WO2004025560B1 - Assay stick comprising coded microbeads - Google Patents

Assay stick comprising coded microbeads

Info

Publication number
WO2004025560B1
WO2004025560B1 PCT/US2003/028875 US0328875W WO2004025560B1 WO 2004025560 B1 WO2004025560 B1 WO 2004025560B1 US 0328875 W US0328875 W US 0328875W WO 2004025560 B1 WO2004025560 B1 WO 2004025560B1
Authority
WO
WIPO (PCT)
Prior art keywords
grating
vessel
refractive index
substrate
particle
Prior art date
Application number
PCT/US2003/028875
Other languages
French (fr)
Other versions
WO2004025560A1 (en
Inventor
Martin A Putnam
John Moon
Tuo Li
Original Assignee
Cyvera Corp
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US10/645,686 external-priority patent/US20040075907A1/en
Application filed by Cyvera Corp filed Critical Cyvera Corp
Priority to AU2003270655A priority Critical patent/AU2003270655A1/en
Priority to US10/661,115 priority patent/US20040126875A1/en
Priority to EP03752362A priority patent/EP1540590A1/en
Priority to CA002498913A priority patent/CA2498913A1/en
Priority to PCT/US2003/028875 priority patent/WO2004025560A1/en
Publication of WO2004025560A1 publication Critical patent/WO2004025560A1/en
Publication of WO2004025560B1 publication Critical patent/WO2004025560B1/en

Links

Classifications

    • G—PHYSICS
    • G03—PHOTOGRAPHY; CINEMATOGRAPHY; ANALOGOUS TECHNIQUES USING WAVES OTHER THAN OPTICAL WAVES; ELECTROGRAPHY; HOLOGRAPHY
    • G03H—HOLOGRAPHIC PROCESSES OR APPARATUS
    • G03H1/00—Holographic processes or apparatus using light, infrared or ultraviolet waves for obtaining holograms or for obtaining an image from them; Details peculiar thereto
    • G03H1/02—Details of features involved during the holographic process; Replication of holograms without interference recording
    • G03H1/0272—Substrate bearing the hologram
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/502761—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/508—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above
    • B01L3/5085—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above for multiple samples, e.g. microtitration plates
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00457—Dispensing or evacuation of the solid phase support
    • B01J2219/00459—Beads
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00457—Dispensing or evacuation of the solid phase support
    • B01J2219/00459—Beads
    • B01J2219/00461—Beads and reaction vessel together
    • B01J2219/00463—Directed sorting
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00457—Dispensing or evacuation of the solid phase support
    • B01J2219/0047—Pins
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase supports
    • B01J2219/005—Beads
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/0054—Means for coding or tagging the apparatus or the reagents
    • B01J2219/00547—Bar codes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/0054—Means for coding or tagging the apparatus or the reagents
    • B01J2219/00572—Chemical means
    • B01J2219/00576—Chemical means fluorophore
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/00702—Processes involving means for analysing and characterising the products
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/06—Fluid handling related problems
    • B01L2200/0636—Focussing flows, e.g. to laminate flows
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/06—Fluid handling related problems
    • B01L2200/0647—Handling flowable solids, e.g. microscopic beads, cells, particles
    • B01L2200/0668—Trapping microscopic beads
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/06—Auxiliary integrated devices, integrated components
    • B01L2300/0627—Sensor or part of a sensor is integrated
    • B01L2300/0654—Lenses; Optical fibres
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2400/00—Moving or stopping fluids
    • B01L2400/04—Moving fluids with specific forces or mechanical means
    • B01L2400/0403—Moving fluids with specific forces or mechanical means specific forces
    • B01L2400/0409—Moving fluids with specific forces or mechanical means specific forces centrifugal forces
