Methods, carrier assemblies, and systems for imaging samples for biological or chemical analysis

Patent metadata

Field	Value
Publication number	US-2016281150-A1
Application number	US-201615077182-A
Country	US
Kind code	A1
Filing date	Mar 22, 2016
Priority date	Mar 24, 2015
Publication date	Sep 29, 2016
Grant date	—

Abstract

Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon. The method also includes detecting optical signals from the sample of the second substrate

First claim

What is claimed is:

1 . A method comprising:
positioning a first carrier assembly on a system stage, the first carrier assembly including a support frame having an inner frame edge that defines a window of the support frame, the first carrier assembly including a removable first substrate that is positioned within the window and surrounded by the inner frame edge, the first substrate having a sample thereon that is positioned within an imaging zone of an optical system; detecting optical signals from the sample of the first substrate using the optical system in accordance with a first imaging protocol; replacing the first carrier assembly with a second carrier assembly on the system stage, the second carrier assembly having a removable second substrate, the second substrate having a sample thereon that is positioned within the imaging zone of the optical system, wherein the first and second substrates are different types of substrates; and detecting optical signals from the sample of the second substrate using the optical system in accordance with a second imaging protocol that is different from the first imaging protocol.

2 . The method of claim 1 , wherein the first substrate includes a flow cell, the flow cell including a flow channel that extends between inlet and outlet ports of the flow cell, the inlet and outlet ports being fluidically coupled to a manifold for flowing a liquid through the flow channel.

3 . The method of claim 1 , further comprising iteratively flowing reagents through the flow cell to conduct a sequencing-by-synthesis (SBS) protocol.

4 . The method of claim 1 , wherein the first and second imaging protocols include moving an objective lens and/or the system stage relative to each other along different respective paths.

5 . The method of claim 1 , wherein the second substrate is an open-face substrate having biological or chemical substances immobilized to an exterior surface of the open-face substrate, wherein the open-face substrate includes a microarray along the exterior surface, wherein the microarray includes a plurality of feature stripes that extend parallel to each other, each of the feature stripes having an array of reaction sites.

6 . The method of claim 1 , wherein each of the first and second carrier assemblies includes apertures that extend into the respective carrier assembly, the apertures receiving corresponding datums when the respective carrier assembly is positioned on the system stage, wherein the first substrate engages the datums and the second substrate does not engage the datums.

7 . The method of claim 1 , wherein the optical system includes an objective lens, wherein detecting the optical signals from the first substrate includes moving the objective lens and the first substrate relative to each other, wherein detecting the optical signals from the second substrate includes moving the objective lens and the second substrate relative to each other, wherein the optical system detects the optical signals from the first substrate along a first imaging zone, the optical system detecting the optical signals from the second substrate along a second imaging zone, the first and second imaging zones being sized differently.

8 . The method of claim 7 , wherein the first and second imaging protocols include automatically moving the objective lens relative to the first and second substrates, respectively, along different paths.

9 . A method comprising:
positioning a first carrier assembly on a system stage, the first carrier assembly including a support frame having an inner frame edge that defines a window of the support frame, the first carrier assembly including a first substrate that is positioned within the window and surrounded by the inner frame edge, the first substrate having a sample thereon that is positioned within an imaging zone of an optical system; detecting optical signals from the sample of the first substrate using the optical system; replacing the first carrier assembly with a second carrier assembly on the system stage, the second carrier assembly including a support frame and an adapter plate coupled to the support frame, the second carrier assembly having a second substrate held by the adapter plate that has a sample thereon, the sample of the second substrate being positioned within the imaging zone of an optical system; and detecting optical signals from the sample of the second substrate using the optical system.

10 . The method of claim 9 , wherein the first substrate is slidable within the window along an XY-plane that extends parallel to the inner frame edge and wherein the adapter plate is slidable within the window along the XY-plane.

11 . The method of claim 9 , wherein the system stage includes a plurality of datums, the datums engaging the first substrate and engaging the adapter plate during the positioning and replacing operations.

12 . The method of claim 9 , wherein the adapter plate includes an inner plate edge that defines a pocket, the second substrate being disposed within the pocket and engaging the plate edge.

13 . The method of claim 9 , wherein replacing the first carrier assembly with the second carrier assembly includes removing the first substrate from the support frame and positioning the second substrate within the adapter plate.

14 . The method of claim 9 , wherein the first carrier assembly includes a holding mechanism that includes a movable datum block that is disposed within a portion of the pocket, the method further comprising pressing the datum block, positioning the second substrate within the pocket, and releasing the datum block, the datum block engaging the second substrate to hold the second substrate in the pocket.

15 . A carrier assembly comprising:
a support frame having an inner frame edge that defines a window of the support frame; an adapter plate coupled to the support frame and positioned within the window, the adapter plate including a plate body having an inner plate edge that defines a pocket for receiving a substrate that is sized smaller than the window, the inner plate edge also defining a holding recess that opens to the pocket; and a movable datum block positioned within the holding recess, the datum block being movable between a retracted position and an engaged position, the datum block configured to engage the substrate when the datum block is in the engaged position and press the substrate against an opposing surface of the adapter plate to hold the substrate within the pocket.

16 . The carrier assembly of claim 15 , wherein the adapter plate extends parallel to an XY plane and faces in a direction along a Z axis, the datum block providing a holding force that is directed along the XY plane.

17 . The carrier assembly of claim 15 , wherein the pocket at least one of coincides with a receiving plane that intersects the inner frame edge or is positioned below the receiving plane.

18 . The carrier assembly of claim 15 , wherein the adapter plate is slidable along an XY plane within the window.

19 . A carrier assembly comprising:
a support frame having an inner frame edge that defines a window of the support frame; and an adapter plate coupled to the support frame and positioned within the window, the inner frame edge defining a substrate-receiving recess positioned above the adapter plate, the substrate-receiving recess being configured to receive a first planar substrate, the adapter plate including a plate body having an inner plate edge that defines a pocket for receiving a second p

Assignees

• Illumina Inc
• Illumina Cambridge Ltd

Inventors

• Rawlings Stephen
• Rao Venkatesh Mysore Nagaraja
• Ang Beng Keong
• Udpa Nitin

Classifications

• G01N35/04

  Details of the conveyor system {(G01N35/021 - G01N35/028 take precedence)} · CPC title

• B01L9/52

  Supports specially adapted for flat sample carriers, e.g. for plates, slides, chips · CPC title

• B01L2300/0654

  Lenses; Optical fibres · CPC title

• G01N21/253

  for batch operation, i.e. multisample apparatus (analytical automats G01N35/00) · CPC title

• G01N35/1095

  for supplying the samples to flow-through analysers (for a specific analyser see relevant groups, e.g. under G01N15/00, G01N21/00, G01N27/00, G01N30/00, H01J49/00) · CPC title