阅读说明：本技术 用于病理试样的移动数字空间剖析的方法、装置、系统和设备 (Method, apparatus, system and device for mobile digital spatial profiling of pathological specimens ) 是由 J·M·比彻姆 D·杜纳维 J·郑 P·舒尔茨 E·索辛 G·特雷梅尔 于 2019-12-20 设计创作，主要内容包括：本公开的实施例针对一种紧凑、移动的数字空间剖析(DSP)系统以及相关联的装置、设备和方法,该数字空间剖析(DSP)系统被配置为对一个或多个感兴趣区域(ROI)成像,并且然后使用UV光从例如一个或多个ROI中的抗体切割掉寡聚物(“光切割”),并收集光切割的寡聚物用于随后的杂交和计数。(Embodiments of the present disclosure are directed to a compact, mobile Digital Spatial Profiling (DSP) system configured to image one or more regions of interest (ROIs) and then use UV light to cleave off oligomers from, for example, antibodies in the one or more ROIs ("photocleavage") and collect the photocleaved oligomers for subsequent hybridization and counting, and associated devices, apparatuses, and methods.)

1. A Digital Space Profiling (DSP) system, comprising:

a housing or other structure for containing at least one component of a DSP system, comprising:

a power source;

a processor;

a UV source (UVS);

a Visible Light Source (VLS) for bright field imaging;

a photomask device configured to selectively illuminate the tissue sample with UV light from the UV source and/or visible light from the visible light source;

a chamber configured to hold at least a portion of a slide having tissue thereon, wherein the chamber is configured with a liquid environment for the tissue;

and

an optical device configured to at least one of: directing and/or focusing UVS and/or VLS onto at least one of tissue, a chamber, a photomask device, and a camera sensor operably linked to a personal mobile computing device (PMD),

wherein the housing and/or the chamber are configured for removable attachment to the PMD such that the camera sensor can image the tissue.

2. The system of claim 1, further comprising a wireless communication device.

3. The system of claim 1, wherein:

the photomask device comprises an LCD with a backlight, and wherein the VLS comprises an LCD backlight or an external VLS,

the optical apparatus comprises a first set for UVS comprising a condenser lens or a scan lens, a dichroic mirror, and a second set of optics comprising an objective lens,

the dichroic mirror is configured to redirect light from a plurality of sources to one optical axis;

the photomask apparatus includes an LCD configured as a programmable aperture to configure at least one of UV light and visible light to reach tissue only in a region of interest (ROI);

the chamber includes a slot configured to receive a slide;

and/or

The photomask includes at least one of: digital Micromirror Device (DMD), liquid crystal on silicon (LCoS) display, Organic Light Emitting Diode (OLED), and micro light emitting diode(s) ((R))LED) array, fiber optic bundle, Liquid Crystal Display (LCD), scanning laser, and physical barrier.

4. The system of claim 3, wherein:

the photomask device includes an LCD comprising a grid of pixels, and wherein the LCD is disposed at a predetermined distance from the tissue;

the predetermined distance is configured such that the tissue is not obscured by the pixel grid;

the predetermined distance is selected to be between about 0.01 to 5 mm, 0.50 to 2.5 mm, 0.75 to 2.25 mm, or 1 to 2 mm;

and/or

The predetermined distance is configured to provide clear visibility of the tissue, and/or to minimize diffusion of UV light.

5. The system of claim 1, wherein:

the system further comprises:

a pump system configured to provide a flow of solution to a slide,

and/or

A software application configured to operate on the processor and configured to cause the mobile device to display a Graphical User Interface (GUI) configured to receive user input to select at least one region of interest (ROI) of a tissue image obtained via the camera sensor and presented on a display of the PMD,

the photomask apparatus is configured to provide at least one of: illumination resolution between about 50 and 300 nm, about 5-12 cm²A field of view in between, and a magnification of between about 1-5 x;

at least one of the housing, the chamber, and the slot is configured to receive and/or retrieve at least one solution,

the housing comprises or contains a plurality of holders, a PMD frame, at least one objective frame, at least one slide frame, a photomask frame, at least one light gathering frame, and at least one thermal management device,

the housing is configured to removably receive a single objective frame of a plurality of objective frames, each objective frame having a different objective lens and corresponding magnification,

and/or

The system is further configured for at least one of dark field microscopy, bright field microscopy, phase contrast microscopy, fluorescence microscopy, and microscopy with ultraviolet surface excitation.

6. The system of any of claims 1-5, wherein the photomask apparatus is configured to provide at least one of: illumination resolution between about 50 and 300 nm, about 5-12 cm²A field of view in between and a magnification of between about 1-5 x.

7. The system of any of claims 1-6, wherein at least one of the housing, the chamber, and the slot is configured to enable movement of the slide relative thereto.

