U.S. patent application number 14/865349 was filed with the patent office on 2016-01-14 for sample applicator sensing and positioning.
The applicant listed for this patent is Roche Diagnostics Hematology, Inc.. Invention is credited to Stephen Conroy, Eric Leknes, Frank L. Pawlowski, David Zahniser, Michael Zahniser, Russell Zahniser.
Application Number | 20160011223 14/865349 |
Document ID | / |
Family ID | 46651589 |
Filed Date | 2016-01-14 |
United States Patent
Application |
20160011223 |
Kind Code |
A1 |
Zahniser; Russell ; et
al. |
January 14, 2016 |
SAMPLE APPLICATOR SENSING AND POSITIONING
Abstract
Systems and methods for positioning a sample applicator relative
to a substrate include: (a) obtaining an image of the sample
applicator in proximity to the substrate, where the image includes
a direct image region corresponding to the sample applicator and a
first reflected image region corresponding to an image of the
sample applicator reflected from a surface of the substrate; (b)
determining a position of an edge of the sample applicator in the
direct image region; (c) determining a position of a reflected edge
of the sample applicator in the first reflected image region; (d)
determining a distance between the edge of the sample applicator
and the reflected edge of the sample applicator; and (e)
determining the position of the sample applicator relative to the
substrate based on the distance between the edges.
Inventors: |
Zahniser; Russell;
(Dorchester, MA) ; Zahniser; David; (Wellesley,
MA) ; Conroy; Stephen; (Maynard, MA) ; Leknes;
Eric; (Manchester, NH) ; Zahniser; Michael;
(Jamaica Plain, MA) ; Pawlowski; Frank L.;
(Amherst, NH) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Roche Diagnostics Hematology, Inc. |
Westborough |
MA |
US |
|
|
Family ID: |
46651589 |
Appl. No.: |
14/865349 |
Filed: |
September 25, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
13549251 |
Jul 13, 2012 |
9146247 |
|
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14865349 |
|
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|
|
61510728 |
Jul 22, 2011 |
|
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Current U.S.
Class: |
382/106 |
Current CPC
Class: |
G06K 9/0014 20130101;
G06T 2207/30004 20130101; G06T 7/12 20170101; G01N 35/00584
20130101; G01N 35/1011 20130101; G06T 7/50 20170101; G06T 7/11
20170101; G01N 35/00029 20130101; G06T 7/70 20170101; G01B 11/14
20130101; G01N 1/31 20130101 |
International
Class: |
G01N 35/00 20060101
G01N035/00; G06K 9/00 20060101 G06K009/00; G06T 7/00 20060101
G06T007/00 |
Claims
1. A method for positioning a sample applicator relative to a
substrate, the method comprising: obtaining an image of the sample
applicator in proximity to the substrate, the image comprising a
direct image region corresponding to the sample applicator and a
first reflected image region corresponding to an image of the
sample applicator reflected from a surface of the substrate;
determining a position of an edge of the sample applicator in the
direct image region; determining a position of a reflected edge of
the sample applicator in the first reflected image region;
determining a distance between the edge of the sample applicator
and the reflected edge of the sample applicator; and determining
the position of the sample applicator relative to the substrate
based on the distance between the edges.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation application of U.S.
patent application Ser. No. 13/549,251, filed on Jul. 13, 2012,
which claims priority under 35 U.S.C. .sctn.119(e) to U.S.
Provisional Patent Application No. 61/510,728, filed on Jul. 22,
2011. The entire contents of each of these applications are
incorporated by reference in their entirety.
TECHNICAL FIELD
[0002] This disclosure relates to methods and systems for
positioning sample applicators for dispensing a sample onto a
substrate.
BACKGROUND
[0003] Conventional methods for analyzing biological samples such
as blood or body fluids typically include two steps. First, an
automated system performs a quantitative analysis of sample
characteristics on the sample in a liquid state. For example, a
flow cytometer using impedance, fluorescence, and/or scattered
light-based measurements processes a sample of blood suspended in a
fluid steam to count red blood cells, white blood cells, platelets,
and to derive other parameters of a complete blood count. Second,
to the extent the flow system detects any abnormalities in the
sample (e.g., an abnormally high white blood cell count), the
system flags the sample and a laboratory technician reviews the
sample manually by examining a dried and stained preparation of the
sample on a microscope slide.
[0004] To facilitate manual review, the technician typically
prepares a "wedge" smear of the blood sample. Smear preparations
yield samples with highly variable thicknesses and distribution of
blood constituents. The wedge smear often has only a single narrow
band with an appropriate cell density for examination and analysis,
and the location and shape of this band varies from slide to slide.
In addition, due to a lack of uniformity, smear preparations often
preclude absolute quantitation of sample properties for a given
patient. In general, only relative proportions can be assessed
within the smear itself.
[0005] A sample preparation method that produces a uniform,
high-quality specimen would make visual evaluation of the sample
both easier and more accurate. Furthermore, for specimens prepared
using a known volume of the sample in a highly consistent manner,
it is possible to automate the quantitation of sample properties
directly from the specimen, replacing the first step of sample
analysis traditionally performed using flow-based systems.
SUMMARY
[0006] The systems and methods disclosed herein are used during
automated sample preparation in which sample applicators are used
to dispense fluid samples onto substrates such as microscope
slides. Successfully dispensing fluids to obtain samples of
relatively uniform distribution across a substrate depends, in
part, on controlling the position of the sample applicator relative
to the surface of the substrate that receives the sample. To
achieve precise control over the sample applicator, the methods and
systems disclosed herein are configured to determine the position
of the sample applicator relative to the substrate surface based on
one or more images of the applicator, including images reflected
from the substrate surface. The image(s) include both a direct
image region that corresponds to a direct (e.g., non-reflected)
image of the sample applicator above the substrate, and a first
reflected image region that corresponds to an image of the sample
applicator that is reflected from the substrate surface.
[0007] The position of the applicator relative to the substrate
surface can be determined based on the distance between the edges
of the sample applicator in the direct image region and the first
reflected image region. The methods and the systems that implement
the methods can be extended to determine the position of the sample
applicator at multiple transverse locations relative to the
substrate. By initially determining a set of suitable positions of
the applicator relative to the substrate surface (e.g., at the
corners of the substrate), suitable control signals for producing
desired applicator positions can be interpolated at other locations
on the substrate surface. In this manner, precise control over the
position of the sample applicator relative to the substrate surface
can be achieved during dispensing of a fluid sample onto the
substrate.
[0008] In general, in a first aspect, the disclosure features
methods of positioning a sample applicator relative to a substrate,
the methods including: (a) obtaining an image of the sample
applicator in proximity to the substrate, the image including a
direct image region corresponding to the sample applicator and a
first reflected image region corresponding to an image of the
sample applicator reflected from a surface of the substrate; (b)
determining a position of an edge of the sample applicator in the
direct image region; (c) determining a position of a reflected edge
of the sample applicator in the first reflected image region; (d)
determining a distance between the edge of the sample applicator
and the reflected edge of the sample applicator; and (e)
determining the position of the sample applicator relative to the
substrate based on the distance between the edges.
[0009] Implementations of the methods can include any one or more
of the following features.
[0010] Obtaining the image of the sample applicator in proximity to
the substrate can include orienting a detector at an angle relative
to the surface of the substrate, and recording the image using the
detector.
[0011] The position of the sample applicator relative to the
substrate can include a height of the sample applicator above the
surface of the substrate. Determining the height of the sample
applicator above the surface of the substrate can include
calculating the height based on reference information that includes
correlation information relating the distance between the edge of
the sample applicator and the reflected edge of the sample
applicator to the height.
[0012] The methods can include measuring a set of distances between
the edge of the sample applicator and the reflected edge of the
sample applicator, where measuring each member of the set of
distances includes: (a) translating the sample applicator to a new
height above the surface of the substrate; (b) obtaining a second
image of the sample applicator at the new height in proximity to
the substrate, the second image including a direct image region
corresponding to the sample applicator and a first reflected image
region corresponding to an image of the sample applicator reflected
from the surface of the substrate; (c) determining a position of an
edge of the sample applicator in the direct image region of the
second image; (d) determining a position of a reflected edge of the
sample applicator in the first reflected image region of the second
image; and (e) determining a distance between the edge of the
sample applicator in the direct image region and the reflected edge
of the sample applicator in the first reflected image region of the
second image.
[0013] The methods can include determining a control setting
associated with a target position of the sample applicator by
interpolating between distances in the measured set of distances.
The methods can include storing in a storage unit the control
setting and information about a location of the sample applicator
relative to the substrate. The set of distances can include at
least two distances (e.g., at least ten distances).
[0014] The methods can include: (a) translating the sample
applicator in a direction perpendicular to a central axis of the
applicator to a new location relative to the substrate; (b)
measuring a set of distances between the edge of the sample
applicator and the reflected edge of the sample applicator; (c)
determining a control setting associated with a target position of
the sample applicator at the new location; and (d) storing the
control setting and information about the new location in the
storage unit. The methods can include repeating the steps of
translating the sample applicator in a direction perpendicular to
the central axis of the sample applicator to a new location
relative to the substrate, measuring a set of distances between the
edge of the sample applicator and reflected edge of the sample
applicator, determining a control setting associated with a target
position of the sample applicator at the new location, and storing
the control setting and information about the new location in the
storage unit, until a number of locations about which information
is stored is three or more (e.g., six or more).
[0015] The methods can include determining coefficients of an
equation of a surface of the substrate. The methods can include
determining an orientation of the substrate relative to a plane
perpendicular to the central axis of the sample applicator.
Determining an orientation of the substrate can include determining
a slope of the substrate surface relative to the plane
perpendicular to the central axis of the sample applicator.
[0016] Determining a position of an edge of the sample applicator
in the direct image region can include: (a) selecting columns of
pixels in the direct image region that extend in a direction
parallel to a central axis of the sample applicator; (b) for each
selected column, determining a position of maximum intensity change
within the column; (c) determining the position of the edge of the
sample applicator based on the positions of maximum intensity
change in each selected column of pixels. Determining the position
of maximum intensity change within each selected column can
include: (a) for each pair of adjacent pixels in the selected
column, determining a change in intensity; (b) determining a
maximum intensity change between pairs of adjacent pixels in the
selected column; and (c) fitting a functional form to the maximum
intensity change between pairs of adjacent pixels to determine the
position of maximum intensity change within the selected column.
