Systems and methods for multi-modal imaging

Abstract

The system may comprise a first light source configured to illuminate a sample: a second light source configured to illuminate the sample; a first solid-state optical path configured to image the sample, the optical path configured with an objective lens optically coupled to the first light source and a first photodetector; a second solid-state optical path configured to image a sample, the optical path configured with light from a second light source and the objective lens optically coupled to the second light source, wherein the objective lens is a common element in both the first solid-state optical path and the second- state optical path; and a controllable element capable of modulating the illumination of the sample by the second light source.

Description

SYSTEMS AND METHODS FOR MULTI-MODAL IMAGING

[0001] The present disclosure provides for systems and methods for multi-modal imaging. In some instances it may be beneficial to combine brightfield maging modality with one or more fluorescence based imaging modality into a system with a common optical axis. Reduction in mechanical and optical complexity may have benefits in improving optical imaging quality and production of units required for biological interrogation.INCORPORATION BY REFERENCE

[0002] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.BRIEF DESCRIPTION OF THE DRAWINGS

[0003] The novel features of a device of this disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of this disclosure will be obtained by reference to the following detailed description that sets forth illustrative examples, in which the principles of a device of this disclosure are utilized, and the accompanying drawings of which:

[0004] Fig. 1 is a representative schematic of a system of the present disclosure.DETAILED DESCRIPTION OF THE DISCLOSUREI. General Overview

[0005] In some aspects, the system comprises a first light source configured to illuminate a sample; a second light source configured to illuminate the sample; a first solid-state optical path configured to image the sample, the optical path configured with an objective lens optically coupled to the first light source and a first photodetector; a second solid-state optical path configured to image a sample, the optical path configured with light from a second light source and the objective lens optically coupled to the second light source, wherein the objective lens is a common element in both the first solid-state optical path and the second-state optical path; and a controllable clement capable of modulating the illumination of the sample by the second light source.

[0006] The imaging system described herein provides for an optical design that may combine fluorescent and brightfield imager built with a single solid-state optical path. This may be accomplished with two mechanisms. In one example, the system may be configured by placing a beam splitter immediately after the objective lens to create separate solid state optical paths, one for fluorescent imaging, and one for brightfield imaging.

[0007] In some examples, to minimize the amount of lost emission light from fluorescent dyes through the beam splitter when the system is being used in its fluorescent imaging mode, the beam splitter may be configured to heavily bias light transmission to the fluorescent optical path rather than the brightfield optical path. In some cases a beam splitter with a ratio of 90:10 may be used. In some cases a beam splitter with a ratio of 80:20 may be used. In some cases a beam splitter with a ratio of 70:30 may be used. In some cases a beam splitter with a ratio of 60:40 maybe used. In some cases a beam splitter with a ratio of 50:50 may be used. In some instances, less light transmitted to the brightfield optical path can be compensated for by increasing the brightness I intensity of the brightfield backlight and increasing the brightfield camera exposure time. Compared to when less light is transmitted to the fluorescent optical path, in some instances, increasing brightness I intensity of the excitation laser or increasing fluorescent camera exposure time now comes at the cost of the photobleaching of the fluorescent dyes.

[0008] In some examples, compensation may also be achieved by placing an LED brightfield backlight underneath the sample, but with a mechanical shutter coated with a black beam stopping material between the sample and the backlight. This allows a controllable element, such as a shutter to toggle between two states, one to allow for the backlight to be exposed to the sample during brightfield imaging, but another to hide the LED brightfield backlight from the optical path during fluorescent imaging. The shutter may be able to cover the backlight during the fluorescent imaging. In some instances, the shutter may be useful to protect the phosphor coating on the surface of the LED from the laser excitation, which would cause undesired white light to be emitted back up into the optical path, and some in some cases to provide a black beam stop behind the sample to minimize reflections and scattering of the excitation beam.IL. Software and Computer Systems for the imaging system

[0009] In various examples, the methods and systems of the invention may further comprise software programs on computer systems and use thereof. Accordingly, computerized control for the synchronization of system functions such as laser system operation, fluid control function, and / or data acquisition steps are within the bounds of the invention. The computer systems may be programmed to control the timing and coordination of delivery of sample to a detection system, and to control mechanisms for diverting selected samples into a different flow path. In some examples of the invention, the computer may also be programmed to store thedata received from a detection system and / or process the data for subsequent analysis and display.