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2400/00—Moving or stopping fluids
    • B01L2400/04—Moving fluids with specific forces or mechanical means
    • B01L2400/0403—Moving fluids with specific forces or mechanical means specific forces
    • B01L2400/0457—Moving fluids with specific forces or mechanical means specific forces passive flow or gravitation
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2400/00—Moving or stopping fluids
    • B01L2400/04—Moving fluids with specific forces or mechanical means
    • B01L2400/0475—Moving fluids with specific forces or mechanical means specific mechanical means and fluid pressure
    • B01L2400/0487—Moving fluids with specific forces or mechanical means specific mechanical means and fluid pressure fluid pressure, pneumatics
    • G—PHYSICS
    • G03—PHOTOGRAPHY; CINEMATOGRAPHY; ANALOGOUS TECHNIQUES USING WAVES OTHER THAN OPTICAL WAVES; ELECTROGRAPHY; HOLOGRAPHY
    • G03H—HOLOGRAPHIC PROCESSES OR APPARATUS
    • G03H2210/00—Object characteristics
    • G03H2210/50—Nature of the object
    • G03H2210/53—Coded object not directly interpretable, e.g. encrypted object, barcode
    • G—PHYSICS
    • G03—PHOTOGRAPHY; CINEMATOGRAPHY; ANALOGOUS TECHNIQUES USING WAVES OTHER THAN OPTICAL WAVES; ELECTROGRAPHY; HOLOGRAPHY
    • G03H—HOLOGRAPHIC PROCESSES OR APPARATUS
    • G03H2230/00—Form or shape of the hologram when not registered to the substrate
    • G03H2230/10—Microhologram not registered to the substrate
    • G—PHYSICS
    • G03—PHOTOGRAPHY; CINEMATOGRAPHY; ANALOGOUS TECHNIQUES USING WAVES OTHER THAN OPTICAL WAVES; ELECTROGRAPHY; HOLOGRAPHY
    • G03H—HOLOGRAPHIC PROCESSES OR APPARATUS
    • G03H2270/00—Substrate bearing the hologram
    • G03H2270/20—Shape
    • G—PHYSICS
    • G03—PHOTOGRAPHY; CINEMATOGRAPHY; ANALOGOUS TECHNIQUES USING WAVES OTHER THAN OPTICAL WAVES; ELECTROGRAPHY; HOLOGRAPHY
    • G03H—HOLOGRAPHIC PROCESSES OR APPARATUS
    • G03H2270/00—Substrate bearing the hologram
    • G03H2270/20—Shape
    • G03H2270/24—Having particular size, e.g. microscopic

Abstract

An assay stick 7 includes a transparent reaction vessel or tube 14 having one or more microbeads 8 disposed therein. The microbeads 8 have a plurality of unique identification digital codes based on a diffraction grating 12 disposed therein that are detected when illuminated by incident light 24. The incident light 24 may be directed transversely onto the side or onto an end of the tube 14 with a narrow band (single wavelength) or multiple wavelength source, in which case the code is represented by a spatial distribution of light or a wavelength spectrum, respectively. The assay stick 7 may be reused or disposed upon completion of the assay. Instead of beads, cells or molecules may be spotted or grown directly on the tube.

Claims

45
AMENDED CLAIMS
[received by the International Bureau on 03 April 2004 (03.04.04); original claims 1-20 replaced by amended claims 1-159]
What is claimed is:
1. An apparatus for reading an encoded optical identification element, comprising: a column-shaped vessel; at least one substrate disposed within said vessel; each of said substrates having at least one diffraction grating disposed therein, said grating having a resultant refractive index variation at a grating location; and said grating providing an output optical signal indicative of a code when jjlumi-oated by an incident light signal-
2. The apparatus of claim 1 comprising a plurality of said substrates.
3. The apparatus of claim 1 wherein said vessel is made of a glass or plastic material.
4. The apparatus of claim 1 wherein said vessel is made of a material that is transparent to said incident light.
5. The apparatus of claim 1 wherein said vessel comprises a tube.
6. The apparatus of claim 1 wherein said substrates are stacked in said vessel.
7. The apparatus of claim 1 wherein said vessel comprises a syringe or pipette tip.
8. The apparatus of claim 1 wherein said refractive index variation comprises at least one refractive index pitch superimposed at said grating location.
