesa, with the top of the
mesa (section of the curve between 1112 and 1114 in FIG. 11)
slanted slightly downward.
[0050] The autofocus mechanism within a molecular array scanner, as
with all electromechanical devices, is not infinitely precise.
Instead, the autofocus mechanism is capable of maintaining the
distance of the illuminated portion of a molecular array surface
within a small range of distances by controlling the z-position of
the stage. Thus, despite the autofocus mechanism, the z-position,
functionally related to the focus distance, varies slightly over
the course of a molecular array scan. FIG. 12 illustrates the
variation in signal intensity I with z-position z in the vicinity
of the peak of the I curve. In FIG. 12, the z coordinate for the
peak, zp, is plotted on the z axis 1202. The total variation in
z-position during a scan is shown by the interval .DELTA.z 1204
plotted from z.sub.l to z.sub.r on the z axis 1206-1207. The signal
intensity varies over the interval .DELTA.z 1204 by a corresponding
signal intensity interval .DELTA.I. Note that, for the typical I/z
functional relationship illustrated in FIG. 12, the signal
intensity varies over the entire .DELTA.I interval 1208 within the
portion of the .DELTA.z interval to the left of the peak position
Z.sub.p, while varying only relatively slightly in the portion of
the .DELTA.z interval to the right of the peak position Z.sub.p.
Thus, because of the asymmetry of the I/z curve with respect to the
peak position Z.sub.p, small fluctuations in the focus distance
corresponding to Z.sub.p may result in relatively large variation
in signal intensity.
[0051] It is desirable to select a focus distance that provides a
relatively slight variation in signal intensity corresponding to
slight variations in focus distance during scanning of a molecular
array. It is the goal of an autofocus mechanism to help maintain a
constant system sensitivity for a constant quantity of flurophore
over the entire surface of a molecular array. FIG. 13 illustrates
selection of an optimal focus distance Z.sub.f. As shown in FIG.
13, if the optimal focus distance Z.sub.f is chosen roughly
centered in the interval representing the top of the mesa of the
I/z curve, producing a .DELTA.z interval 1302 within the top of the
mesa, then the variation in signal intensity .DELTA.I 1304 over the
interval .DELTA.z is relatively small compared with the .DELTA.I
interval (1208 in FIG. 12) resulting from selection of the focus
distance at the peak of the I/z curve Z.sub.p.
[0052] If, by contrast, the scanner geometry and photo-detection
apparatus produces a symmetrical, Gaussian-like I/z functional
curve, selection of a focus distance corresponding to the
z-position of the curve peak Z.sub.p may result in the smallest
possible signal intensity variation. FIG. 14 illustrates the signal
intensity variation over a z-position variation centered about the
peak of the I/z curve.
[0053] Thus, either a focus distance corresponding to a z-position
at a positive offset from the peak z-position may be selected, for
I/z curves having slanted mesa forms, or a focus distance
corresponding to the peak z-position may be optimal for
symmetrical, Gaussian-like I/z functional relationships. In either
case, the optimal focus distance is a focus distance that gives a
relatively large signal intensity that varies relatively slightly
with variation in the focus distance.
[0054] The method for optimal focus distance selection that
represents one embodiment of the present invention relies on a
single-pass, automated scan of a reference molecular array. The
reference molecular array is prepared by precisely coating the
surface of a molecular array substrate with a
polymethylmethacrylate polymer ("PMMA") containing a fluorescent or
chemiluminescent dye. The PMMA polymer can be spun onto the surface
of a slide and, if necessary, planarized, using
PMMA-substrate-preparation techniques commonly employed in the
manufacture of semiconductors. PMMA-based reference arrays are far
more uniform than previously employed cyanine-dye reference arrays.
The U.S. patent application Ser. No. 10/008598 entitled "Devices
For Calibrating Optical Scanners And Methods Of Using The Same" by
Holcomb et al. (filed Dec. 4, 2001) details the PMMA-based
reference arrays, and is herein incorporated by reference.