[0010] The computer systems may be understood as a logical apparatus that can read instructions from media and / or a network port, which can optionally be connected to server having fixed media. The system can include a CPU, disk drives, optional input devices such as keyboard and / or mouse and optional monitor. Data communication can be achieved through the indicated communication medium to a server at a local or a remote location. The communication medium can include any means of transmitting and / or receiving data. For example, the communication medium can be a network connection, a wireless connection or an internet connection. Such a connection can provide for communication over the World Wide Web. It is envisioned that data relating to the present disclosure can be transmitted over such networks or connections for reception and / or review by a party.

[0011] A computer system can be used in connection with examples of the present invention. The example computer system can include a processor for processing instructions. Non- limiting examples of processors include: Intel XeonTM processor, AMD OpteronTM processor, Samsung 32-bit RISC ARM 1176]Z(F)-S vl .OTM processor, ARM Cortex-A8 Samsung SSPC100TM processor, ARM Cortex- A8& Apple A4TM processor, Marvell PXA 930TM processor, or a functionally-equivalent processor. Multiple threads of execution can be used for parallel processing. In some examples, multiple processors or processors with multiple cores can also be used, whether in a single computer system, in a cluster, or distributed across systems over a network comprising a plurality of computers, cell phones, and / or personal data assistant devices.

[0012] A high speed cache can be connected to, or incorporated in, the processor toprovide a high speed memory for instructions or data that have been recently, or are frequently, used by processor. The processor is connected to a north bridge by a processor bus. The north bridge is connected to random access memory (RAM) by a memory bus and manages access to the RAM by the processor. The north bridge is also connected to a south bridge by a chipset bus. The south bridge is, in turn, connected to a peripheral bus. The peripheral bus can be, for example, PCI, PCI-X, PCI Express, or other peripheral bus. The north bridge and south bridge are often referred to as a processor chipset and manage data transfer between the processor, RAM, and peripheral components on the peripheral bus. In some alternative architectures, the functionality of the north bridge can be incorporated into the processor instead of using a separate north bridge chip.

[0013] In some examples, a system can include an accelerator card attached to the peripheral bus. The accelerator can include field programmable gate arrays (FPGAs) or other hardware for accelerating certain processing. For example, an accelerator can be used for adaptive data restructuring or to evaluate algebraic expressions used in extended set processing.

[0014] Software and data are stored in external storage and can be loaded into RAM and / or cache for use by the processor. The system includes an operating system for managing system resources; non-limiting examples of operating systems include: Linux, WindowsTM, MACOSTM, BlackBerry OSTM, iOSTM, and other functionally- equivalent operating systems, as well as application software running on top of the operating system for managing data storage and optimization in accordance with example examples of the present invention.

[0015] In some examples, a system also includes network interface cards (NICs) and connected to the peripheral bus for providing network interfaces to externalstorage, such as Network Attached Storage (NAS) and other computer systems that can be used for distributed parallel processing.

[0016] Also disclosed is a network with a plurality of computer systems, and, a plurality of cell phones and personal data assistants, and Network Attached Storage (NAS). In example examples, systems can manage data storage and optimize data access for data stored in Network Attached Storage (NAS) and. A mathematical model can be used for the data and be evaluated using distributed parallel processing across computer systems, and cell phone and personal data assistant systems. Computer systems and cell phone and personal data assistant systems can also provide parallel processing for adaptive data restructuring of the data stored in Network Attached Storage (NAS). This is an example only, and a wide variety of other computer architectures and systems can be used in conjunction with the various examples of the present invention. For example, a blade server can be used to provide parallel processing. Processor blades can be connected through a back plane to provide parallel processing. Storage can also be connected to the back plane or as Network Attached Storage (NAS) through a separate network interface.