Determining the position of the edge of the sample applicator can
include fitting the positions of maximum intensity change within
each selected column to a functional form. Determining the position
of the edge of the sample applicator can include determining an
apex point of the sample applicator based on the fitted functional
form.
[0017] Determining the position of the reflected edge of the sample
applicator in the first reflected image region can include: (a)
selecting rows of pixels in the first reflected image region that
extend in a direction perpendicular to an elongated axis of the
sample applicator image; (b) for each selected row, determining an
average of an m highest pixel intensities in the row, and
determining an average of a k lowest pixel intensities in the row;
(c) determining a contrast level associated with the row as a
difference between the average of the m highest pixel intensities
and the average of the k lowest pixel intensities; and (d)
determining the position of the reflected edge of the sample
applicator based on the contrast level in each selected row.
Determining the position of the reflected edge of the sample
applicator based on the contrast level in each selected row can
include: (a) identifying a first portion of the first reflected
image region based on a contrast level in each selected pixel row,
where the first portion does not include the image of the sample
applicator; (b) identifying a second portion of the first reflected
image region based on a contrast level in each selected pixel row,
where the second portion includes the image of the sample
applicator; and (c) determining the position of the reflected edge
of the sample applicator based on a difference in contrast levels
between the first and second portions of the first reflected image
region. The quantity m can correspond to at least one fifth of a
total number of pixels in each selected row, the quantity k can
correspond to at least one fifth of the total number of pixels in
each selected row, and there may be no pixels in each selected row
that are common to the m pixels and the k pixels.
[0018] The surface of the substrate is an upper surface of the
substrate closest to the sample applicator. The image of the sample
applicator in proximity to the substrate can include a second
reflected image region corresponding to an image of the sample
applicator reflected from a lower surface of the substrate, and the
methods can include: (a) determining a position of a reflected edge
of the sample applicator in the second reflected image region; (b)
determining a distance between the reflected edges of the sample
applicator in the first and second reflected image regions; and (c)
determining a thickness of the substrate based on the distance
between the reflected edges of the sample applicator in the first
and second reflected image regions. Determining the thickness of
the substrate can include calculating the thickness based on
reference information that includes correlation information
relating the distance between the reflected edges of the sample
applicator to the thickness.
[0019] Determining a position of a reflected edge of the sample
applicator in the second reflected image region can include: (a)
selecting rows of pixels in the second reflected image region that
extend in a direction perpendicular to an elongated axis of the
sample applicator image; (b) for each selected row, determining an
average of a p highest pixel intensities in the row, and
determining an average of a q lowest pixel intensities in the row;
(c) determining a contrast level associated with the row as a
difference between the average of the p highest pixel intensities
and the average of the q lowest pixel intensities; and (d)
determining the position of the reflected edge of the sample
applicator in the second reflected image region based on a
difference between the contrast level in each selected pixel row in
the second reflected image region and the contrast level in each
selected pixel row in the first reflected image region. The
quantity p can correspond to at least one fifth of a total number
of pixels in each selected row, the quantity q can correspond to at
least one fifth of the total number of pixels in each selected row,
and no pixels in each selected row may be common to the p pixels
and the q pixels.
[0020] The methods can include calibrating the correlation
information, where calibrating the correlation information includes
determining an offset control signal value that causes an actuator
of the sample applicator to provide an upward force that will just
be overcome by the force of gravity, storing the offset control
signal value, translating the sample applicator toward the
substrate until a signal associated with a translation error of the
actuator is within an error threshold, and storing the position of
the sample applicator when the signal associated with the
translation error of the actuator is within the error threshold.
Calibrating the correlation information can include setting the
height of the sample applicator to zero at the stored position. The
methods can include calibrating the correlation information, where
calibrating the correlation information includes determining an
offset control signal value that causes an actuator of the sample
applicator to provide an upward force that will just barely be
overcome by the force of gravity (e.g., in some implementations
about 0.5, 1, 2, 3, 4, or 5% less than gravity); storing the offset
control signal value; lowering the sample applicator slowly until a
control signal of the actuator is within an error threshold of the
offset control signal; and storing the position of the sample
applicator when the control signal of the actuator is within the
error threshold of the offset control signal.
[0021] Various implementations and embodiments of the methods can
also include any one or more of the other features disclosed
herein, in any combination, as appropriate.
[0022] In another aspect, the disclosure features systems that
include a sample applicator, a stage configured to support a
substrate, a detector, and an electronic processor, where the
system is configured so that when a substrate is supported by the
stage: (a) the detector is configured to obtain an image of the
sample applicator in proximity to the substrate, the image
including a direct image region corresponding to the sample
applicator and a first reflected image region corresponding to an
image of the sample applicator reflected from a surface of the
substrate; and (b) the electronic processor is configured to: (i)
determine a position of an edge of the sample applicator in the
direct image region; (ii) determine a position of a reflected edge
of the sample applicator in the first reflected image region; (iii)
determine a distance between the edge of the sample applicator and
the reflected edge of the sample applicator; and (iv) determine the
position of the sample applicator relative to the substrate based
on the distance between the edges.
[0023] Various implementations and embodiments of the systems can
include any one or more of the following features.
[0024] The position of the sample applicator relative to the
substrate can include a height of the sample applicator above the
surface of the substrate, and the electronic processor can be
configured to determine the height of the sample applicator based
on reference information that includes correlation information
relating the distance between the edge of the sample applicator and
the reflected edge of the sample applicator to the height.
[0025] The electronic processor can be configured to measure a set
of distances between the edge of the sample applicator and the
reflected edge of the sample applicator by: (a) translating the
sample applicator to a new height above the surface of the
substrate; (b) obtaining a second image of the sample applicator at
the new height in proximity to the substrate, the second image
including a direct image region corresponding to the sample
applicator and a first reflected image region corresponding to an
image of the sample applicator reflected from the surface of the
substrate; (c) determining a position of an edge of the sample
applicator in the direct image region of the second image; (d)
determining a position of a reflected edge of the sample applicator
in the first reflected image region of the second image; and (e)
determining a distance between the edge of the sample applicator in
the direct image region and the reflected edge of the sample
applicator in the first reflected image region of the second
image.
[0026] The electronic processor can be configured to determine a
control setting associated with a target position of the sample
applicator by interpolating between distances in the measured set
of distances. The system can include a storage unit connected to
the electronic processor, where the electronic processor is
configured to store the control setting and information about a
location of the sample applicator relative to the substrate in the
storage unit.
[0027] The electronic processor can be configured to: (a) translate
the sample applicator in a direction perpendicular to a central
axis of the sample applicator to a new location relative to the
substrate; (b) measure a set of distances between the edge of the
sample applicator and the reflected edge of the sample applicator;
(c) determine a control setting associated with the target position
of the sample applicator at the new location; and (d) store the
control setting and information about the new location in the
storage unit. The electronic processor can be configured to
determine coefficients of an equation of a plane corresponding to a
surface of the substrate based on the stored control settings. The
electronic processor can be configured to determine an orientation
of the substrate relative to a plane perpendicular to the central
axis of the sample applicator based on the stored control
settings.
[0028] Implementations and embodiments of the system can also
include any one or more of the other features disclosed herein, in
any combination, as appropriate.
[0029] As used herein, the term "sample applicator" refers to a
device that dispenses a sample onto a substrate. Typically,
although not always, sample applicators include a fluid conduit for
dispensing fluid samples. Sample applicators can include pipettes,
needles, and tubes, for example.
[0030] A "sample" is a solution, a suspension, a liquid, or another
type of fluid sample dispensed by the sample applicator onto a
surface of the substrate. A sample can be a biological specimen
such as blood, for example.
[0031] A "substrate" is a member onto which a sample can be
dispensed. Typically, but not always, substrates have a planar
receiving surface onto which the sample can be dispensed by the
sample applicator. An example substrate is a microscope slide, or
any other reflective material capable of supporting a sample.
[0032] The "upper surface" of the substrate corresponds to the
substrate surface closest to the sample applicator. The "lower
surface" of the substrate corresponds to the substrate surface
opposite to the upper surface.
[0033] A "direct image region" corresponds to a region in an image
that includes a direct image of the sample applicator. A direct
image is an image that has not been reflected from a surface of the
substrate. A "first reflected image region" is a region, typically
from the same image, that includes an image of the sample
applicator that has been reflected from a surface of the substrate
(either the upper surface or the lower surface). A "second
reflected image region" is a region, typically from the same image,
that includes an image of the sample applicator that has also been
reflected from a surface of the substrate. In some embodiments, the
first and second reflected image regions correspond to images of
the sample applicator that have been reflected from different
surfaces of the substrate (e.g., the upper and lower surfaces,
respectively).
[0034] An "edge of the sample applicator" refers to a boundary, in
the direct image region, that demarcates the sample applicator from
other features in the direct image region. A "reflected edge of the
sample applicator" refers to a boundary, in the first reflected
image region, that demarcates the reflected image of the sample
applicator from other features in the first reflected image
region.
[0035] When comparing the intensities I(1) and I(2) of pixels 1 and
2, respectively, in a given image region, the "change in intensity"
corresponds to I(2)-I(1). Typically, the sample applicator in an
image region appears as a dark feature against a brighter
background (e.g., the background is of higher intensity).
Accordingly, the change in intensity will be positive when pixel 2
is a background pixel and pixel 1 corresponds to the sample
applicator.
[0036] The quantity "contrast level" is a measure of the intensity
variability among a set of pixels. Contrast level can be calculated
as follows: first, by selecting from the pixel set a first subset
of pixels with the highest intensities among the pixels in the set,
and a second subset with the lowest intensities among pixels in the
set; and second, by calculating the difference between the average
intensities for the two subsets. The subsets can be a fixed number
of pixels or proportional to the size of the pixel set (e.g., 1/5
of the pixels in the set). For example, the average intensity for
the subset of pixels with the highest intensities can correspond to
the average of the n largest pixel intensities for a particular row
of pixels in an image. The average intensity for the subset of
pixels with the lowest intensities can correspond to the average of
the m smallest pixel intensities for the particular row. The values
of n and m can be different, or the same. For example, n can have a
value of 10, but can range from 1 through the total number of
pixels for the row. In addition, m can have a value of 10, but can
range from 1 through the total number of pixels for the row.