[0055] FIG. 15 illustrates the scan pattern employed in a preferred
embodiment of the present invention. In FIG. 15, a molecular array
1502 is abstractly represented with horizontal rows, such as row
1504. The scan pattern involves scanning a fixed number of
contiguous rows n at each z-position over a range of z-positions
Z.sub.max.sup.- to Z.sub.max.sup.+. The z-position is incremented
by an increment i over this range of z-positions. For example, as
shown in FIG. 15, a contiguous block of n rows is first scanned at
z-position z=-7i, a second block of n contiguous rows is scanned at
z-position z=-6I 1508, and so on, up through scanning of the
continuous block of n rows 1510 at z-position z=7i. The number of
rows scanned at each z-position n, the z-position increment i, and
the range Z.sub.max.sup.- to Z.sub.max.sup.+ may all be specified
in a configuration file for the automated focus-distance
determination. Note that there are many alternative possible
focus-distance-determination scan patterns. In one embodiment of
the present invention, z positions ranging from -20.mu. (microns)
to +20.mu. are scanned at 0.25.mu. increments, with ten rows
scanned for each z-position.
[0056] In the following discussion, the described embodiment
relates to a two-channel molecular array scanner that measures
emitted light in red and green regions of the visible spectrum.
Thus, the following discussion refers to red and green channels and
red and green signals. However, the present invention is equally
applicable to single-channel molecular array scanners or to
molecular array scanners that measure more than two types of
signals, or measure signals from different parts of the
electromagnetic radiation spectrum.
[0057] FIG. 16 is a flow-control diagram for the optimal
focus-distance determination method "focus_distance" that
represents one embodiment of the present invention. In step 1602,
the scanner is initialized. Initialization involves checking the
scanner to make sure that the scanner is properly physically
configured, setting the photodetector voltages to default voltages,
initializing a stage motion controller(s), and loading the
reference molecular array into the scanner and verifying, via a bar
code imprinted on the surface of the molecular array, that the
reference molecular array is the appropriate reference molecular
array for the optimal focus-distance determination. In step 1604,
the optimal focus-distance determination configuration file is
input, specifying various parameters for the optimal focus-distance
determination, including the parameters n, i, Z.sub.max.sup.- and
Z.sub.max.sup.30 parameters described with reference to FIG. 15,
above. In step 1606, the reference array is scanned as specified by
the configuration-file parameters input in step 1604. The
reference-array scan results in a computer encoding of signal
intensities measured for discrete regions covering the surface of
the molecular array. In many molecular array scanners, these
signal-intensity results are encoded as integer or floating-point
values associated with pixels within the scanned image of the
molecular array. In the for-loop comprising steps 1608, 1610, and
1612, focus_distance filters and averages the signal intensities
for each block of n rows. The rows are filtered to remove saturated
pixels, or, in other words, pixels with intensity values that
exceed the linear range of the electronics (due, for example, to
dust), and the signal intensities of the remaining pixels are
averaged to produce an average intensity value corresponding to the
z-position at which the rows were scanned. Note that, if the number
of saturated pixels exceeds some specified threshold, the scan may
be rejected, and an indication displayed by the molecular array
scanner to a user indicating that the molecular array scanner needs
to be reconfigured in order to produce signal intensities within
appropriate ranges.
[0058] Next, in step 1614, the average intensity values for each
z-position are assembled into a computer-encoded format
corresponding to the I/z graphs shown in FIGS. 11-13 and 14, above.