8. The system of claim 7, wherein the relative movement of the slides is for tissue imaging.

9. The system of any one of claims 1-8, wherein at least one of the housing, the chamber, and the slot is configured to receive and/or retrieve at least one solution.

10. The system of claim 9, wherein the receiving and/or retrieving of the at least one solution is via fluid delivery.

11. The system of claim 10, wherein fluid delivery comprises at least one of pipetting and capillary action, and wherein pipetting may be manual or automated via robotic means.

12. The system of any of claims 1-11, wherein the housing comprises or contains a plurality of racks, a PMD frame, at least one objective frame, at least one slide frame, a photomask frame, at least one light gathering frame, and at least one thermal management device.

13. The system of claim 12, wherein the thermal management device comprises at least one of a heat sink, a heat pump, a fan, a liquid cooling system, and a peltier device.

14. The system of any of claims 1-13, wherein the housing is configured to removably receive a single objective frame of a plurality of objective frames, each objective frame having a different objective lens and corresponding magnification.

15. The system of claim 14, wherein each objective frame is configured so as to provide a different spacing from the camera sensor.

16. The system of claim 15, wherein the at least thermal management device comprises a plurality of heat dissipation clips.

17. The system of any of claims 1-16, further comprising a PMD.

18. The system of claim 17, wherein the PMD includes a PMD processor, a display, a camera sensor for imaging tissue disposed on the slide, and a first wireless communication device for transmitting information to a remote device, either directly or via a network, and optionally a second wireless communication device for communicating with a local device.

19. The system of claim 18, wherein the second wireless communication device comprises at least one of bluetooth, Wi-Fi, or infrared.

20. The system of any of claims 1-19, further comprising a software application operating on the processor and configured to cause the mobile device to display a Graphical User Interface (GUI) configured to receive user input to select a region of interest (ROI) of a tissue image obtained via a camera sensor of the tissue slide and presented on a display of the PMD.

21. The system of any of claims 1-20, wherein the system is further configured for at least one of dark field microscopy, bright field microscopy, phase contrast microscopy, fluorescence microscopy, and microscopy with ultraviolet surface excitation.

22. The system of any of claims 6-21, further comprising a pump system configured to provide a flow of solution to a slide.

23. The system of claim 22, wherein the solution is a buffer.

24. The system of claim 1, further comprising a temperature sensor configured to determine a temperature in at least one of the enclosure and the chamber.

25. The system of any of claims 2-23, further comprising a temperature sensor configured to determine a temperature in at least one of the enclosure and the chamber.

26. The system of claim 25, wherein the processor is configured to:

receiving an input from a temperature sensor corresponding to a sensed temperature, and at least one of:

when the sensed temperature is greater than the predetermined temperature, turning off the UVS; and

providing at least one of a visual and an audible warning when the sensed temperature is greater than a predetermined amount.

27. The system of any of claims 1-26, further comprising:

sealing means for maintaining a liquid environment over tissue, and/or

A manual fluid collection guide disposed proximate to the tissue configured to enable pipetting of a solution from the tissue.

28. The system of claim 27, wherein the manual fluid collection guide comprises a microarray.

29. The system of claim 28, wherein:

the microarray is configured as or has a flow cell, and/or is arranged within or near the chamber; and/or

The manual fluid collection guide includes a mesh barrier.

30. The system of claim 29, wherein the grid barrier is disposed within or adjacent to the sealing device.

31. A digital space profiling system, comprising:

a Portable Mobile Device (PMD) having a processor, a display, a camera sensor for imaging tissue disposed on a slide, and a communication means for transmitting information to a remote device, either directly or via a network;

a software application operating on the processor and configured to cause the mobile device to display a Graphical User Interface (GUI) configured to receive a user input to select a region of interest (ROI) of a tissue image obtained via a camera sensor of a tissue slide and presented on the display;

and

a housing or other structure for containing at least one component of a DSP system, comprising:

a UV source (UVS);

a Visible Light Source (VLS) for bright field imaging;

a photomask device configured to selectively illuminate tissue with UV light from a UV source or visible light from a visible light source;

a slot configured to receive a slide;

a chamber configured to receive at least a portion of a slide having tissue thereon via a slot, wherein the chamber is configured with an aqueous environment for the tissue;

and

an optical device configured to at least one of: directing and/or focusing the UVS and/or VLS onto at least one of a tissue, a chamber, a photomask device, and a camera sensor;

wherein the housing, slot, and/or cavity are configured for removable attachment to the PMD such that the camera sensor can image the tissue.