Typically, the values of n and m are selected for the set of pixels
so that none of the pixels selected is common to both the first and
second subsets.
[0037] The "height" of the sample applicator refers to the minimum
distance between the upper surface of the substrate and the portion
of the sample applicator nearest to the upper surface. For an
applicator with an extended central axis (e.g., a pipette or tube)
oriented perpendicular to the substrate surface, the height is
measured along a direction parallel to the central axis. For an
applicator without an extended central axis or a central axis that
is not oriented perpendicular to the substrate surface, the height
is measured in a direction parallel to a surface normal of the
substrate surface.
[0038] The "location" of the sample applicator relative to the
substrate corresponds to the applicator's two-dimensional
displacement, in a plane parallel to the upper surface of the
substrate, relative to a reference position on the substrate
surface.
[0039] The "thickness" of the substrate corresponds to a maximum
dimension of the substrate measured between the upper and lower
surfaces in a direction perpendicular to the plane of the upper
surface.
[0040] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention belongs. Although
methods and materials similar or equivalent to those described
herein can be used in the practice or testing of the present
invention, suitable methods and materials are described below. All
publications, patent applications, patents, and other references
mentioned herein are incorporated by reference in their entirety.
In case of conflict, the present specification, including
definitions, will control. In addition, the materials, methods, and
examples are illustrative only and not intended to be limiting.
[0041] The details of one or more embodiments are set forth in the
accompanying drawings and the description below. Other features and
advantages will be apparent from the description, drawings, and
claims.
DESCRIPTION OF DRAWINGS
[0042] FIG. 1A is a schematic diagram showing a side view of a
sample applicator positioned perpendicular to an upper surface of a
substrate.
[0043] FIG. 1B is a schematic diagram showing a side view of a
sample applicator positioned at an angle with respect to an upper
surface of a substrate.
[0044] FIG. 2 is a schematic diagram showing a side view of a
sample applicator positioned relative to a substrate and a detector
that captures a direct and a reflected image of the sample
applicator.
[0045] FIG. 3 is a schematic representative image showing a direct
image of a sample applicator within a direct image region and two
reflected images of the sample applicator within reflected image
regions.
[0046] FIG. 4 is a flow chart that includes a series of steps for
determining an apex position of a direct image of a sample
applicator.
[0047] FIG. 5A is a schematic representative direct image of a
sample applicator showing locations of maximum intensity change in
each column of pixels.
[0048] FIG. 5B is a graph showing change in intensity plotted as a
function of position for a column of pixels in the image of FIG.
5A.
[0049] FIG. 6 is a flow chart that includes a series of steps for
determining an apex position of a reflected image of a sample
applicator.
[0050] FIG. 7A is a schematic representative reflected image of a
sample applicator.
[0051] FIG. 7B is a graph showing contrast level plotted as a
function of row position for each row of pixels in the image of
FIG. 7A.
[0052] FIG. 7C is a schematic representative image of a sample
applicator showing apex positions of the sample applicator.
[0053] FIG. 8 is a schematic graph showing image separation plotted
as a function of a manipulator control setting.
[0054] FIG. 9 is a schematic diagram of a substrate showing the
determination of a control setting associated with the sample
applicator at a plurality of locations relative to the upper
surface of the substrate.
[0055] FIG. 10 is a schematic diagram of an automated sample
processing system.
[0056] Like reference symbols in the various drawings indicate like
elements.
DETAILED DESCRIPTION
[0057] To accurately quantify results directly from a prepared
sample on a substrate, the composition, configuration, and height
or thickness of the deposited sample should be as highly uniform as
possible across the substrate surface so that each analyzed
sub-area of the sample is representative of the sample prepared on
the substrate as a whole as well, and of the patient from whom the
sample was extracted. In addition, highly consistent and uniformly
prepared samples provide a basis to directly compare samples and
analysis results across multiple patients. By preparing samples in
a uniform manner, automated methods can be used for analysis,
significantly improving throughput.
[0058] A variety of different methods can be used to prepare
samples in automated fashion for subsequent analysis. To improve
uniformity, a known quantity of a fluid sample (e.g., liquids,
suspensions, solutions, and other mixtures such as human or animal
blood or bodily fluids, with or without diluent, e.g., cells from
bone marrow, urine, vaginal tissue, epithelial tissue, tumors,
semen, spittle, and other body fluids) can be dispensed onto a
substrate surface in a controlled manner to ensure that fluid does
not build up or spread too thinly at particular locations on the
substrate surface (e.g., to achieve, as closely as possible,
uniformity in the sample deposited on the substrate). By way of
example, the following discussion refers to the dispersal and
analysis of blood samples on microscope slides. However, the
methods and systems disclosed herein can be applied to the
preparation and analysis of a wide variety of fluid samples, as
described above, on a wide variety of substrates. Substrates can
include, but are not limited to, glass or plastic microscope
slides, polished or mirrored ceramic slides, polished metal
substrates, plastic or other flexible specimen films, and/or any
other reflective materials capable of supporting a sample.
Sample Application Systems and Methods
[0059] The methods and systems disclosed herein can be used with
automated sample preparation systems that dispense a known quantity
of blood onto the surface of a microscope slide using a sample
applicator. Typically, the applicator moves in relation to the
surface of the slide, continuously dispensing blood while moving
relative to the slide. The blood can be dispensed in a variety of
patterns according to the movement of the sample applicator. In
some embodiments, for example, a stage holding the substrate moves
the slide in a raster pattern under the sample applicator, which
results in a continuous "painting" of rows of blood on the
substrate surface. In certain embodiments, the applicator or stage
can move in a spiral or boustrophedon pattern with each
successively painted row next to the previous row painted in the
opposite direction across the sample surface. By way of example,
the following discussion refers to dispensing blood in a
boustrophedon pattern on the substrate surface. However, more
generally, the methods and systems disclosed herein can be applied
to dispense fluids in a wide variety of patterns including, but not
limited to, raster patterns and spiral patterns as either or both
of the sample applicator or the stage supporting the substrate move
during the sample deposition process.
[0060] In some embodiments, when blood is dispensed in a
boustrophedon pattern, the sample applicator--positioned at a
certain height above the substrate surface--sweeps across the
sample surface in successive rows, dispensing a continuous volume
of blood as it moves. As the rows of blood dry on the substrate
surface, they coalesce to form a continuous film of blood. The
uniformity of the film depends on the manner in which the rows of
blood are dispensed onto the substrate. The rate at which the blood
is dispensed and the spacings or overlap between successive rows of
blood are chosen so that adjacent rows of blood, when they spread
laterally and merge, form a film with a cellular distribution
across the substrate that is as uniform as possible, e.g., one cell
in thickness. Ideally, the cells within the film are deposited at a
desired thickness on the substrate as densely as possible while
maintaining consistent spacing between cells to minimize overlap or
contact between adjacent cells (e.g., a layer of cells uniformly
distributed across the surface of the substrate where each cell is
separated from adjacent cells by half of the cell's thickness).
[0061] An important factor that influences the uniformity of the
overall film is the uniformity of the width of the individual rows
of blood deposited on a substrate. Typically, the greater the
uniformity of the width of each row, the greater the uniformity of
the overall film that is formed on the substrate. The width of a
given row of dispensed blood is related to the height of the
applicator above the substrate upper surface as the applicator is
translated to new locations relative to the surface because of
capillary forces within sample on the substrate contiguous with the
sample being dispensed from the applicator. To achieve a uniform
film with a monolayer of cells on the surface of the substrate, the
capillary forces within the sample are balanced against the
dispersive forces that tend to cause spreading of the dispensed
rows on the substrate surface. By balancing these forces, adjacent
rows merge to form a uniform film on the sample surface in which
the cells and other sample constituents are dispersed neither too
thinly nor too irregularly.
[0062] In addition to controlling the width of a dispensed row of
blood by controlling the height of the applicator above the
substrate, the viscosity of the fluid sample and the rate of speed
at which the applicator and substrate are moving with respect to
each other influence the width of a given row of blood dispensed
onto the substrate. In general, the greater the height of the
applicator above the surface (e.g., the larger the gap between the
applicator and the surface), the greater the width of the dispensed
rows. That is, the rate at which blood is dispensed onto the
surface of the slide is related to the volume of the region between
the applicator and the substrate surface. Variations in the volume
of this region are therefore related to variations in height of the
applicator above the substrate surface. Thus, to dispense rows that
are as nearly uniform in width, height, and cellular distribution
as possible, it is important: (a) to maintain as uniform a height
of the applicator above the substrate surface as possible as the
applicator is translated or moved from location to location
relative to the substrate surface; and (b) to dispense the sample
at a flow rate that neither succumbs to the capillary forces
present in the sample deposited on the substrate and contiguous
with the sample in the applicator, nor overpowers these capillary
forces. In addition, depositing slightly overlapping rows (e.g.,
overlapping by 1/8, 1/4, 1/2, or 1/3 of the sample applicator
diameter) can improve the overall uniformity of a sample deposited
on a substrate.
[0063] Because the viscosity and surface tension of blood are both
relatively high, the amount of lateral spreading of the dispensed
rows is smaller than would occur for rows of a fluid with smaller
surface tension, such as water or a sample of blood mixed with a
diluent. Thus, the viscosity and surface tension can be determined
and monitored to ensure that the spacing between rows of blood is
suitable to achieve the desired overall coverage.
[0064] It has been determined through careful experimentation that
for a sample applicator having an outer diameter of about 1500 to
500 microns and an inner diameter of about 500 to 100 microns
(e.g., a sample applicator with an outer diameter of about 812
microns and an inner diameter of about 431 microns), used to
dispense rows of blood that cover an area of 600 square millimeters
on the surface of a glass substrate, a suitable height for the
applicator above the surface of the substrate (e.g., a microscope
slide) is about 8 to 20 microns (e.g., 10, 12, 14, 16, or 18
microns). On average, for example, the height of the sample
applicator above the surface of the glass substrate can be
maintained at about 12 microns. At this height, to ensure that rows
of blood are dispensed with sufficient uniformity, the height of
the applicator above the substrate surface should vary by no more
than 2 microns.