Note that each type of signal, such as the red and green signals
described above, in the background section, are measured to produce
separate I/z functional relationship for each type of signal, or
channel. The computer-encoded data representing the I/z functional
relationship for each channel can then be scanned with respect to
z-position to determine the I and z coordinates of the peak of the
I/z curve. In step 1616, focus_distance determines whether the
z-positions of the I/z peaks for all channels fall within an
acceptable range of z-position values. If not, then focus_distance
displays an error message in step 1618 indicating the need for
resetting the coarse adjustment of the z-component of the autofocus
mechanism, or another resetting or reconfiguration of the molecular
array scanner, and then returns an error. If all the peaks fall
within an acceptable z-position range, then a focus routine is
called in step 1620. The focus routine called depends on the
geometry and configuration of the molecular array scanner. For
molecular array scanners that produce mesa-shaped I/z functional
curves, the routine "window_focus" is called. Alternatively, if the
molecular array scanner produces symmetrical, Gaussian-like curves,
as shown in FIG. 14, then the focus routine "peak_intensity_focus"
is called. Molecular scanners that produce other types of I/z
curves may need other, specific focus routines. The focus function
called in step 1620 produces an optimal z-position corresponding to
an optimal focus distance, Z.sub.f, that can be used by the
molecular array scanner for one or more data-acquisition scans.
[0059] Next, in step 1622, focus_distance graphically displays the
results of the optimal focus-distance determination to a user. If
the user wishes they can review the displayed information and can
input acceptance or rejection of the optimal focus-distance
determination. If the method is found to be robust enough for any
particular configuration of scanner, this step can be skipped and
the process be fully automated. If the optimal focus-distance
determination is accepted, as determined in step 1624, then the
optimal focus distance is stored into non-volatile memory within
the array scanner in step 1626, and focus_distance returns success.
The optimal focus distance may be stored in flash memory, for
example, or in other non-volatile memory storage, such as a mass
storage device. If the optimal focus distance is rejected, as
determined in step 1624, then the user is prompted for input as to
whether to retry the optimal focus-distance determination. If the
user elects not to retry the optimal focus-distance determination
then focus_distance returns an error. Otherwise, control flows back
to the initial step, step 1602.
[0060] For molecular scanners that produce Gaussian-like, roughly
symmetrical I/z curves, as shown in FIG. 14, the focusing routine
"peak_intensity_focus" is called from step 1620 of focus_distance,
described with reference to FIG. 16. FIGS. 17-21 illustrate
operation of the routine "peak_intensity_focus" with reference to
I/z functional curves. FIG. 22 is a flow-control diagram for the
routine "peak_intensity_focus." Note that the I/z curves shown in
FIGS. 17-21 are mesa-shaped curves characteristic of one class of
molecular array scanners. Although the routine
"peak_intensity_focus" provides best results for symmetrical,
Gaussian-like I/z curves, it can also be applied to the mesa-shaped
curves shown in FIGS. 17-21.
[0061] FIG. 17 is a graph of the I/z curve for the red channel 1702
and the I/z curve for the green channel 1704 of a two-channel
molecular array scanner. The routine "peak_intensity_focus" first
determines the z-position Z.sub.p 1706 of the peak in intensity for
the red-channel I/z curve 1702, as shown in FIG. 17. Next, as shown
in FIG. 18, peak_intensity_focus begins from the z-position
Z.sub.max.sup.- and proceeds rightward, as shown by arrow 1802,
searching for a Z.sub.l z-position at which the corresponding
signal intensity rises to a threshold percentage of the signal
intensity corresponding to the Z.sub.p peak z-position. After
finding the z-position Z.sub.l, peak_intensity_focus starts at
z-position Z.sub.p 1804 and proceeds rightward, as indicated by
arrow 1806, evaluating the signal intensities of successive
z-positions until peak_intensity_focus identifies a position
Z.sub.r 1808 at which the corresponding signal intensity falls
below the threshold value. As shown in FIG. 19, the z-positions
Z.sub.l 1803 and Z.sub.r 1808 define endpoints of a red-channel
plateau interval P.sub.r 1902 for the red-channel I/z curve. In
similar fashion, peak_intensity_focus applies the plateau-finding
technique to identify a green-channel plateau interval P.sub.g
shown as interval 1202 in FIG. 20. Finally, as shown in FIG. 21,
peak_intensity_focus determines whether the overlap 2102 between
the red-channel plateau interval P.sub.r 1902 and green-channel
plateau interval P.sub.g 2002 is greater than or equal to a
threshold length, in microns, and determines whether or not each of
plateau intervals P.sub.r and P.sub.g are also greater than or
equal to a threshold width, in microns. In one embodiment, the
threshold width for both the overlap 2102 and the plateau intervals
1902 and 2002 is four microns. If the overlap and plateau intervals
do not meet the threshold requirements, then peak_intensity_focus
returns an error value. Otherwise, in one embodiment,
peak_intensity_focus returns a focus Z.sub.f corresponding to the
z-position of the midpoint of the red-channel plateau interval
1902.