9. The apparatus of claim 1 wherein said refractive index variation comprises a plurality of refractive index pitches superimposed at said grating location.
10. The apparatus of claim 1 wherein said substrate is made of a material selected from the group: glass, silica, plastic, rubber, and polymer.
11. The apparatus of claim 1 wherein said code comprises a plurality of digital bits. 46
12. The apparatus of claim 1 wherein said code comprises at least a predetermined number of bits, said number being: 3, 5, 7, 9, 10, 12, 14, 16, 18, 20, 24, 28, 30, 40, 50, or 100.
13. The apparatus of claim 1 wherein said code comprises a plurality of bits, each bit having a plurality of states.
14. The apparatus of claim 1 wherein said code comprises a plurality of bits, each bit having a corresponding spatial location and each bit in said code having a value related to the intensity of said output optical signal at the spatial location of each bit.
15. The apparatus of claim 14 wherein the value of each bit corresponds to the magnitude of refractive index variation of a corresponding refractive index pitch in said grating.
16. The apparatus of claim 1 wherein said code comprises a plurality of digital bits, each bit having a corresponding spatial location and each bit in said code having a binary value related to the intensity of said output optical signal at the spatial location of each bit.
17. The apparatus of claim 16 wherein the value of each bit corresponds to the presence or absence of a corresponding refractive index pitch in said grating.
1.8. The apparatus of claim 1 wherein said incident light comprises a single wavelength.
19. The apparatus of claim 1 wherein said incident light comprises a plurality of wavelengths or a single wavelength scanned over a predetermined wavelength range.
20. The apparatus of claim 19 wherein said code comprises a plurality of bits, and each bit in said code having a value related to the intensity of said output optical signal at a wavelength corresponding to each bit.
21. The apparatus of claim 20 wherein the value of said intensity is related to the magnitude of refractive index variation of a corresponding refractive index pitch in said grating.
22. The apparatus of claim 21 wherein said code comprises a plurality of digital bits, and each bit in said code having a binary value related to the intensity of said output optical signal at the wavelength corresponding to each bit. 47
23. The apparatus of claim 22 wherein the value of said intensity is related to the presence or absence of a corresponding refractive index pitch in said grating.
24. The apparatus of claim 1 wherein said substrate has a length that is less than about 500 microns.
25. The apparatus of claim 1 wherein said substrate has a diameter that is less than about 125 microns.
26. The apparatus of claim 1 wherein said substrate has a reflective coating disposed thereon.
27. The apparatus of claim 1 wherein said substrate has a coating disposed on at least a portion of said substrate, at least a portion of said coating being made of a material that allows sufficient amount of said incident light signal to pass through said material to alJow detection of said code.
28. The apparatus of claim 1 wherein said substrate has a coating material disposed on at least a portion of said substrate, said coating comprising a polymer.
29. The apparatus of claim 1 wherein said substrate has a magnetic or electric charge polarization.
30. The apparatus of claim 1 wherein said substrate has geometry having holes therein or having protruding sections therein.
31. The apparatus of claim 1 wherein at least a portion of said substrate has an end cross sectional geometry selected from the group: circular, square, rectangular, elliptical, clam-shell, D-sh ped, and polygon.
32. The apparatus of claim 1 wherein at least a portion of said substrate has a side view geometry selected from the group: circular, square, rectangular, elliptical, clam-shell, D-shaped, and polygon.
33. The apparatus of claim 1 wherein at least a portion of said substrate has a 3-D shape selected from the group: a cylinder, a sphere, a cube, and a pyramid.
34. The apparatus of claim 1 wherein said substrate has a grating region where said grating is located and a non-grating region where said grating is not located; and wherein said substrate has a plurality of grating regions.
35. The apparatus of claim 1 wherein said substrate has a grating region where said grating is located and a non-grating region where said grating is not located; and wherein said grating region has a refractive index that is greater than that of said non- grating region.