[0065] In addition, it has been observed that ordinary microscope
slides can vary in thickness from slide to slide by as much as 25
microns between the upper and lower slide surfaces. The variation
in microscope slide thicknesses can significantly alter the
consistency or uniformity of samples deposited on a slide if the
applicator is fixed in position in a laboratory frame of reference,
without regard to the thickness of the substrate. If the thickness
of the substrate varies, then maintaining the applicator at a fixed
position along an axis normal to the substrate surface may result
in variations in the height of the applicator above the substrate
surface as the applicator and substrate move relative to one
another due to the varying thickness of the substrate. Further,
although substrates such as microscope slides are maintained in an
orientation such that the surface of the slide is planar and
nominally orthogonal to a central axis of the applicator, in
practice, a substrate can be oriented such that its upper surface
is angled somewhat with respect to the central axis of the
applicator, further complicating the task of maintaining a constant
applicator height.
[0066] Given the above constraints, methods and systems that can
determine the height of the sample applicator above the upper
surface of the substrate are important for ensuring that automated
methods can be used to prepare blood samples that correspond to a
consistent volume of analyte (e.g., 1 microliter of blood)
dispersed in a sample uniformly distributed across the surface of a
substrate. Further, because of the relatively small tolerance for
variations in the applicator height, it is important that the
applicator height be determined without allowing the applicator to
physically contact the substrate during sample deposition or
outside a calibration process. Uncontrolled or unintended physical
contact between the applicator and the substrate could potentially
damage the applicator tip or displace the substrate from its
original position, precluding an accurate determination of the
applicator position. In addition, if the applicator tip includes a
drop of sample and the drop contacts the substrate before the
applicator deposits the sample onto the substrate, additional cells
may be deposited onto the substrate surface, thereby erroneously
affecting the quantitative results for a sample of expected
volume.
[0067] The methods and systems disclosed herein can be used to
determine both the height of the sample applicator above the
substrate surface and the thickness of the substrate. Typically,
height measurements are performed at one or more substrate surface
locations. At each location, the sample applicator is scanned
through a series of displacements relative to the substrate
surface. At each displacement value, the height of the applicator
above the substrate surface is determined, and correlated with a
particular setting of the applicator manipulator that controls
displacement of the applicator. At each location, a manipulator
setting is determined that corresponds to the targeted height
(e.g., 8, 10, 12, 14, 16, 18, or 20 microns) of the applicator
above the substrate surface. In this manner, suitable positions for
the applicator are determined at multiple locations on the
substrate surface. At each location, the thickness of the substrate
can also be determined to further refine the positional height data
for the applicator.
[0068] After this information has been determined for the
substrate, the applicator can dispense rows of blood without making
any further measurements of the applicator height. In effect, the
initial set of height measurements used to determine suitable
settings for the applicator manipulator functions as calibration
data for the dispensing operation. By calibrating prior to the
dispensing operation, a known quantity of blood can be dispensed
continuously (e.g., in rows) without performing applicator height
measurements, while enabling a continuous, controlled height
adjustment of the applicator to ensure that the blood is dispensed
regularly and uniformly, and each row is allowed to dry for the
same amount of time before an adjacent row is dispensed. This
pattern of regular, uniform row dispensing helps to ensure that the
resulting blood sample is as uniform as possible when it has
dried.
Sample Applicator Height Determination Systems and Methods
[0069] FIG. 1A shows a schematic diagram of a system 50 that
features a sample applicator 100 positioned above an upper surface
of a substrate 102. Sample applicator 100 dispenses a fluid sample
104 onto substrate 102. Substrate 102 has a thickness t, and sample
applicator 100 is positioned at a height h above the upper surface
of substrate 102. Both t and h are measured along a direction
parallel to the central axis 108 of sample applicator 100. A
detector 106 is positioned to detect light rays 110 from sample
applicator 100 and/or substrate 102 that propagate at an angle to
central axis 108 of sample applicator 100. Sample applicator 100 is
mechanically connected to a manipulator 150, and substrate 102 is
supported by a stage 152. Manipulator 150 and stage 152 are
electrically (e.g., by wires or wirelessly) connected to control
unit 160, which includes an electronic processor 162.
[0070] In FIG. 1A, the central axis 108 of sample applicator 100 is
nominally orthogonal to the plane of substrate 102. In certain
embodiments, the central axis of sample applicator 100 may not be
orthogonal to the plane of substrate 102. FIG. 1B shows a schematic
diagram of a sample applicator 100 that dispenses fluid 104 onto
the surface of substrate 102. In FIG. 1B, substrate 102 is oriented
at an angle .theta. with respect to a plane perpendicular to
central axis 108 of sample applicator 100. The angle .theta.
corresponds to the tilt angle of substrate 102 in an external
coordinate system, such as the coordinate system of manipulator
150. In FIG. 1B, axis 112 corresponds to a direction along which
sample applicator 102 is translated by manipulator 150. Manipulator
150 can also translate sample applicator 102 along a second axis
orthogonal to the plane of FIG. 1B and to axis 112; substrate 102
can be un-tilted with respect to the second axis (e.g., as in FIG.
1A), or substrate 102 can be tilted with respect to the second
axis. In general, the tilt angle with respect to the second axis
can be the same as, or different from, the tilt angle with respect
to axis 112.
[0071] FIG. 2 shows an enlarged view of the embodiment of FIG. 1A.
In FIG. 2 (as in FIG. 1A), a sample applicator 100 is positioned at
a height h above an upper surface of substrate 102. Fluid
104--dispensed by applicator 100--is not shown in FIG. 2 for
clarity. Light rays emerging from multiple points on sample
applicator 100 are captured by detector 106. By way of
illustration, a series of light rays are shown emerging from point
100a on the surface of sample applicator 100. Rays 110a, 110b, and
110c emerge from point 100a and are detected directly by detector
106; these rays form a direct (e.g., unreflected) image of point
100a. In an image formed on detector 106, rays 110a-c form a
portion of a direct image region that corresponds to the direct
image of applicator 100.
[0072] Rays 110d, 110e, and 110f also emerge from point 100a.
However, rays 100d-f initially propagate downwards toward upper
surface 102a of substrate 102. Upon encountering upper surface
102a, a portion of each of rays 110d-f is reflected from the upper
surface toward detector 106. The reflected portions correspond to
rays 110g, 110h, and 110i. These rays form an indirect (e.g.,
reflected) image of point 100a in a first reflected image region of
the image formed on detector 106.
[0073] Portions of rays 110d-f in FIG. 2 undergo refraction rather
than reflection at upper surface 102a. These refracted rays
propagate through substrate 102, and are reflected from lower
surface 102b of substrate 102. Upon encountering upper surface 102a
a second time, the rays again undergo refraction at the upper
surface, emerge from substrate 102, and propagate toward detector
106 as rays 110j, 110k, and 110l. Rays 110j-l form a second
indirect (e.g., reflected) image of point 100a in a second
reflected image region of the image formed on detector 106.
[0074] FIG. 3 shows a schematic, exemplary image 300 formed on
detector 106. Image 300 includes a direct image 302 of sample
applicator 100, a first reflected image 304 of sample applicator
100, and a second reflected image 306 of sample applicator 100.
First reflected image 304 is formed by rays reflected from upper
surface 102a of substrate 102 (e.g., rays 110g-i). Second reflected
image 306 is formed by rays reflected from lower surface 102b of
substrate 102 (e.g., rays 110j-l).
[0075] As is evident from FIGS. 2 and 3, the direct image
corresponding to rays 110a-c is displaced laterally from the
reflected image corresponding to the bundle of rays 110g-i in the
plane of the image formed on detector 106 by an amount .mu.h that
is related to the height h of sample applicator 100 above surface
102a of substrate 102. As sample applicator 100 is moved closer to
upper surface 102a, the displacement .mu.h between the direct and
reflected images of sample applicator 100 is reduced. Conversely,
as h increases, the image displacement .mu.h also increases.
[0076] In similar fashion, the reflected image corresponding to
rays 110g-i is displaced laterally from the reflected image
corresponding to rays 110j-l in the image plane on detector 106 by
an amount .mu.t that is related to the thickness t of substrate
102. For thicker substrates (e.g., where the distance between
surfaces 102a and 102b is larger), the displacement .mu.t is also
larger. For thinner substrates, .mu.t is reduced.
[0077] Accordingly, by determining displacements between the direct
and reflected images of sample applicator 100 in one or more images
captured by detector 106, the height h of sample applicator above
substrate 102 and the thickness t of substrate 102 can be
estimated. Further, by calibrating image pixel measurements with
known linear displacements, pixel-based measurements of height and
thickness can be converted into length units (e.g., microns).
[0078] To determine the position of sample applicator 100 relative
to substrate 102 (e.g., the height of sample applicator 100 above
substrate 102), the displacement .mu.h between images 302 and 304
in FIG. 3 is determined. The first step in measuring this distance
is to determine an apex position for the direct image 302 of sample
applicator 100. FIG. 4 is a flow chart 400 that includes a series
of steps for determining an apex position of a direct image of a
sample applicator. In a first step 402 in flow chart 400, a direct
image of sample applicator 100 is analyzed to select pixel subsets
that will be used to calculate an intensity gradient along the
central axis 108 of the applicator. FIG. 5A shows a half-image 500
of a sample applicator 100. The central axis 108 of the applicator
shown in the half-image is coincident with the right-most edge of
image 500. In FIG. 5A, pixel columns 502, 504, 506, 508, 510, and
512 extend parallel to central axis 108. Accordingly, each of these
pixel columns is selected in step 402 for further analysis.
[0079] Next, in step 404, each subset (e.g., column) of pixels
identified in step 402 is separately analyzed by calculating an
intensity gradient along the column. In certain embodiments, the
gradient is calculated along the pixel column using an edge
detection kernel (e.g., a four-pixel kernel of [1, 3, -3, -1]). In
some embodiments, the gradient can be calculated by determining the
intensity differences between each adjacent pixel in the column.