[0017] In some example examples, processors can maintain separate memory spaces and transmit data through network interfaces, back plane or other connectors for parallel processing by other processors. In other examples, some or all of the processors can use a shared virtual address memory space.

[0018] Also disclosed is a multiprocessor computer system using a shared virtual address memory space in accordance with an example of the system of the disclosure. The system includes a plurality of processors that can access a shared memory subsystem. The system incorporates a plurality of programmable hardware memory algorithm processors (MAPs) in the memory subsystem. Each MAP cancomprise a memory and one or more field programmable gate arrays (FPGAs). The MAP provides a configurable functional unit and particular algorithms or portions of algorithms can be provided to the FPGAs for processing in close coordination with a respective processor. For example, the MAPs can be used to evaluate algebraic expressions regarding the data model and to perform adaptive data restructuring in example examples. In this example, each MAP is globally accessible by all of the processors for these purposes. In one configuration, each MAP can use Direct Memory Access (DMA) to access an associated memory, allowing it to execute tasks independently of, and asynchronously from, the respective microprocessor. In this configuration, a MAP can feed results directly to another MAP for pipelining and parallel execution of algorithms.

[0019] The above computer architectures and systems are examples only, and a wide variety of other computer, cell phone, and personal data assistant architectures and systems can be used in connection with example examples, including systems using any combination of general processors, co-processors, FPGAs and other programmable logic devices, system on chips (SOCs), application specific integrated circuits (ASICs), and other processing and logic elements. In some examples, all or part of the computer system can be implemented in software or hardware. Any variety of data storage media can be used in connection with example examples, including random access memory, hard drives, flash memory, tape drives, disk arrays, Network Attached Storage (NAS) and other local or distributed data storage devices and systems.

[0020] In example examples, the computer system can be implemented using software modules executing on any of the above or other computer architectures and systems. In other examples, the functions of the system can be implemented partially or completely in firmware, programmable logic devices such as field programmable gate arrays (FPGAs), system on chips (SOCs), application specific integrated circuits (ASICs), or other processing and logic elements. For example, theSet Processor and Optimizer can be implemented with hardware acceleration through the use of a hardware accelerator card.III. Terminology

[0021] The terminology used therein is for the purpose of describing particular examples only and is not intended to be limiting of a device of this disclosure. As used herein, the singular forms an” and "the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. Furthermore, to the extent that the terms "including”, "includes”, "having”, "has”, "with”, or variants thereof are used in either the detailed description and / or the claims, such terms are intended to be inclusive in a manner similar to the term "comprising”.

[0022] Several aspects of a device of this disclosure are described above with reference to example applications for illustration. It should be understood that numerous specific details, relationships, and methods are set forth to provide a full understanding of a device. One having ordinary skill in the relevant art, however, will readily recognize that a device can be practiced without one or more of the specific details or with other methods. This disclosure is not limited by the illustrated ordering of acts or events, as some acts may occur in different orders and / or concurrently with other acts or events. Furthermore, not all illustrated acts or events are required to implement a methodology in accordance with this disclosure.

[0023] Ranges can be expressed herein as from "about” one particular value, and / or to "about” another particular value. When such a range is expressed, another example includes from the one particular value and / or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent "about,” it will be understood that the particular value forms another example. It will be further understood that the endpoints of each of the ranges are significantboth in relation to the other endpoint, and independently of the other endpoint. The term "about” as used herein refers to a range that is 15% plus or minus from a stated numerical value within the context of the particular usage. For example, about 10 would include a range from 8.5 to 11.5.