36. The apparatus of claim 1 wherein said substrate has a grating region where said grating is located and a non-grating region where said grating is not located; and wherein said grating region has a refractive index that is not greater than that of said non- grating region.
37. The apparatus of claim 1 wherein said incident light is incident on said substrate along a longitudinal grating axis of said grating.
38. The apparatus of claim 1 wherein said incident light is incident on said substrate at an angle to a longitudinal grating axis of said grating.
39. The apparatus of claim 1 wherein said incident light comprises laser light.
40. The apparatus of claim 1 wherein said grating comprises a thin grating or a blazed grating.
41. The apparatus of claim 1 wherein said substrate comprises a plurality of said gratings.
42. The apparatus of claim 1 wherein said substrate comprises a plurality of said gratings each at different locations within said substrate.
43. The apparatus of claim 1 wherein said chemical comprises at least one gene, oligonucleotide, protein, antibody, peptide, amino acid, NDA, cDNA, R.NA, nucleic acid oligomer, polymer, or biological cell, or portion thereof.
44. An apparatus for reading an encoded particle, comprising: a column-shaped vessel; at least one particle disposed within said vessel; each of said particles having at least one diffraction grating disposed therein, said grating having a resultant refractive index variation at a grating location; and said grating providing an output optical signal indicative of a code when illuminated by an incident light signal.
45. The apparatus of claim 1 comprising a plurality of said particles.
46. The apparatus of claim 1 wherein said vessel is made of a glass or plastic material. 49
47. The apparatus of claim 1 wherein said vessel is made of a material that is transparent to said incident light.
48. The apparatus of claim 1 wherein said vessel comprises a tube.
49- The apparatus of claim I wherein said particles are stacked in said vessel.
50. The apparatus of claim I wherein said vessel comprises a syringe or pipette tip.
51. The apparatus of claim 1 wherein said refractive index variation comprises at least one refractive index pitch superimposed at said grating location.
52. The apparatus of claim 1 wherein said refractive index variation comprises a plurality of refractive index pitches superimposed at said grating location.
53. The apparatus of claim 44 wherein said particle is made of a material selected from the group: glass, silica, plastic, rubber, and polymer.
54. The apparatus of claim 44 wherein said code comprises a plurality of digital bits.
55. The apparatus of claim 44 wherein said code comprises at least a predetermined number of bits, said number being: 3, 5, 7, 9, 10, 12, 14, 16, 18, 20, 24, 28, 30, 40, 50, or 100.
56. The apparatus of claim 44 wherein said code comprises a plurality of bits, each bit having a plurality of states.
57. The apparatus of claim 44 wherein said code comprises a plurality of bits, each bit having a corresponding spatial location and each bit in said code having a value related to the intensity of said output optical signal at the spatial location of each bit.
58. The apparatus of claim 5 wherein the value of each bit corresponds to the magnitude of refractive index variation of a corresponding refractive index pitch in said grating.
59- The apparatus of claim 44 wherein said code comprises a plurality o f digital bits, each bit having a corresponding spatial location and each bit in said code having a binary value related to the intensity of said output optical signal at the spatial location of each bit.
60. The apparatus of claim 59 wherein the value of each bit corresponds to the presence or absence of a corresponding refractive index pitch in said grating. 50
61. The apparatus of claim 44 wherein said incident light comprises a single wavelength.
62. The apparatus of claim 44 wherein said incident light comprises a plurality of wavelengths or a single wavelength scanned over a predeteπnined wavelength range.
63. The apparatus of claim 62 wherein said code comprises a plurality of bits, and each bit in said code having a value related to the intensity of said output optical signal at a wavelength corresponding to each bit.
64. The apparatus of claim 63 wherein the value of said intensity is related to the magnitude of refractive index variation of a corresponding refractive index pitch in said grating.
65. The apparatus of claim 64 wherein sai d code comprises a plurality of digital bits, and each bit in said code having a binary value related to the intensity of said output optical signal at the wavelength corresponding to each bit.
66. The apparatus of claim 65 wherein the value of said intensity is related to the presence or absence of a corresponding refractive index pitch in said grating.
