Flow cell alignment methods and systems
First Claim
1. An alignment method for use by an imager imaging deoxyribonucleic acid (DNA) fragments on a flow cell, the imager capturing intensity values at DNA fragment bead locations in tiles with each tile having a reference location in the flow cell, the method comprising:
- during a first imaging session;
positioning the flow cell on an xy stage with the flow cell facing an imaging axis, the xy stage being movable along an x-axis and a y-axis, the x-axis being perpendicular to the y-axis, and the imaging axis being perpendicular to the x-axis and the y-axis,illuminating the flow cell from the side of the flow cell with a first light to cause the first light to strike the DNA fragment beads from above the xy stage and at an angle relative to the imaging axis, and reflect off the DNA fragment bead locations,operating the xy stage to reposition the flow cell to obtain a respective first image of each of a first tile and a second tile during a first imaging session, the respective first image comprising reflections of the first light, andidentifying a first reference constellation of bead locations within the first tile and a second reference constellation of bead locations within the second tile during the first imaging session; and
during a second imaging session;
identifying a first pattern of light corresponding to the first reference constellation in the first tile, and a second pattern of light corresponding to the second reference constellation in the second tile,determining a first offset between the first reference constellation during the first imaging session and the first pattern of light during the second imaging session,determining a second offset between the second reference constellation during the first imaging session and the second pattern of light during the second imaging session,moving the xy stage to alter the reference location of at least one tile during the second imaging session to correct for the first offset, andapplying at least one correction factor for reading out intensity values from the imager for the bead locations in the flow cell to correct for an angular offset determined from the first offset and the second offset.
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Accused Products
Abstract
Imagers and alignment methods for use by imagers imaging deoxyribonucleic acid (DNA) fragments on a flow cell are disclosed. The imagers capture intensity values at DNA fragment bead locations in tiles with each tile having a reference location in the flow cell. Flow cells may be aligned by obtaining a dark field image of each tile during a first imaging session, identifying dark field constellations of bead locations within two separate tiles during the first imaging session, identifying corresponding constellations during a second imaging session, altering the reference location of at least one tile during the second imaging session to correct for a linear offset in the corresponding constellations, and applying at least one correction factor for reading out intensity values from the imager for the bead locations in the flow cell to correct for an angular offset determined from offsets in the corresponding constellations.
299 Citations
29 Claims
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1. An alignment method for use by an imager imaging deoxyribonucleic acid (DNA) fragments on a flow cell, the imager capturing intensity values at DNA fragment bead locations in tiles with each tile having a reference location in the flow cell, the method comprising:
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during a first imaging session; positioning the flow cell on an xy stage with the flow cell facing an imaging axis, the xy stage being movable along an x-axis and a y-axis, the x-axis being perpendicular to the y-axis, and the imaging axis being perpendicular to the x-axis and the y-axis, illuminating the flow cell from the side of the flow cell with a first light to cause the first light to strike the DNA fragment beads from above the xy stage and at an angle relative to the imaging axis, and reflect off the DNA fragment bead locations, operating the xy stage to reposition the flow cell to obtain a respective first image of each of a first tile and a second tile during a first imaging session, the respective first image comprising reflections of the first light, and identifying a first reference constellation of bead locations within the first tile and a second reference constellation of bead locations within the second tile during the first imaging session; and during a second imaging session; identifying a first pattern of light corresponding to the first reference constellation in the first tile, and a second pattern of light corresponding to the second reference constellation in the second tile, determining a first offset between the first reference constellation during the first imaging session and the first pattern of light during the second imaging session, determining a second offset between the second reference constellation during the first imaging session and the second pattern of light during the second imaging session, moving the xy stage to alter the reference location of at least one tile during the second imaging session to correct for the first offset, and applying at least one correction factor for reading out intensity values from the imager for the bead locations in the flow cell to correct for an angular offset determined from the first offset and the second offset. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29)
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12. An imager for imaging deoxyribonucleic acid (DNA) fragments on a flow cell, the imager capturing intensity values at DNA fragment bead locations in tiles with each tile having a reference location in the flow cell, the imager comprising:
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an xy stage supporting the flow cell with the flow cell facing an imaging axis, the xy stage being movable along an x-axis and a y-axis, the x-axis being perpendicular to the y-axis, and the imaging axis being perpendicular to the x-axis and the y-axis; a dark field light emitting diode positioned along the y-axis to one side of the flow cell, the dark field light emitting diode being configured to illuminate the flow cell with a first light that strikes the flow cell from above the xy stage and a direction that is angled relative to the imaging axis; a camera configured to capture images of flow cell tiles; and a processor coupled to the xy stage and the camera, the processor configured to position the xy stage at a plurality of tile locations along the x-axis and the y-axis, and control the camera to; reposition the xy stage to obtain a first image of each tile during a first imaging session, the first image comprising reflections from the first dark field LED; identify a first reference constellation of bead locations within a first tile and a second reference constellation of bead locations within a second tile during the first imaging session; identify, during a second imaging session, a first pattern of light corresponding to the first reference constellation and a second pattern of light corresponding to the second reference constellation; determine a first offset between the first reference constellation during the first imaging session and the first pattern of light during the second imaging session; determine a second offset between the second reference constellation during the first imaging session and the second pattern of light during the second imaging session; alter the reference location of at least one tile during the second imaging session when positioning the xy stage to correct for the first offset; and apply at least one correction factor for reading out intensity values from the camera for the bead locations in the flow cell to correct for an angular offset determined from the first offset and the second offset.
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13. An alignment method for use by an imager imaging deoxyribonucleic acid (DNA) fragments in a flow cell, the method comprising:
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providing a flow cell chip that extends in a horizontal plane having an imaging axis extending perpendicular thereto, the flow cell chip having a flow cell comprising a plurality of tiles, wherein each tile comprises a respective reference location and a respective plurality of DNA fragment beads; positioning the flow cell chip on an xy stage, the xy stage being movable along an x-axis and a y-axis the x-axis being perpendicular to the y-axis and the imaging axis being perpendicular to the x-axis and the y-axis during a first imaging session; directing a first light from a side of the flow cell chip in relation to the imaging axis, such that the first light strikes the flow cell chip from above the xy stage and at an angle relative to the imaging axis, to thereby illuminate the flow cell chip from the side, positioning the flow cell chip with a reference location of a first tile at a predetermined position in relation to a camera, and obtaining an image of reflections along the imaging axis of the first light from DNA fragment beads in the first tile with each reflection indicating the position of a respective DNA fragment bead, and identifying a group of the reflections of the first light from the DNA fragment beads in the first tile as a first reference constellation; after the first imaging session, repositioning the flow cell chip in relation to the camera; during a second imaging session; attempting to position the flow cell chip with the reference location of the first tile at the predetermined position in relation to the camera, and examining DNA fragment bead locations in the first tile to determine the location of the first reference constellation; and comparing the location of the first reference constellation during the second imaging session to the location of the first reference constellation during the first imaging session to determine a first offset between the position of the first tile in relation to the camera during the first imaging session and the position of the first tile in relation to the camera during the second imaging session. - View Dependent Claims (14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
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Specification