Optical scanning systems for in situ genetic analysis

Patent metadata

Field	Value
Publication number	US-2016109693-A1
Application number	US-201514884631-A
Country	US
Kind code	A1
Filing date	Oct 15, 2015
Priority date	Oct 16, 2014
Publication date	Apr 21, 2016
Grant date	—

Abstract

Presented herein are systems and methods for performing sequencing, including fluorescence in situ sequencing. In one embodiment, a confocal time delay and integration (TDI) line scan imaging system may include various pinhole and/or slit aperture mechanisms in front of the image sensor. The system may also include structures with focusing strips on a substrate in contact with the tissue sample to be imaged. Alternatively, these strips may be cut into the tissue sample. The system may also include configurations and methods of placing a tissue sample inside a reaction chamber of a flow cell during the assembly of the flow cell and then performing chemistry operations on the tissue sample. The flow cells may use an open container for performing chemistry operations on the tissue sample.

First claim

What is claimed is:

1 . A confocal TDI line scan imaging system comprising:
a light source aperture; an optical beam splitter; a lens; a TDI image sensor and a sensor aperture mechanism.

2 . The TDI line scan imaging system of claim 1 , wherein the sensor aperture mechanism is positioned in an optically conjugate plane in front of the TDI image sensor.

3 . The TDI line scan imaging system of claim 1 , wherein the sensor aperture mechanism comprises pinholes.

4 . The TDI line scan imaging system of claim 1 , wherein the sensor aperture mechanism comprises slits.

5 . The TDI line scan imaging system of claim 1 , wherein the TDI image sensor comprises a long linear sensor.

6 . The TDI line scan imaging system of claim 1 , wherein the sensor aperture mechanism is positioned in an intermediate image plane conjugating to the TDI image sensor.

7 . The TDI line scan imaging system of claim 1 , wherein the sensor aperture mechanism comprises a first set of apertures and a second set of apertures having switchable positions.

8 . The TDI line scan imaging system of claim 7 , wherein the first set of apertures is positioned with respect to a corresponding first set of pixels on the TDI image sensor and the second set of apertures is positioned with respect to a corresponding second set of pixels on the TDI image sensor.

9 . The TDI line scan imaging system of claim 1 , wherein the aperture mechanism comprises at least one aperture plate formed of a material that is not optically transparent to the wavelengths detected by the TDI image sensor, the plate further comprising a plurality of slits.

10 . The TDI line scan imaging system of claim 9 , wherein the position of the slits substantially corresponds to the positions of a plurality of pixel columns of the TDI image sensor.

11 . The TDI line scan imaging system of claim 9 , wherein a first aperture plate and a second aperture plate are switchable in a rotating or shifting fashion.

12 . The TDI line scan imaging system of claim 11 , wherein a first aperture plate substantially corresponds to even numbered pixel columns and a second aperture plate substantially corresponds to odd numbered pixel columns, such that as switching occurs, only one aperture plate is in front of the TDI image sensor at any given time.

13 . The TDI line scan imaging system of claim 1 , comprising a switch cycle synchronized to the TDI line scan speed of one switch cycle or an integer number of cycles in a TDI scan readout.

14 . The TDI line scan imaging system of claim 13 , wherein in a first imaging half-cycle, a first aperture plate is switched into position in front of the TDI image sensor whereby odd pixel columns are open and even pixel columns are blocked.

15 . The TDI line scan imaging system of claim 13 , wherein in a second imaging half-cycle, a second aperture plate is switched into position in front of the TDI image sensor whereby even pixel columns are open and odd pixel columns are blocked.

16 . The TDI line scan imaging system of claim 1 , the system comprising a substrate having one or more focus tracking mechanisms provided thereon.

17 . The TDI line scan imaging system of claim 1 , the system comprising a substrate having one or more focus tracking mechanisms provided thereon.

18 . The TDI line scan imaging system of claim 17 , wherein the focus tracking mechanism comprises a focusing strip.

19 . The TDI line scan imaging system of claim 18 , wherein the focusing strip comprises a high-reflection material.

20 . The TDI line scan imaging system of claim 17 , wherein the focus tracking mechanism comprises a groove cut into a tissue sample.

21 . The TDI line scan imaging system of claim 20 , wherein the groove exposes the surface of a bottom substrate.

22 . The TDI line scan imaging system of claim 17 , the substrate having an exposed side comprising a tissue sample disposed in direct contact with the focus tracking mechanism on the same surface of the substrate.

23 . The TDI line scan imaging system of claim 22 , wherein the substrate further comprising a laser-based focusing mechanism provided on the opposite side of the exposed side.

24 . The TDI line scan imaging system of claim 1 , further comprising a flow cell, the flow cell comprising a first substrate upon which a tissue sample to be imaged can be disposed.

25 . The TDI line scan imaging system of claim 24 , further comprising a second substrate, the first and second substrate separated by a gap, whereby the first substrate, second substrate and gap define a reaction chamber.

26 . The TDI line scan imaging system of claim 25 , wherein the flow cell comprises an inlet and an outlet for flowing liquid into and through the reaction chamber.

27 . A method of processing a tissue sample comprising:
providing a first substrate of a flow cell; placing a sample tissue on the first substrate; providing a second substrate and assembling the second substrate to the first substrate, wherein a reaction chamber is formed around the sample tissue; and performing chemistry operations on the sample tissue in the reaction chamber

28 . The method of claim 27 , wherein the reaction chamber comprises a spacer disposed between the first and second substrates.

29 . The method of claim 28 , wherein the spacer comprises an O-ring.

30 . The method of claim 28 , wherein the spacer comprises an adhesive layer.

31 . The method of claim 27 , wherein the flow cell comprises liquid and an imaging lens is immersed in the liquid.

32 . The method of claim 31 , wherein the flow cell is substantially drained of liquid and the imaging lens is not immersed in the liquid.

Assignees

• Illumina Inc

Inventors

• Feng Wenyi

Classifications

• C12Q1/6841

  In situ hybridisation · CPC title

• H04N23/54

  Mounting of pick-up tubes, electronic image sensors, deviation or focusing coils · CPC title

• H04N23/55

  Optical parts specially adapted for electronic image sensors; Mounting thereof · CPC title

• G02B21/006 Primary

  focusing arrangements; selection of the plane to be imaged · CPC title

• G02B21/0076 Primary

  arrangements using fluorescence or luminescence · CPC title