[0062] The routine "peak_intensity_focus" is alternatively
described by the flow-control diagram of FIG. 22. In step 2202,
peak_intensity_focus receives the I/z for each channel scanned by
the molecular array scanner. In the for-loop comprising steps
2204-2209, peak_intensity_focus determines the plateau interval for
each channel. In step 2205, peak_intensity_focus determines the
z-position Z.sub.p corresponding to the peak intensity for the
currently considered channel c. In steps 2206 and 2207,
peak_intensity_focus determines the Z.sub.l and Z.sub.r z-positions
for the plateau interval for the currently considered channel c, as
described above with reference to FIGS. 18-19. Then, in step 2208,
peak_intensity_focus reports and stores the plateau interval
P.sub.c for the currently considered channel c. In step 2209,
peak_intensity_focus determines whether or not the plateau for
another channel needs to be computed and, if so, control flows back
to step 2205. When all the plateau interval shave been computed,
peak_intensity_focus, in step 2210, determines the overlap between
the calculated and stored plateau intervals for all channels
considered in the for-loop comprising steps 2204-2209. In step
2212, peak_intensity_focus determines whether or not each plateau
interval is greater than or equal to a threshold value, in one
embodiment, 4 microns. If not, then an error is returned.
Otherwise, in step 2214, peak_intensity_focus determines whether or
not the overlap, calculated in step 2210, is greater than or equal
to a threshold value, in one embodiment, also 4 microns. If not,
then an error is returned. Otherwise, a focus z-position Z.sub.f is
selected in step 2216. In one embodiment, the midpoint of the
red-channel plateau interval is selected as the focus Z.sub.f. In
other embodiments, a centroid z-position for the plateau intervals
or for the overlap may be selected as the focus Z.sub.f. In all
embodiments, peak_intensity_focus returns the final selected focus
Z.sub.f in step 2218.
[0063] An alternate focus-finding routine is the focus-finding
routine "window_focus," also called in step 1620 of the routine
focus_distance illustrated in FIG. 16. The routine "window_focus"
is more suitable for the mesa-shaped I/z curves characteristic of
one class of molecular array scanners, for reasons described above
with respect to FIGS. 12 and 13. FIGS. 23-29 illustrate operation
of window_focus using graphical representations of I/z curves.
FIGS. 30-31 show flow-control diagrams that describe operation of
window_focus.
[0064] In a first step, as shown in FIG. 23, window_focus computes
the z-positions Z.sub.P.sub..sub.r and Z.sub.P.sub..sub.g 2302 and
2304 for the red-channel I/z curve 1306 and the green-channel I/z
curve 1308, respectively. FIGS. 23-29 assume a two-channel
molecular array scanner. Then, window_focus checks to make sure
that these peak positions Z.sub.P.sub..sub.r and Z.sub.P.sub..sub.g
fall within a range of z-position values 1310 and 1312 that
represents 80 percent of the range
Z.sub.max.sup.+-Z.sub.max.sup.-.If the peak z-positions
Z.sub.P.sub..sub.r and Z.sub.P.sub..sub.g fall outside this range,
an error is returned.
[0065] Next, window_focus divides the z-position range
Z.sub.max.sup.+-Z.sub.max.sup.- into a number of evenly sized
increments. In one embodiment of the present invention, each
increment represents a 1/4 micron change in the z-position. The
window_focus algorithm places the left edge of a window, or
z-position interval, at each discrete z-position increment, with
the last few increments near Z.sub.max.sup.+ omitted, as truncated
windows would result. Therefore, there nearly as many windows as
there are depth settings. FIG. 24 illustrates the windows initially
constructed by window_focus. A first window is defined by vertical
lines 2402-2403. A second window is defined by vertical dashed
lines 2404-2405. A third window is defined by vertical
dashed-and-crossed lines 2406-2407.