67. The apparatus of claim 44 wherein said particle has a length that is less than about 500 microns.
68. The apparatus of claim 44 wherein said particle has a diameter that is less than about 125 microns.
69. The apparatus of claim 44 wherein said particle has a reflective coating disposed thereon.
70. The apparatus of claim 44 wherein said particle has a coating disposed on at least a portion of said particle, at least a portion of said coating being made of a material that allows sufficient amount of said incident light signal to pass through said material to allow detection of said code.
71. The apparatus of claim 44 wherein said particle has a coating material disposed on at least a portion of said particle, said coating comprising a polymer.
72. The apparatus of claim 44 wherein said particle has a magnetic or electric charge polarization. 51
73. The apparatus of claim 44 wherein said particle has geometry having holes therein or having pτotruding sections therein.
74. The apparatus of claim 44 wherein at least a portion of said particle has an end cross sectional geometry selected from the group: circular, square, rectangular, elliptical, clam-shell, D-shaped, and polygon.
75. The apparatus of claim 44 wherein at least a portion of said particle has a side view geometry selected from the group: circular, square, rectangular, elliptical, clam-shell, D-shaped, and polygon.
76. The apparatus of claim 44 wherein at least a portion of said particle has a 3-D shape selected from the group: a cylinder, a sphere, a cube, and a pyramid.
77. The apparatus of claim 44 wherein said particle has a grating region where said grating is located and a non-grating region where said grating is not located; and wherein said particle has a plurality of grating regions.
78. The apparatus of claim 44 wherein said particle has a grating region where said grating is located and a non-grating region where said grating is not located; and wherein said grating region has a refractive index that is greater than that of said non- grating region.
79. The apparatus of claim 44 wherein said particle has a grating region where said grating is located and a non-grating region where said grating is not located; and wherein said grating region has a refractive index that is not greater than that of said non- grating region.
80. The apparatus of claim 44 wherein said incident light is incident on said particle along a longitudinal grating axis of said grating.
81. The apparatus of claim 44 wherein said incident light is incident on said particle at an angle to a longitudinal grating axis of said grating.
82. The apparatus of claim 44 wherein said incident light comprises laser light.
83. The apparatus of claim 44 wherein said grating comprises a thin grating or a blazed grating.
84. The apparatus of claim 44 wherein said particle comprises a plurality of said gratings. 52
85. The apparatus of claim 44 wherein said particle comprises a plurality of said gratings each at different locations within said particle.
86. The apparatus of claim 44 wherein said chemical comprises at least one gene, oUgonucIeotide, protein, antibody, peptide, amino acid, NDA, cDNA, RNA, nucleic acid oligomer, polymer, or biological cell, or portion thereof,
87. An apparatus for performing an assay, comprising: a column-shaped vessel; a plurality of particles each having at least one diffraction grating disposed therein, said grating having a resultant refractive index variation at a grating location; said particles being disposed within said vessel; at least one probe being attached to at least one of said particles, thereby providing functionalized particles; said functionalized particles being in contact with at least one analyte, said analyte having a corresponding label disposed thereon; said particle providing a first output light signal indicative of a code and a second output light signal indicative of said label when illuminated with at least one incident light; and said first output light signal being indicative of said code; and said second output light signal being indicative of said label.
88. The apparatus of claim 86 comprising a plurality of said substrates.
89. The apparatus of claim 86 wherein said vessel is made of a glass or plastic material.
90. The apparatus of claim 86 wherein said vessel is made of a material that is transparent to said incident light.
91. The apparatus of claim 86 wherein said vessel comprises a tube.
92. The apparatus of claim 86 wherein said substrates are stacked in said vessel.
93. The apparatus of claim 86 wherein said vessel comprises a syringe or pipette tip. 53
94. The apparatus of claim 86 wherein said refractive index variation comprises at least one refractive index pitch superimposed at said grating location.
95. The apparatus of claim 86 wherein said refractive index variation comprises a plurality of refractive index pitches superimposed at said grating location.