Claims

WHAT IS CLAIMED IS:

1. An optical imaging system comprising: a first light source configured to illuminate a sample; a second light source configured to illuminate the sample; a first solid-state optical path configured to image the sample, the optical path configured with an objective lens optically coupled to the first light source and a first photodetector; a second solid-state optical path configured to image a sample, the optical path configured with light from a second light source and the objective lens optically coupled to the second light source, wherein the objective lens is a common element in both the first solid-state optical path and the second- state optical path; and a controllable element capable of modulating the illumination of the sample by the second light source.

2. The system of claim 1, wherein the first light source is coherent light.

3. The system of claim 1, wherein the first light source is a laser.

4. The system of claim 1, wherein the first light source is a continuous wave laser.

5. The system of claim 1, wherein the first light source is a pulsed laser.

6. The system of claim 1, wherein the first light source is an amplified laser.

7. The system of claim 1, where in the first light source configured to illuminate the sample produces a fluorescent signal.

8. The system of claim 1, wherein the second light source illuminates the sample through epi-fluorescent illumination.

9. The system of claim 1, wherein the second light source illuminates the sample with non-coherent light.

10. The system of claim 1, wherein the second light source illuminates the sample with bright-field illumination.

11. The system of claim 1, wherein the second light source illuminates the sample through transmission illumination.

12. The system of claim 1, wherein the first solid-state optical path configured to image the sample with an objective lens optically coupled to the first light source and a first photodetector is optically coupled with a beam splitter.

13. The system of claim 12, wherein the beam splitter is configured to produce a ratio of 90:10 ofthe first light source and the second light source.

14. The system of claim 1, wherein the objective lens is perpendicular to the imaging plane ofthe sample.

15. The system of claim 1, wherein the first solid-state optical path comprises at least one dichroic mirror.

16. The system of claim 1, wherein the first solid-state optical path comprises at least one tube lens.

17. The system of claim 1, wherein the second solid-state optical path comprises at least one tube lens.

18. The system of claim 1, wherein the photodetector is a fluorescent camera.

19. The system of claim 1, wherein the photodetector is a CCD image sensor.

20. The system of claim 1, wherein the photodetector is a CMOS sensor.

21. The system of claim 1, wherein the first solid-state optical path comprises at least one of transmitted light, reflected light, and scattered light from the sample.

22. The system of claim 1, wherein the second solid-state optical path comprises at least one of transmitted light, reflected light, and scattered light from the sample.

23. The system of claim 1, wherein the second light source comprises one or more light-emitting diodes.

24. The system of claim 1, wherein the controllable element is a shutter operatively coupled to the optical imaging system.

25. The system of claim 1, wherein the controllable element is a mechanical device capable of modulating the illumination intensity of the second light source.

26. The system of claim 1, wherein the modulating the illumination of the sample by the second light source is determined by the objective lens optically coupled to the first light source.

27. The system of claim 1, wherein the controller element modulating the illumination of the sample by the second light source variably adjusts the light intensity of the second light source.

28. The system of claim 1, wherein the first solid-state optical path and second solid- state optical path comprise an objective focus element.

29. The system of claim 1, wherein the sample is a biological specimen.

30. The system of claim 1, wherein the sample comprises one or more analytes.

31. The system of claim 1, wherein the sample comprises biological tissue.

32. The system of claim 1, wherein the controllable element capable of modulating the illumination intensity of the second light source is performed by physically blocking the second light source.

33. The system of claim 1, wherein the controllable element capable of modulating the illumination intensity of the second light source is performed by exposing the second light source to the second solid-state optical path.

34. The system of claim 1, wherein the sample comprises RNA, DNA or protein.

35. A method of imaging a sample comprising: illuminating a sample with a first light source in an optical system; generating an image from the sample via light through a first solid-state optical path configured with an objective lens optically coupled to the first light source and a first photodetector; illuminating the sample with a second light source in an optical system; generating an image from the sample via light through a second solid-state optical path configured with an objective lens optically coupled to the second light source and a second photodetector, wherein the objective lens is a common element in both the first solid-state optical path and the second-state optical path; activating a controllable element that modulates the illumination of the sample by a second; light source during the illuminating of the sample with the first light source or the second light source.

Images