The change in intensity .DELTA.I between any two adjacent pixels 1
and 2 is calculated as .DELTA.I=I(2)-I(1), where I(1) and I(2) are
the measured intensities of pixels 1 and 2, respectively. This
procedure is illustrated in FIG. 5B for pixel column 506, where the
change in intensity is plotted along the upper (horizontal) axis
against column position on the left-hand (vertical) axis. For
example, the uppermost plotted point 514 along the vertical axis
corresponds to the change in intensity between the first pixel 516
and the second pixel 518 in column 506. The vertical coordinate of
point 514 corresponds to the dividing line between the pixels; the
horizontal coordinate of point 514 corresponds to the calculated
change in intensity between the pixels. As the intensity of second
pixel 518 in column 506 is greater than the intensity of first
pixel 516 (e.g., the second pixel appears brighter than the first),
the change in intensity is positive. As is evident from FIG. 5B,
the largest change in intensity in column 506 occurs between fourth
pixel 520 and fifth pixel 522; this change in intensity is
represented by point 524 in FIG. 5B.
[0080] Returning to FIG. 4, in step 406, the position of the
maximum change in intensity is determined for each pixel column.
For each pixel column, the process of determining the position of
the maximum change in intensity is generally accomplished by
fitting a functional form to the change in intensity values
calculated between adjacent pixels of the column in step 404. This
process is illustrated in FIG. 5B, where curve 526 has been fitted
to some of the calculated change in intensity values. In general, a
variety of different functional forms can be used to determine the
position of the maximum change in intensity. In FIG. 5B, a
parabolic functional form was fitted to the maximum change in
intensity between adjacent pixels (e.g., point 524) and to the
calculated change in intensity values on either side of the
maximum. As shown in FIG. 5B, the position of maximum change in
intensity for pixel column 506 was then interpolated as the peak of
the fitted parabolic curve, point 528. In the example of FIG. 5B,
the position of the maximum change in intensity, point 528, did not
correspond exactly with the positions of any of the divisions
between adjacent pixels. Instead, the position of maximum intensity
change fell within pixel 520.
[0081] This procedure is repeated for each of the pixel columns in
FIG. 5A to determine a position of maximum intensity change for
each column. The determined maximal positions are shown as lines
530, 532, 534, 536, 538, and 540 in FIG. 5A. As can be seen from
comparing FIGS. 5A and 5B, the maximum position 534 in column 506
corresponds to the position of point 528 in FIG. 5B.
[0082] Returning to FIG. 4, after the positions of maximum
intensity change for each pixel column have been determined in step
406, the apex position of the sample applicator is determined in
step 408. In general, the apex position of the sample applicator
corresponds approximately to the maximum change in intensity that
is furthest from the dark edge among the pixel columns of image 500
in FIG. 5A (i.e., the top horizontal row of pixels shown in FIG.
5A). Referring to FIG. 5A, this dark edge of the sample applicator
image corresponds to the body of the sample applicator, while the
bright edge corresponds to the end of the applicator that is
nearest to substrate 102. Accordingly, the apex position of sample
applicator 100--the point on the direct image of the sample
applicator that is nearest to the reflected images of the sample
applicator--is identified approximately as the position of the
maximum change in intensity, selected from among all of the pixel
columns, that is nearest to the bright edge of the direct image. In
FIG. 5A, the position of maximum change in intensity for pixel
column 512, position 540, is closest to the bright edge of image
500 (i.e., the bottom horizontal row of pixels shown in FIG. 5A).
Accordingly, the apex position of the sample applicator in the
direct image of the applicator is approximately identified as point
540 in FIG. 5A.
[0083] In some embodiments, the apex position of the sample
applicator can be further refined by fitting a functional form to
the positions of maximum change in intensity for each pixel column.
For example, a functional form (e.g., a parabolic functional form)
can be fitted to positions 530, 532, 534, 536, 538, and 540, and
the apex of the sample applicator can be determined as the vertex
of the fitted parabolic form. In FIG. 5A, a parabola fitted to
positions 530, 532, 534, 536, 538, and 540 will have a vertex that
is approximately coincident with position 540. More generally,
however, the fitted functional form may not be exactly coincident
with the any of the positions of maximum change in intensity for
the pixel columns, due to imaging artifacts and irregularities in
the shape of sample applicator 100, for example.
[0084] It has been experimentally determined that a parabolic
functional form typically yields an accurate apex position for the
sample applicator. As discussed above, the apex position of
applicator 100 can be determined from the direct image as the
maximal point of the fitted function (e.g., the apex of the
parabola) closest to the substrate. Other functional forms can also
be used to determine the apex position for the sample applicator.
For example, in some embodiments, an elliptical functional form can
be fitted to the applicator edge locations to determine the apex
position of the sample applicator. Typically, an elliptical
functional form matches the edges of the applicator closely because
the edge profile of the applicator is elliptical in reflected
images.
[0085] Having determined the apex position of the sample applicator
in the direct image using at least one of the foregoing methods,
the process shown in FIG. 4 terminates at step 410.
[0086] The next step in determining the position of sample
applicator 100 relative to substrate 102 is to determine an apex
position for the image of sample applicator 100 that corresponds to
the reflection from upper surface 102a of substrate 102. FIG. 6
shows a flow chart 600 that includes a series of steps for
determining an apex position of a reflected image of the sample
applicator. The first step 602 in flow chart 600 is to identify the
image of the sample applicator that corresponds to the reflection
from upper surface 102a of substrate 102.
[0087] In some embodiments, the procedure disclosed previously in
connection with FIG. 4 for locating the apex of the direct image of
the sample applicator can be used to determine the apex position of
a reflected image of the sample applicator. Alternatively, and
particularly when the reflected image of the sample applicator is
not as well focused as the direct image, other procedures can be
used to determine the apex position. FIG. 7A shows a schematic
representation of a typical image 700 captured by detector 106. A
direct image region 702 of image 700 includes a direct image 704 of
sample applicator 100. A first reflected image region 706 includes
a first reflected image 708 of sample applicator 100. A second
reflected image region 707 includes a second reflected image 710
(overlaid on a portion of the first reflected image) of sample
applicator 100. First reflected image 708 corresponds to reflection
from upper surface 102a of substrate 102, as explained above.
[0088] Returning to FIG. 6, the second step 604 in flow chart 600
is to identify rows of pixels that extend in a direction
perpendicular to the central axis 108 of sample applicator 100 in
the reflected image region. In FIG. 7A, the central axis 108 in the
first and second reflected image regions extends in a direction
parallel to the left- and right-hand edges of image 700;
accordingly, suitable rows of pixels extend in a direction parallel
to the top and bottom edges of image 700.
[0089] The identification of suitable rows of pixels to be used in
finding the apex position of the reflected image of the sample
applicator can also involve excluding certain rows from
consideration. For example, the apex position of the direct image
of the sample applicator, point 712, has already been determined
using the procedure described in flow chart 400. Accordingly, with
reference to image 700, pixel rows above point 712 need not be
further considered, as the reflected image of the sample applicator
will not appear in these rows.
[0090] In certain embodiments, pixel rows can also be foreshortened
to speed up computational operations. For example, referring to
FIG. 7A, the edge positions of the direct image of the sample
applicator can be determined from the analysis of image 704. The
edge positions of the reflected images 708 and 710 of the sample
applicator can be assumed to fall in approximately the same
locations as the edge positions of the direct image 704.
Accordingly, pixel rows that are used to find the apex position of
the reflected image of the sample applicator can be shortened by
applying edge boundaries 714 and 716 in FIG. 7A. Further, edge
boundaries can be selected to exclude other substrate features
(e.g., painted logos, specimen frames, fiducial marks) from the
first reflected image region. Edge boundaries 714 and 716 can be
angled with respect to central axis 108 as shown in FIG. 7A, or can
be parallel to central axis 108. The angle of the edge boundaries
with respect to central axis 108 can be 5.degree. or more (e.g.,
10.degree. or more, 15.degree. or more, 20.degree. or more,
25.degree. or more, 30.degree. or more, 40.degree. or more,
50.degree. or more).
[0091] Returning again to FIG. 6, after suitable rows of pixels
have been identified in step 604 (which can include foreshortening
the identified rows), the contrast level for each row of pixels is
determined in step 606. The contrast level can be determined in a
variety of ways; the following discussion presents a particular
series of steps for performing this calculation, but it is to be
understood that other methods can also be used for measuring the
variability in intensity for each row of pixels.
[0092] In certain embodiments, the first step in determining the
contrast level for a particular row of pixels includes determining
an average intensity for a subset of the brightest (e.g., highest
intensity) pixels within a given row. The determination of an
average intensity for a subset of pixels with the highest intensity
values for a pixel row involves determining the average of the n
largest intensities of pixels in the row. The value of n can be 1
or more (e.g., 2 or more, 3 or more, 4 or more, 5 or more, 6 or
more, 8 or more, 10 or more, 15 or more, 20 or more, 30 or more),
or n can be expressed as a fraction of the total number of pixels
in the row (e.g., 1/4 or less, 1/5 or less, 1/6 or less, 1/7 or
less). Typically, the value of n is chosen so that the subset of
highest intensity pixels does not include pixels that correspond to
the reflected image 708 of the sample applicator.
[0093] The next step in determining the contrast level for the
pixel row is to determine the average intensity for a subset of the
darkest (e.g., lowest intensity) pixels within the row. The average
intensity for the darkest pixels with a row can be calculated as
the average of the m smallest intensities for pixels in the row.
The value of m can be 1 or more (e.g., 2 or more, 3 or more, 4 or
more, 5 or more, 6 or more, 8 or more, 10 or more, 15 or more, 20
or more, 30 or more), or m can be expressed as a fraction of the
total number of pixels in the row (e.g., 1/4 or less, 1/5 or less,
1/6 or less, 1/7 or less). Typically, the value of m is chosen so
that the subset of lowest intensity pixels does not include pixels
that correspond to the background portion of the image (i.e., that
does not contain the reflected image 708 of the sample
applicator).