96. The apparatus of claim 96 wherein said substrate is made of a material selected from the group: glass, silica, plastic, rubber, and polymer.
97. A method of reading an encoded optical identification element, comprising: obtaining a column-shaped vessel; obtaining at least one substrate, each of said substrates having at least one diffraction grating disposed therein, said grating having a resultant refractive index variation at a grating location; said substrate being disposed within said vessel; illuminating said substrate with incident light propagating in free space, said substrate providing an output light signal indicative of a code; and reading said output light signal and detecting said code therefrom.
98. The apparatus of claim 97 comprising a plurality of said substrates.
99. The apparatus of claim 97 wherein said vessel is made of a glass or plastic material.
100. The apparatus of claim 97 wherein said vessel is made of a material that is transparent to said incident light.
101. The apparatus of claim 97 wherein said vessel comprises a tube.
102. The apparatus of claim 97 wherein said substrates are stacked in said reaction vessel.
103. The apparatus of claim 97 wherein said reaction vessel comprises a syringe or pipette tip.
104. The apparatus of claim 97 wherein said refractive index variation comprises at least one refractive index pitch superimposed at said grating location.
105. The apparatus of claim 97 wherein said refractive index variation comprises a plurality of refractive index pitches superimposed at said grating location. 54
106. The method of claim 97 wherein said substrate is made of a material selected from the group: glass, silica, plastic, rubber, and polymer.
107. The method of claim 97 wherein said grating comprises a plurality of refractive index pitches superimposed at said grating location.
108. The method of claim 97 wherein said code comprises a plurality of digital bits.
109. The method of claim 97 wherein said code comprises at least a predetermined number of bits, said number being: 3, 5, 7, , 10, 12, 14, 16, 18, 20, 24, 28, 30, 40, 50, or 100.
110. The method of claim 97 wherein said substrate comprises a particle or bead.
111. The method of claim 97 wherein said substrate has a chemical attached to at least a portion of said substrate.
112. The method of claim 97 wherein said chemical comprises at least one gene, oligonucleotide, protein, antibody, peptide, amino acid, NDA, cDNA, NA, nucleic acid oligomer, polymer, or biological cell, or portion thereof.
113. The method of claim 97 wherein said chemical is attached to said substate after said substrate is disposed within said vessel.
114. The method of claim 97 wherein said chemical is attached to said substate before said substrate is disposed within said vessel.
115. The method of claim 97 wherein said at least one substrate is placed in said vessel after obtaining said vessel.
11 . The method of claim 97 wherein said vessel is obtained with said at least one substrate inside said vessel.
117. A method of reading an encoded particle, comprising: obtaining a column-shaped vessel; obtaining at least one particle, each having at least one diffraction grating disposed therein, said grating having a resultant refractive index variation at a grating location; said particle being disposed within said vessel; 55
illuminating sajd particle with incident light propagating in free space, said particle providing an output light signal indicative of a code; and reading said output light signal and detecting said code therefrom.
118. The method of claim $6 comprising a plurality of said substrates.
119. The method of claim 86 wherein said vessel is made of a glass or plastic material.
120. The method of claim 86 wherein said vessel is made of a material that is transparent to said incident light.
1,21. The method of claim 86 wherein said vessel comprises a tube.
122. The method of claim 86 wherein said substrates are stacked in said reaction vessel.
123. The method of claim 86 wherein said reaction vessel comprises a syringe or pipette tip.
124. The method of claim 86 wherein said refractive index variation comprises at least one refractive index pitch superimposed at said grating location.
125. The method of claim 96 wherein said refractive index variation comprises a plurality of refractive index pitches superimposed at said grating location.
126. The method of claim 117 wherein said particle is made of a material selected from the group: glass, silica, plastic, rubber, and polymer.
127. The method of claim 117 wherein said grating comprises a plurality of refractive index pitches superimposed at said grating location.