[0066] Initially, window_focus employs wider windows to determine
approximate plateau intervals for each channel. In one embodiment,
an initial 8-micron window is used. If the window-based
plateau-interval determination fails to work for wider windows, it
is tried again for narrower windows. FIG. 25 illustrates narrower
windows. The plateau-interval determination is illustrated in FIGS.
26 and 27 for red and green channels, respectively. In FIG. 26,
window_focus starts from the Z.sub.max.sup.- z-position and
proceeds rightward, as indicated by arrow 2602, determining a slope
for each window. This slope can be calculated as the difference
between the largest and smallest signal intensity seen inside the
window expressed as a percentage of maximum intensity for the
entire I/z curve between Z.sub.max.sup.- and Z.sub.max.sup.+.
Various methods can be used to determine the slope for a window,
including applying a differential smoothing operator and then
dividing the difference between the highest and lowest intensity
values within the window by the length of the window increment.
Alternative techniques may also be employed. Window_focus
determines the slope of all initial windows. Window_focus looks for
positions for which the difference between the maximum and minimum
intensity values within the window are less than 2% of the maximum
intensity found anywhere on the entire I/z curve. If window_focus
finds at least one such window, it will return the z-position of
the center of the window with the smallest intensity variation. If
window_focus does not find a window with less than a 2% difference,
then window_focus tries again with smaller-sized windows, in one
embodiment, 6-micron windows If window_focus fails to find a window
with less than a 2% difference, then window_focus tries again with
4 micron windows. If window_focus fails to find a 4-micron window
with less than a 2% difference, then window_focus returns the
4-micron with the smallest intensity variations, using an RMS-like
intensity variation measure discussed below. In FIG. 26, window
2704 is shown as meeting the criteria for a plateau window,
although, as pointed out above, the slope of the plateau in the
figures is exaggerated, and thus appears to create an intensity
variation greater than 2%.
[0067] FIG. 27 illustrates determination of the plateau window 2702
for the green channel. Thus, by the window-based method, a
red-channel plateau interval 2704 and a green-channel plateau
interval 2702 are determined with respect to the z-position
coordinate axis. As shown in FIGS. 28A-B, window_focus determines
an overlap region common to the determined plateau intervals for
each channel. In FIGS. 28A-B, the plateau windows for the red
channel (2802 and 2804) are plotted horizontally in z-position
(with respect to the plateau windows for the green channel (2806
and 2808). Z axis segments (2810-2813) are plotted above and below
the plateau-window plots. In FIG. 28A, the overlap region begins at
z-position 2814 and extends to z-position 2816. In FIG. 28B, the
overlap region begins at z-position 2818 and extends to z-position
2820. When, as in FIG. 28A, the overlap region is less than some
threshold value, in one embodiment four microns, or the signal
intensities within the plateau intervals differ from one another by
greater than some threshold amount, in one embodiment 2 percent,
then, as shown in FIG. 28A, a left boundary Z.sub.l 2822 and a
right boundary Z.sub.r 2824 are chosen as the left-most and
right-most boundaries of the plateau intervals. By contrast, when
the width of the overlap region exceeds a threshold value and the
signal intensities within the plateau intervals differ by less than
a threshold amount, then the left boundary Z.sub.l is chosen as the
left-most point of the overlap 2818 and the right boundary Z.sub.r
is chosen as the right-most point of the overlap region 2820, as
shown in FIG. 28B.
[0068] Window_focus then centers smaller windows, in one
embodiment, 2-micorn windows, at each z-position within the left
and right boundaries, and searches, starting from the center, to
find a small window with acceptable criteria most close to the
center of the Z.sub.l-to- Z.sub.r interval. The criteria used in
one embodiment, for two-micron narrow windows, is that the signal
intensities within the window must differ by less than 1 percent.
In one embodiment, the search first considers narrow window 2902,
next considers window 2904, next considers window 2906, next
considers window 2908, and so forth, in a ping-pong like fashion.