[0094] Finally, the contrast level for the pixel row is calculated
as the difference between the average intensity for the subset of
highest intensity pixels for the row, and the average intensity for
the subset of lowest intensity pixels for the row. The foregoing
process can be repeated for each row of pixels identified in step
604, so that each pixel row has an associated contrast level.
[0095] Then, in step 608, the apex position of the reflected image
of sample applicator 100 can be determined based on the change in
contrast level values between each of the pixel rows. FIG. 7B shows
contrast level (on the upper horizontal axis) plotted as a function
of pixel row (on the left-hand vertical axis) for image 700 in FIG.
7A. Determination of the apex position of the reflected image of
the sample applicator is based on the observation that in pixel
rows that do not correspond to an image of the sample applicator,
the contrast level will be relatively small, and in pixel rows that
do correspond to an image of the sample applicator, the contrast
level will be considerably larger. For example, in FIG. 7A, pixel
row 718 does not correspond to first reflected image 708 of the
sample applicator; as a result, the contrast level in row 718 is
small, as indicated by point 722 in FIG. 7B. In contrast, pixel row
720 does correspond to first reflected image 708; accordingly, the
contrast level in row 720 is larger than in row 718, as indicated
by point 724 in FIG. 7B.
[0096] By plotting the contrast level as a function of pixel row in
FIG. 7B, pixel rows that correspond to no reflected images, to the
first reflected image 708, and to the combination of the first and
second reflected images, 708 and 710, can be identified based on
the changes in contrast level between pixel rows. As shown in FIGS.
7A and 7B, the applicator tip in the first reflected image region
of FIG. 7A corresponds to the largest change in contrast level
between pixel rows in first reflected image region 706, indicated
as point 726 in FIG. 7B. With the apex position of the first
reflected image 708 of the sample applicator determined in step
608, the process in flow chart 600 then terminates at step 610. A
similar process can be repeated, as further described below, to
determine the apex position of second reflected image 710 of the
sample applicator, shown as point 728 in FIG. 7B.
Determining Applicator Height
[0097] Having determined the apex positions of direct image 704 and
of first reflected image 708 from the substrate's upper surface as
described above, the height of sample applicator 100 relative to
substrate 102 can be determined by calculating the separation h
between the apex positions. FIG. 7C shows a schematic
representative image in which the apex position of the direct
image, point 712, and the apex position of the first reflected
image, point 726, have been determined. The separation .mu.h
between the images can be calculated in straightforward fashion (in
image pixel units) from the difference between the apex positions.
If desired, the separation .mu.h can be converted to length units
(e.g., microns) based on previously determined calibration
information.
Calibration--General Considerations
[0098] The calibration information can be determined by correlating
a known separation (in length units such as microns) between the
sample applicator and the upper surface of a substrate based on a
known position of the stage or applicator to a pixel separation
between the applicator and the upper surface of the substrate in a
reflected image region. Thereafter, the calibration information can
be used to interpolate pixel separations and positions of the stage
or applicator to find the desired position of the stage or
applicator that provides the desired pixel separation, and the
position of the stage or applicator can be offset based on the
calibrated separation to achieve the desired separation between the
applicator and the upper surface of the slide. Alternatively,
control unit 160 can (a) correlate manipulator 150 or stage 152
positions to instances when detector 106 acquires an image of the
sample applicator contacting a substrate, and (b) extrapolate the
correlated manipulator or stage positions to a desired separation
between the sample applicator and substrate.
Surface Touch Detection Calibration
[0099] A variety of methods can be used to calibrate the systems
disclosed herein so that measurements of the separation .mu.h
between direct and reflected images of the sample applicator can be
converted to measurements of the height h of the sample applicator
above the surface of substrate 102. One such method is discussed
below, but it is to be understood that other methods can also be
used for calibration.
[0100] In some embodiments, the actuators used to control the
position of the sample applicator (e.g., actuators present in
manipulator 150 and/or stage 152 and controlled by control unit
160) can include non-screw driven linear actuators, such as linear
crossed roller bearings or air-bearing linear actuators, such as
those available from Dover (Westborough, Mass.), in which motor,
bearing, and encoder are not in direct contact. In addition to
permitting movement along an axis when a suitable control signal is
delivered, such actuators can also permit generation and
measurement of force along the direction of motion. When such
actuators are used in the systems disclosed herein, obtaining
calibration information typically occurs according to a two-step
procedure separated into a first "Digital to Analog Converters
("DAC") calibration" step and a second "applicator displacement"
step.
[0101] In the DAC calibration step, with the sample applicator not
in contact with the surface of the slide, the servo loop that
typically drives the actuator is terminated and the actuator's
amplifier is immediately re-enabled with a fixed DAC offset control
signal. This DAC offset signal is delivered to the actuator by
manipulator 150 from control unit 160 to initiate motion of the
actuator in an "upward" direction (e.g., parallel to central axis
108 of the applicator and away from the surface of substrate 102).
As a result, the actuator and sample applicator are together driven
upwards by the fixed DAC offset control signal. After allowing the
fixed DAC offset control signal to move the actuator and sample
applicator for a set period of time, the actuator position is
measured. The calibration routine begins again with a smaller DAC
offset control signal, and continues to repeat until movement of
the actuator, during the set time period, passes a predetermined
threshold condition in the downward direction. The DAC offset
control signal value that satisfies this threshold is stored. The
value of the stored DAC offset control signal, when applied without
an active servo loop, produces sufficient upward force such that
the actuator will just barely be overcome by the force of
gravity.
[0102] Once the DAC offset control signal has been calibrated, the
actuator moves the sample applicator to a position that is known to
be above the surface of the substrate. A fatal following error
threshold is established (e.g., entry by a system operator,
retrieval from a storage medium, or hard-coded into software or
hardware) such that when the servo loop following error exceeds the
fatal following error, the servo loop is terminated. The actuator
and sample applicator are slowly displaced towards the surface of
the substrate, under control of the servo loop, while the servo
loop following error is measured by control unit 160. When the
sample applicator makes physical contact with the surface of the
substrate and continues to drive downward, the servo loop following
error builds up and quickly exceeds the fatal following error; the
servo loop is then terminated. Control unit 160 then re-enables the
actuator's amplifier and activates the calibrated DAC offset
control signal.
[0103] The result of this second stage of calibration is that the
sample applicator comes to rest nearly weightlessly on the surface
of the substrate. After waiting for a period of time for actuator
to settle into position, control unit 160 reads the position of the
actuator and optionally converts the position into position units
(e.g., microns). This value is stored as the position of the
surface of the substrate (e.g., the h=0 position). The sample
applicator can then be translated to a position above the surface
of the substrate, and the position (e.g., measured by reading from
the actuator's encoder) can be correlated with a pixel separation
as disclosed above.
[0104] Such measurements can be repeated as many times as desired
to produce accurate calibration information. It has been found that
calibration information produced in this manner is repeatable to
better than 500 nm, and contact between the sample applicator and
the substrate introduces no more than 1 micron of deflection to the
substrate. Additional features and aspects of using air bearing
actuators for calibration are disclosed, for example, in a document
entitled "Force Generation and Measurement," by Kevin McCarthy,
published in Drives & Controls (March 2002), and available from
Dover Motion on the Internet at "dovermotion.com" under
"WhitePapersPage.aspx," the entire contents of which are
incorporated herein by reference. Further, while servo motors can
be used with manipulator 150 or stage 152 to implement the surface
touch detection calibration technique, other types of motors (e.g.,
stepper motors) can be used to accomplish the technique.
[0105] By way of example, the foregoing surface touch detection
calibration procedure can be performed at initialization of an
automated sample preparation system, at predetermined times during
normal operation or maintenance of such system, or upon receipt of
a system error message relating to the quality of a prepared sample
on a substrate (e.g., a low magnification or high magnification
imaging station cannot accurately identify or count one or more
constituents within a sample).
Determining Substrate Thickness
[0106] The methods and systems disclosed herein can also be used to
determine the thickness of the substrate, e.g., a microscope slide,
by comparing apex positions of the images reflected from the upper
and lower surfaces of a transparent substrate.
[0107] The process disclosed above in flow chart 600 can also be
used to determine an apex position of the image of the sample
applicator that is reflected from lower surface 102b of substrate
102 (i.e., the second reflected image 710 in the second reflected
image region 707). As shown in FIG. 7B, for example, just as there
is a significant difference between the contrast level for pixel
rows that correspond to no reflected image and pixel rows that
correspond to first reflected image 708, there is typically also a
significant difference between the contrast level for pixel rows
that correspond to the overlap of first reflected image 708 and
second reflected image 710, and pixel rows that correspond only to
first reflected image 708. The apex position for second reflected
image 710 is indicated as point 728 in FIGS. 7B and 7C.
[0108] With reference to FIG. 7C, the separation between apex
positions 726 and 728, .mu.t, can then be calculated to provide an
indication of the thickness of substrate 102. As disclosed above in
connection with the separation .mu.h, the value of
.mu.t--determined in pixel units from the image in FIG. 7C--can be
converted to linear units using suitable calibration information,
which can be obtained in a manner similar to the procedure
described above, or in a variety of other ways, including
performing a series of calibration runs with substrates of known
thickness to assemble a calibration table of measured values of
.mu.t and the corresponding known thicknesses t. During subsequent
operation of the systems disclosed herein, a thickness t
corresponding to a measured value of .mu.t can be interpolated from
the values in the calibration table.
Selecting an Appropriate Applicator Height to Dispense a Desired
Sample Distribution
[0109] In the foregoing description, sample applicator 100 is
positioned at a fixed height h above the upper surface 102a of
substrate 102 while the separation .mu.h is determined from an
image such as that shown in FIG. 7C. Sample applicator 100 can be
mechanically connected to a manipulator that controls translation
of sample manipulator 100 in three coordinate dimensions. In the
embodiment shown in FIG. 1A, for example, sample applicator 100 is
connected to manipulator 150. Associated with manipulator 150 is a
coordinate system that corresponds to axes along which sample
applicator 100 can be translated. For example, sample applicator
100 can be translated along a z-coordinate direction of manipulator
150, which extends parallel to central axis 108 of sample
applicator 100--to vary the height h of the sample applicator above
upper surface 102a of substrate 102. Further, sample applicator 100
can be translated along x- and y-coordinate directions, each of
which is perpendicular to the z-coordinate direction. The x- and
y-coordinate directions are each parallel to a plane oriented
perpendicular to central axis 108. When the tilt angle .theta. of
substrate 102 is zero, the x- and y-coordinate directions are also
parallel to the plane formed by substrate 102; translating sample
applicator 100 in either or both of the x- and y-coordinate
directions therefore positions the sample applicator at a new
location relative to substrate 102, but does not change the height
h of sample applicator 100 relative to substrate 102.