128. The method of claim 117 wherein said code comprises a plurality of digital bits.
129. The method of claim 117 wherein said code comprises at least a predetermined number of bits, said number being: 3, 5, 7, 9, 10, 12, 14, 16, 18, 20, 24, 28, 30, 40, 50, or 100.
130. The method of claim 117 wherein a chemical is attached to said particle.
131. The method of claim 117 wherein said chemical comprises at least one gene, ougonucleotide, protein, antibody, peptide, amino acid, NDA, cDNA, RNA, nucleic acid oligomer, polymer, or biological cell, or portion thereof. 56
132. The method of claim 87 wherein said chemical is attached to said substrate after said substrate is disposed within said vessel.
133. The method of claim 87 wherein said chemical is attached to said substrate before said substrate is disposed within said vessel.
134. The method of claim 87 wherein said at least one substrate is placed in said vessel after obtaining said vessel.
135. The method of claim 87 wherein said vessel is obtained with said at least one substrate inside said vessel.
136. A method of performing a multiplexed particle assay, comprising: obtaining a column-shaped vessel; obtaining a plurality of particles each having at least one diffraction grating disposed therein, said grating having a resultant refractive index variation at a grating location; said particles being disposed within said vessel; attaching at least one probe to at least one of said particles, thereby providing functionalized particles; placing said functionalized particles in contact with at least one analyte, said analyte having a corresponding label disposed thereon; illuminating said particles with at least one incident light, said particle providing a first output light signal indicative of a code and a second output light signal indicative of said label; reading said first output light signal and detecting said code therefrom; and reading said second output light signal and detecting said label therefrom.
137. The method of claim 136 comprising a plurality of said substrates.
138. The method of claim 1 6 wherein sajd vessel is made of a glass or plastic material.
139. The method of claim 136 wherein said vessel is made of a material that is transparent to said incident light.
140. The method of claim 136 wherein said vessel comprises a tube. 57
141 The method of claim 136 wherein said substrates are stacked in said reaction vessel
142 The method of claim 136 wherein said reaction vessel comprises a syringe or pipette tip
143 The method of claim 136 wherein said refractive index variation comprises at least one refractive index pitch superimposed at said grating location
144 The method of claim 136 wherein said refractive index variation comprises a plurality of refractive index pitches superimposed at said grating location
145 The method of claim 141 wherein said particle is made of a material selected from the group glass, silica, plastic, rubber, and polymer
146 The method of claim 141 wherein said grating comprises a plurality of refractive index pitches superimposed at said grating location
147 The method of claim 141 wherein said code comprises a plurality of digital bits
148 The method of claim 141 wherein said code comprises at least a predetermined number of bits, said number being 3, 5, 7, 9, 10, 12, 14, 16, 18, 20, 24, 28, 30, 40, 50, or 100
149 The method of claim 141 wherein said particle comprises a plurality of said gratings each at different locations within said particle
150 The method of claim 141 wherein said analyte comprises at least one gene, oligonucleotide, protein, antibody, peptide, am o acid, NDA, cDNA, RNA, nucleic acid oligomer, polymer, or biological cell, or portion thereof
151 The method of claim 141 wherein said probe comprises at least one gene, oligonucleotide, protein, antibody, peptide, amino acid, NDA, cDNA, RNA, nucleic acid oligomer, polymer, or biological cell, or portion thereof
152 The method of claim 141 wherein said label comprises a fluorescent label
153 The method of claim 141 wherein said incident light comprises a first incident light signal providing said output light signal and a second incident light signal providing said second output light signal
154 The method of claim 141 wherein said reading is performed with a CCD device
58
155 The method of claim 87 wherein said probe is attached after said particles are disposed within said vessel
156 The method of claim 87 wherein said probe is attached before said particles are disposed within said vessel
157 The method of claim 87 wherein said particles are placed in said vessel after obtaining said vessel
158 The method of claim 87 wherein said vessel is obtained with said particles inside said vessel
159 The method of claim 87 wherein said vessel is obtained with said particles inside said vessel and with said probe attached to said at least one particle
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US10/645,689 2003-08-20
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