The first window considered that meets the criteria is selected as
the focus window, and the z-position of the window's center is
selected as the focus Z.sub.f.
[0069] FIGS. 30 and 31 show flow-control diagrams for the routine
"window_focus" and the routine "micro_focus," called from the
routine "window_focus." Beginning with FIG. 30 in step 3002,
window_focus receives the I/z data for scans of the reference array
in each channel. In step 3004, window_focus determines the
z-positions for the signal intensity peaks for each channel, as
discussed above with reference to FIG. 23, and checks to see that
they are within the central 80-percent interval of the full
z-position range Z.sub.max.sup.+ to Z.sub.max.sup.30 . If all the
peak positions are not within the 80 percent central range, as
determined by window_focus in step 3006, then an error is returned.
Otherwise, in the nested for-loops comprising steps 3008-3014,
window_focus determines the plateau intervals for each channel, as
described above with reference to FIGS. 26-28B. Then, as discussed
with reference to FIG. 29, window_focus calls the routine
"micro_focus," in step 3024, to compute the z-position
corresponding to the optimal focus distance Z.sub.f, returning the
optimal focus z-position Z.sub.f in step 3026, along with a status
value indicating whether or not the plateau determination carried
out in steps 3008-3014 successfully completed. Step 3008 is the
first step of the outer for-loop of the nested for-loops of steps
3008-3014. The outer for-loop is repeated over a series of
decreasing window sizes, as described with reference to FIGS.
24-25, in order to select plateau intervals for each channel
scanned by the molecular array scanner.
[0070] The inner for-loop comprising steps 3009-3011 determines
plateau intervals for each channel by the method described above
with reference to FIGS. 26 and 17. A flow-control diagram for the
routine "determine_plateau_interval," called from step 3010, is not
provided, as the technique is thoroughly described, above, with
reference to FIGS. 26 and 27. As noted there, plateau intervals
span z-positions corresponding to the top of a mesa, and are
identified as windows with essentially flat or nearly flat slopes
that follow steeply sloped windows that contain the walls of the
mesa.
[0071] When the plateau intervals for all channels have been
determined for a current window size, window_focus determines, in
step 3011, whether the signal variation, or differences, within
each plateau interval is less than 2%. If not, then, in step 3012,
window_focus determines whether or not the current window size is
the smallest window size allowed for the outer for-loop. If not,
then window_focus decrements the window size, in step 3013, and
control returns to step 2009, where the inner for-loop is again
executed. If the smallest window size has been tried, then
window_focus returns, as the plateau window for each channel, the
smallest windows with the least variation in signal intensity,
using an RMS-like measure to be discussed below. Once the plateau
intervals for each channel are found, then, in step 3016,
window_focus computes the overlap between plateau intervals. If the
overlap is acceptable, as determined in step 3018, then, as
described with reference to FIG. 28B, above, window_focus sets the
left and right boundaries Z.sub.l and Z.sub.r respectively, to the
left and right boundaries of the overlap region, in step 3020.
Otherwise, as described above with reference to FIG. 28A,
window_focus sets the Z.sub.l and Z.sub.r boundary z-position
values to the left-most z-position and right-most z-position of the
various plateau intervals, in step 3022. Note that this step may
also set an error return value to indicate an error condition
corresponding to not finding a suitable plateau window for at least
one channel. Following setting of the Z.sub.l and Z.sub.r boundary
z-positions in step 3020 or 3022, window_focus calls the routine
"micro_focus" in step 3018.
[0072] FIG. 31 shows a flow-control diagram for the routine
"micro_focus," called from step 3018 of FIG. 30. In step 3102,
micro_focus computes the center of the Z.sub.l-to-Z.sub.r interval
Z.sub.c. Next, in step 3104, micro_focus applies the small windows
to each increment within the Z.sub.l-to-Z.sub.r interval, starting
with the center of the Z.sub.l-to- Z.sub.r interval Z.sub.c. In one
embodiment of the present invention, 2-micron windows are used. In
step 3106, micro_focus determines whether there are an odd number
of windows in the Z.sub.l-to-Z.sub.r z-position range. If so, then
in step 3108, micro_focus determines whether the center window has
acceptable characteristics. As discussed above with reference to
FIG. 29, acceptable characteristics may include a variation of
signal intensities within the center window less than 1 percent.