[0110] Alternatively, in some embodiments, stage 152 can be used to
translate substrate 102 in the x-, y, and z-coordinate directions
relative to sample applicator 102. Further, in certain embodiments,
both stage 152 and manipulator 150 can be used to translate sample
applicator 100 relative to substrate 102, with motion in the in x-,
y, and z-coordinate directions apportioned between stage 152 and
manipulator 150. In the following disclosure, adjustment of the
sample applicator's height via manipulator 150 is discussed;
however, it should be understood that the methods disclosed can
also be implemented via adjustment of the height of sample
applicator 100 using stage 152 alone, or by using stage 152 in
combination with manipulator 150.
[0111] In the methods disclosed above for determining the
separation .mu.h, sample applicator 100 remains at both a fixed
height and a fixed location relative to substrate 102. However, as
discussed above, careful experimentation has determined suitable
heights for dispensing certain fluids onto certain substrates. In
particular, it has been determined that for dispensing blood onto
microscope slides to form a film that is approximately one-cell
thick, sample applicator 100 should be maintained at a height of
about 12 microns above the surface of the slide. This height value
was determined for a specific rate of sample dispensing (e.g.,
translation speed of sample applicator 100 relative to substrate
102) and for a specific sample viscosity. More generally, sample
applicator 100 should be maintained at a height of between 8
microns and 20 microns above the surface of the slide (e.g., at a
height of about 8 microns, about 10 microns, about 12 microns,
about 14 microns, about 16 microns, or about 18 microns, or within
a range of 10 to 14, 16, or 18 microns) when dispensing blood onto
microscope slides.
[0112] In general, the following factors influence the ability to
dispense a sample uniformly on a substrate at an even distribution,
and therefore have an effect on the appropriate height of the
sample applicator above the surface of the substrate:
[0113] (1) the flow rate of the sample dispensed from the
applicator should equal the desired volume of sample to be
dispensed during the sample dispensing period;
[0114] (2) as the sample applicator translation speed relative to
the substrate increases, the applicator height above the substrate
should decrease proportionally (although the proportionality
relationship may not be linear, and the applicator height should
not decrease below a minimum height below which damage occurs to
cells);
[0115] (3) as the sample viscosity increases relative to the
surface tension of the sample dispensed onto the substrate, the
applicator height above the surface of the substrate should
decrease to prevent disruptions or "tears" in the sample flow as it
is deposited on the substrate;
[0116] (4) as the substrate wettability increases, the sample
applicator height above the substrate should decrease to maintain
under the applicator a constant volume of sample being dispensed
onto the substrate; and
[0117] (5) as the sample applicator inner diameter increases, the
applicator height above the substrate should decrease (although not
below the minimum height below which damage occurs to cells) to
maintain under the applicator a constant volume of sample being
dispensed onto the substrate.
[0118] In some embodiments, to ensure that sample applicator 100 is
positioned at a suitable height above substrate 102 when fluid 104
is later dispensed onto the substrate, sample applicator 100 is
maintained at a specific location relative to substrate 102 (e.g.,
at a particular x- and y-coordinate position in the coordinate
system of the manipulator), and the height of sample applicator 100
above substrate 102 is varied (e.g., sample applicator 100 is
translated along the z-coordinate direction in the coordinate
system of manipulator 150). At each new height setting of the
manipulator, the steps disclosed above in flow charts 400 and 600
are repeated to determine the separation .mu.h.
[0119] Then, using calibration information that relates the
measured image separation .mu.h to the actual height h of sample
applicator 100 above substrate 102 and/or to particular control
settings of manipulator 150, a suitable control setting for the
manipulator is selected to yield a sample applicator height that
corresponds to the desired target applicator height at a particular
location of sample applicator 100 relative to substrate 102.
[0120] This procedure is illustrated with reference to FIG. 8,
which shows a calibration curve 800 that relates control settings
V.sub.i of manipulator 150 (or stage 152) to a series of measured
image separations .mu.h. To generate the points shown in FIG. 8,
sample applicator 100 was positioned at a series of six different
heights above upper surface 102a of substrate 102 by applying six
different control settings to manipulator 150 (or stage 152) using
control unit 160. The location of sample applicator 100 in the x-y
plane relative to substrate 102 was the same for each different
height (along the z axis). At each different height, an image was
obtained by detector 106 showing both a direct image of sample
applicator 100 and a reflected image of sample applicator 100. The
separation between the direct and reflected images, .mu.h, was
determined. The six measured image separations,
.mu.h.sub.1-.mu.h.sub.6, are plotted on the vertical axis of FIG. 8
as a function of the six different control settings V.sub.1-V.sub.6
applied to manipulator 150 (or stage 152) to position sample
applicator 100 at the six different heights.
[0121] It is known from previously determined calibration
information that target separation .mu.h.sub.t corresponds to the
desired target height ht of sample applicator 100 above substrate
102. For example, for dispensing a blood sample onto a microscope
slide, previous calibration steps have determined that a target
sample applicator height ht above the surface of substrate 102
(e.g., 12 microns) corresponds to a particular z coordinate
position of manipulator 150 (or stage 152). As shown in FIG. 8,
target separation .mu.h.sub.t falls in between measured separations
.mu.h.sub.3 and .mu.h.sub.4, which correspond to manipulator (or
stage) control settings V.sub.3 and V.sub.4, respectively.
[0122] To determine the manipulator (or stage) control setting that
yields the target sample applicator height h.sub.t (e.g., 12
microns), interpolation between the measured points (V,.mu.h) can
be used. In particular, interpolation between points
(V.sub.3,.mu.h.sub.3) and (V.sub.4,.mu.h.sub.4) can be used to
determine the control setting V.sub.t that yields the target
separation .mu.h.sub.t. Because the target separation .mu.h.sub.t
corresponds to the target applicator height h.sub.t, control
setting V.sub.t applied to manipulator 150 (or stage 152) yields
the desired target sample applicator height h.sub.t.
[0123] Although a total of six different manipulator (or stage)
settings were used in FIG. 8 to determine target control setting
V.sub.t, more generally, any number of manipulator (or stage)
height settings can be used. For example, the number of sample
applicator height settings (which is the same as the number of
manipulator or stage control settings) can be 2 or more (e.g., 3 or
more, 4 or more, 6 or more, 8 or more, 10 or more, 15 or more, 20
or more).
[0124] For a particular location of sample applicator 100 relative
to substrate 102, the process disclosed herein yields a control
setting V.sub.t of the manipulator (or stage) that will ensure that
sample applicator 100 is positioned at a desired height above upper
surface 102a of substrate 102 at that location. As shown in FIG. 9,
the process disclosed above can be repeated for multiple different
locations 902, 904, 906, and 908 of sample applicator 100 relative
to substrate 102. At each location, the height of sample applicator
above substrate 102 can be varied by translating manipulator 150
(or stage 152) along the z-coordinate axis of the manipulator by
applying different control settings to the manipulator (or stage).
The measured image separations .mu.h at the different heights can
be used to determine a target control setting V.sub.t of the
manipulator (or stage) that will ensure that sample applicator 100
is positioned at a desired height above substrate 102 at that
location.
[0125] Suitable control settings can be determined at any number of
locations of sample applicator 100 relative to substrate 102. In
FIG. 9, suitable control settings are determined at four different
locations. More generally, however, the number of locations can be
one or more (e.g., two or more, three or more, four or more, six or
more, eight or more, ten or more, 15 or more, 20 or more, or 30 or
more).
[0126] After suitable control settings have been determined at a
fixed number of locations, suitable control settings can be
estimated at other locations by using, e.g., interpolation
techniques. For example, referring to FIG. 9, suitable control
settings V.sub.t are determined at locations 902 and 904. A
suitable control setting V.sub.t that yields a sample applicator
height of, e.g., 10 microns, above substrate 102 can be estimated
at location 903 by interpolating between the control settings
determined at locations 902 and 904.
[0127] The thickness of substrate 102 can also be measured at any
of locations 902, 904, 906, and 908 using the steps disclosed above
in connection with flow chart 600. In particular, the separation
.mu.t between the two reflected images of sample applicator 100
need only be determined once at each location; this separation does
not change as sample applicator 100 is translated along the
z-coordinate axis of manipulator 150 (or stage 152). Accordingly,
.mu.t can be determined at a single height. The image separation
.mu.t can be converted to yield a thickness t measured in linear
units (e.g., microns) using calibration information if desired.
[0128] With suitable control settings for the manipulator (or
stage) determined at specific locations of sample applicator 100
relative to substrate 102, manipulator 150 (or stage 152) can be
positioned such that sample applicator 100 is positioned at any
location relative to substrate 102, and the height of the sample
applicator above the substrate's upper surface can be maintained at
a desired value. Thus, fluid 104 can be dispensed from nearly a
constant height above substrate 102, ensuring that rows of the
dispensed fluid are as nearly uniform as possible. In this manner,
the samples produced are of greater uniformity than those produced
using, e.g., manual methods.
Determining Substrate Orientation
[0129] In some embodiments, the orientation of substrate 102 can be
determined. With reference to FIG. 1B, determining the orientation
of substrate 102 can include determining the tilt angle .theta.
between the plane defined by substrate 102 and a plane orthogonal
to central axis 108 of sample applicator 100. Determining the
orientation of substrate 102 can also include determining
parameters associated with an equation f(x,y) that describes upper
surface 102a of substrate 102 as a function of position in the
(x,y) coordinate plane of manipulator 150 (or stage 152). In
general, the orientation of a plane can be determined when three
points on the plane are known. Accordingly, when the number of
stored control settings (which typically corresponds to the number
of distinct locations of sample applicator 100 relative to
substrate 102 at which control settings are determined) is three or
more, the equation of the plane describing surface 102a can be
determined directly from the stored control settings. In some
embodiments, the stored control settings are first converted to
displacement values expressed in linear units (e.g., microns) using
calibration information, and then the displacement values are used
to determine the coefficients of the equation of the plane of
surface 102a. It has been observed that as a result of the slope of
the plane of substrate 102 supported by stage 152, the vertical
coordinate of surface 102a of the substrate (in the coordinate
system of manipulator 150 or stage 152) can vary by as much as 30
microns between (x,y) locations on opposite ends of the substrate.
The equation of the plane that describes surface 102a can also be
used, for example, to determine the tilt angle of surface 102a.
Additionally, with four or more stored control settings, it is
possible to track non-planar surface substrates such as a slightly
curved substrate by fitting a more complex equation f(x,y)
describing a curved surface to the values of the control settings.
Methods for determining an equation of a plane describing or
relative to a surface are found in co-pending U.S. patent
application Ser. No. 13/019,118, filed on Feb. 1, 2011, the entire
contents of which are incorporated herein by reference.
System Components
[0130] Returning again to FIG. 1A, manipulator 150 can include a
variety of different devices. In general, manipulator 150 functions
to translate sample applicator 100 in three different, orthogonal
coordinate directions. Suitable manipulators include, for example,
actuators activated by step-and-repeat motors, and piezoelectric
actuators.
[0131] Detector 106 can include a variety of devices for capturing
images of sample applicator 100. In some embodiments, for example,
detector 106 can include a CCD array detector. In certain
embodiments, detector 106 can include a CMOS-based array detector.
Detector 106 can also include other optical imaging elements such
as filters, lenses, beam splitters, and dispersive optical
elements.
[0132] Stage 152 is configured to support substrate 102 during
dispensing of fluid 104. In certain embodiments, stage 152 is
formed of a rigid material such as a metal (e.g., aluminum and/or
stainless steel) and/or a plastic material (e.g., a
Teflon.RTM.-based material). Stage 152 can also include actuators
for translating substrate 102 (and part or all of stage 152) in one
or more coordinate directions, e.g., in the x-y plane, while
applicator 100 remains stationary to dispense the sample fluid. In
some embodiments, stage 152 can include actuators for changing an
orientation of substrate 102 and part or all of stage 152. Control
unit 160 is connected to stage 152 and can issue control signals to
stage 152 to initiate translation and/or re-orientation of
substrate 102.
[0133] In some embodiments, system 50 can include a light source
170 for directing incident light onto sample applicator 100. Light
source 170 can be electrically connected to control unit 160 as
shown in FIG. 1A. Light source 170 can include, for example, one or
more incandescent, fluorescent, diode-based, and/or laser sources.
Incident light produced by light source 170 can include wavelengths
in one or more of the ultraviolet, visible, and infrared regions of
the electromagnetic spectrum.
[0134] Control unit 160 includes electronic processor 162, which
can be configured to control various components in system 50 and
perform any of the method steps disclosed herein. For example,
electronic processor 162 can be configured to direct detector 106
to capture one or more images of sample applicator 100 as described
herein. Further, electronic processor 162 can be configured to
direct light source 170 to emit incident light that illuminates
sample applicator 100 during image capture.
[0135] Electronic processor 162 can be further configured to
transmit control signals to manipulator 150 to cause manipulator
150 to translate sample applicator 100 and/or stage 152 as
disclosed herein. In particular, control signals from electronic
processor 162 can direct manipulator 150 to translate sample
applicator 100 along the x- and/or y-coordinate directions of
manipulator 150 to a new location relative to substrate 102.
Alternatively or in addition, electronic processor 162 can transmit
control signals to stage 152 to translate substrate 102 in the x-
and/or y direction, while the applicator 100 remains stationary.
Electronic processor 162 can also transmit control signals that
direct manipulator 150 to translate sample applicator 100 along the
z-coordinate direction of manipulator 150 to a new height above
substrate 102, and can transmit control signals to stage 152 to
translate substrate 102 (e.g., while sample applicator 100 remains
stationary) to change the height of applicator 100 above substrate
102.
[0136] In some embodiments, control unit 160 includes a storage
unit 164. Storage unit 164 can include, for example, one or more of
a variety of different devices for storing information optically,
electrically, and/or magnetically. Exemplary devices include, but
are not limited to, magnetic storage devices such as hard drives
and floppy disks, optical storage devices such as CD and/or DVD
drives and their storage media, and electronic devices such as
flash memory devices and solid state drives. Storage unit 164 can
be configured to store any of the values or quantities disclosed
herein, including the locations of sample applicator 100 relative
to substrate 102, control settings determined for the sample
applicator that ensure the applicator is maintained at a constant
height above the upper surface 102a of substrate 102, the measured
heights of the sample applicator above substrate 102, the
separations .mu.h and/or .mu.t between images, the measured
thicknesses of substrate 102, and software containing instructions
that, when executed, cause processor 162 to perform any one or more
of the functions or steps disclosed herein.
Automated Sample Preparation Systems
[0137] The systems and methods disclosed herein can be used with a
variety of different automated sample preparation systems.
Exemplary systems are disclosed, for example, in U.S. patent
application Ser. No. 13/293,050, filed on Nov. 9, 2011, and now
published as U.S. Patent Application Publication No. US
2012/0149050, the entire contents of which are incorporated herein
by reference.
[0138] FIG. 10 shows a schematic diagram of an embodiment of an
automated sample preparation system 1000. System 1000 includes
multiple sub-systems for storing substrates, depositing samples on
substrates, inspecting samples prepared on substrates, and storing
prepared samples.
[0139] Substrate storage sub-system 1010 is configured to store
substrates prior to the deposition of samples thereon. Substrates
can include, for example, microscope slides, coverslips, and
similar planar, optically transparent substrates. The substrates
can be formed from a variety of different amorphous or crystalline
materials including various types of glasses. Sub-system 1010 can
include a manipulator that selects individual substrates from a
storage container and transfers the selected substrates to sample
deposition sub-system 1020.
[0140] Sample deposition sub-system 1020 deposits a selected
quantity of a sample of interest--such as a blood sample--onto a
substrate. Sub-system 1020 includes, in general, a variety of fluid
transfer components (e.g., pumps, fluid tubes, valves) configured
to deposit the sample.
[0141] The fluid transfer components can also be configured to
expose the substrate to solutions of various types, including wash
solutions, one or more stains that bind to the sample, fixing
solutions, and buffer solutions. Sub-system 1020 can also feature
fluid removal components (e.g., a vacuum sub-system) and a drying
apparatus to ensure that the sample is fixed to the substrate. A
substrate manipulator can transfer the substrate supporting the
sample to imaging sub-system 1030.
[0142] As discussed above, the methods and systems disclosed herein
permit the determination of the thickness of substrate 102 based on
images of the sample applicator that are reflected from lower
surface 102b of the substrate. This thickness information can be
used by sample deposition sub-system 1020. For example, as
described in U.S. patent application Ser. No. 13/293,050
(incorporated by reference above), substrate thickness information
can be used to determine how to orient the substrate in a specimen
processing position, and the extent of agitation that occurs during
the deposition process.
[0143] Inspection sub-system 1030 includes various components for
obtaining images of samples on substrates, and for analyzing the
images to determine information about the samples. For example,
inspection sub-system 1030 can include one or more light sources
(e.g., light emitting diodes, laser diodes, and/or lasers) for
directing incident light to a sample. Imaging sub-system 1030 can
also include an optical apparatus (e.g., a microscope objective)
for capturing transmitted and/or reflected light from a sample. A
detector (e.g., a CCD detector) coupled to the optical apparatus
can be configured to capture images of the sample. Information
derived from analysis of the images of the sample can be stored on
a variety of optical and/or electronic storage media for later
retrieval and/or further analysis.
[0144] Following inspection, a substrate manipulator can transfer
the substrate to storage sub-system 1040. Storage sub-system 1040
can label individual substrates, for example, with information
relating to the source of the sample applied to the substrate, the
time of analysis, and/or any irregularities identified during
analysis. Storage sub-system can also store processed substrates in
multi-substrate racks, which can be removed from system 1000 as
they are filled with substrates.
[0145] As shown in FIG. 10, each of the various sub-systems of
system 1000 can be linked to a common electronic processor 1050
(which can be the same as electronic processor 162, or a different
electronic processor). Processor 1050 can be configured to control
the operation of each of the sub-systems of system 1000 in
automated fashion, with relatively little (or no) input from a
system operator. Results from the analysis of samples can be
displayed on system display 1060 for a supervising operator.
Interface 1070 permits the operator to issue commands to system
1000 and to manually review the automated analysis results.
Hardware and Software Implementation
[0146] The method steps and procedures described herein can be
implemented in hardware or in software, or in a combination of
both. In particular, an electronic processor (e.g., electronic
processor 162) can include software and/or hardware instructions to
perform any of the methods discussed above. The methods can be
implemented in computer programs using standard programming
techniques following the method steps and figures disclosed herein,
and stored on a variety of non-transitory media such as magnetic
disks, optical storage media such as compact discs and DVDs, solid
state memory devices such as flash memory, and mechanical storage
media such as hard disks. Program code is applied to input data to
perform the functions described herein. The output information is
applied to one or more output devices such as a printer, or a
display device, or a web page on a computer monitor with access to
a website, e.g., for remote monitoring.
[0147] Each program is preferably implemented in a high level
procedural or object oriented programming language to communicate
with a processor. However, the programs can be implemented in
assembly or machine language, if desired. In any case, the language
can be a compiled or interpreted language. Each computer program
can be stored on a storage medium or device (e.g., an electronic
memory) readable by the processor, for configuring and operating
the processor to perform the procedures described herein.
OTHER EMBODIMENTS
[0148] A number of embodiments have been described. Nevertheless,
it will be understood that various modifications may be made
without departing from the spirit and scope of the disclosure.
Accordingly, other embodiments are within the scope of the
following claims.
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