Alternatively, a slope-based method or another method for
determining the degree of signal-intensity constancy within the
window may be employed. If the center window is acceptable, then,
in step 3110, micro_focus sets the z-position corresponding to the
optimal focus distance, Z.sub.f to the z-position of the center of
the center window and returns success. Otherwise, in the for-loop
comprising steps 3112-3116, micro_focus carries out a ping-pong
search of windows, out from the central z-position Z.sub.c, to find
an acceptable window closest to the center Z.sub.c. The index i is
set to the first window to the right of the center, and the index j
is set to index the first window to the left of the center. In each
iteration of the for-loop, the index i is incremented and the index
j is decremented by 1 increment, in step 3116. In step 3113,
micro_focus determines whether the window index by index i is
acceptable, according to the criteria described above for
acceptability of the center window in step 3108. If so, then
control flows to step 3110, where the z-position corresponding to
the optimal focus distance Z.sub.f is set to the center of the
window indexed by variable i. Otherwise, if the window indexed by
index j is acceptable according to the criteria applied to the
central window in step 3108, then the z-position corresponding to
the optimal focus distance is set to the center of the window
indexed by j, in step 3110. Otherwise, if there are more windows to
consider in the range Z.sub.l-to-Z.sub.r, as determined in step
3115, then the indices are incremented and decremented in step 3116
and another iteration of the for-loop is carried out. If an
acceptable window is not found following termination of the
for-loop then, in step 3118, micro_focus computes a
root-mean-square-like ("RMS-like") value, 1 ( ( max ( I r ) - min (
I r ) ) / I r max ) 2 + ( ( max ( I g ) - min ( I g ) - min ( I g )
) / I g max ) 2 ,
[0073] for each window, where max(I.sub.r) is maximum red-channel
intensity for the window, min(I.sub.r) is the minimum red-channel
intensity for the window, I.sub.rmax is the maximum red intensity
of the red-channel I/z function, max(I.sub.g) is maximum
green-channel intensity for the window, min(I.sub.g) is the minimum
green-channel intensity for the window, and I.sub.gmax is the
maximum green intensity of the green-channel I/z function.
Micro_focus then selects the window with the smallest RMS-like
value in step 3120. The z-position of the center of the selected
window is returned as the z-position corresponding to the optimal
focus distance Z.sub.f.
[0074] Although the present invention has been described in terms
of a particular embodiment, it is not intended that the invention
be limited to this embodiment. Modifications within the spirit of
the invention will be apparent to those skilled in the art. For
example, many different scan patterns may be used to construct the
I/z data employed by the automated focus-distance determination
routines. Different ranges of window sizes may be employed, and
different orderings in window searching may be employed. The
automated focus-distance determination routines can be implemented
in many different languages, or hardware circuits, in an almost
limitless number of ways, using different modular organizations and
control logic. The methods was generally described in flow-control
diagrams to include an arbitrary number of channels, and is
intended to be applicable for 1-channel, 2-channel, and
many-channel molecular array scanners.
[0075] The foregoing description, for purposes of explanation, used
specific nomenclature to provide a thorough understanding of the
invention. However, it will be apparent to one skilled in the art
that the specific details are not required in order to practice the
invention. The foregoing descriptions of specific embodiments of
the present invention are presented for purpose of illustration and
description. They are not intended to be exhaustive or to limit the
invention to the precise forms disclosed. Obviously many
modifications and variations are possible in view of the above
teachings. The embodiments are shown and described in order to best
explain the principles of the invention and its practical
applications, to thereby enable others skilled in the art to best
utilize the invention and various embodiments with various
modifications as are suited to the particular use contemplated. It
is intended that the scope of the invention be defined by the
following claims and their equivalents:
* * * * *