32. The system of claim 31, wherein the communication device is a wireless communication device.

33. A Digital Space Profiling (DSP) method, comprising:

optionally providing a system according to any one of claims 1-43;

launching a software application on the PMD;

inserting a slide with a tissue sample, the tissue having been previously conjugated with an antibody solution and, prior to insertion, covered in a buffer solution such that it is received by the chamber for imaging and alignment with the photomask;

providing illumination light to the tissue;

imaging the tissue sample with a camera sensor of the PMD and displaying the image via a PMD display;

selecting a plurality of marks of a photomask displayed via the GUI, such selection forming an outline of a rectangle;

selecting the ROI via the GUI;

wirelessly connecting the PMD to a DSP system;

stopping irradiation;

exposing the tissue to UV radiation for a predetermined period of time sufficient to cleave oligomers in the tissue;

and

the solution is collected from the tissue comprising the cleavage oligomer.

34. The method of claim 33, further comprising imaging the photomask prior to inserting the slide to calibrate the photomask and/or to change the size of the rectangle outlined by the selected indicia.

35. The method of claim 34, wherein the changed size corresponds to one of a plurality of specified sizes.

36. A non-transitory computer readable medium having stored thereon instructions for enabling one or more computer processors to perform one or more steps of method embodiments disclosed herein.

Technical Field

Embodiments of the present disclosure relate to mobile digital spatial profiling for biochemical characterization of pathological specimens.

Background

In biological research and clinical pathology, information on the spatial arrangement of biomolecules in tissues is crucial for determining disease state and etiology. However, current methods are either "low complexity" -that is, not quantitative, destructive, or lack spatial information. To meet this demand, Digital Spatial Profiling (DSP) methods have been developed to quantify the relative number of biological species in fixed tissue samples. Such methods target DNA, RNA, and proteins, and are "highly complex" -that is, because of the use of DNA-based fluorescent barcodes, a sufficient (or greater) amount of information is collected to determine the disease state and/or etiology. Each barcode is associated with an oligonucleotide that is bound to a molecular recognition moiety that can be cleaved using UV light and recovered in solution. The barcodes are then used to determine the relative number of molecules in the sample. Although this approach has many advantages, there is room in the market for lightweight alternatives.

Summary of some embodiments

Embodiments of the present disclosure are directed to a reduced size Digital Spatial Profiling (DSP) system, and associated apparatus, devices, and methods. All of the foregoing can be configured to image one or more regions of interest (ROIs) of tissue, cleave oligomers (i.e., "photocleavage") from antibodies in the one or more ROIs using UV light, and collect the photocleaved oligomers, which can then be hybridized and counted (using, for example, Nanostring nCounter technology). In some embodiments, such functionality may also be provided in a mobile form, and furthermore (in some embodiments) in a compact form.

Thus, in some embodiments, such a compact mobile DSP system may include a housing or other structure for containing at least one component of the DSP system, including, for example: a power source, a processor, a UV light Source (UVs), a Visible Light Source (VLS) for bright field imaging such as, for example, an LED array, a fluorescent bulb, an incandescent bulb, an arc lamp, a metal halide lamp, a photomask device configured to selectively illuminate a tissue sample with UV light from the UV source and/or visible light from the visible light source, a chamber configured to hold at least a portion of a slide having tissue thereon, wherein the chamber may be configured with a liquid environment for the tissue, and an optical device (in some embodiments, the optical device may be provided outside the chamber) configured to at least one of: the UVS and/or VLS is directed and/or focused onto at least one of a tissue, a slide, a chamber, a photomask device, and a camera sensor operably linked to a personal mobile computing device (PMD). PMDs may include cell phones, tablet computers, notebook computers, and desktop computers. The operatively linked camera sensor can be internal to or integrated within the PMD, or external to the PMD. At least one of the housing and the chamber is configured for removable attachment to the PMD such that the camera sensor can image tissue.

Such embodiments may additionally include at least one or more (in some embodiments, a plurality of, in further embodiments, all) of the following features, structures, functions, steps and/or descriptions, resulting in yet further embodiments:

the photomask arrangement may comprise an LCD optionally with a backlight

The VLS may comprise an LCD backlight or a separate external visible light source;

the optical device may comprise a first set for UVS, which may comprise at least one, more or all of: a second set of condenser lenses, scan lenses, dichroic mirrors, and optics that may include an objective lens;

the o-dichroic mirror may be configured to redirect light from multiple sources to one optical axis;

the photo mask device may comprise an LCD configured as a programmable aperture to configure at least one of UV light and visible light to reach tissue only in a region of interest (ROI);

the chamber may comprise a slot configured to receive a slide;

the photomask may comprise at least one of: digital Micromirror Device (DMD), liquid crystal on silicon (LCoS) display, Organic Light Emitting Diode (OLED), micro light emitting diode (μ LED) array, fiber bundle, Liquid Crystal Display (LCD), scanning laser, and physical barrier;

the photomask device may comprise an LCD comprising a grid of pixels, and wherein the LCD is arranged at a predetermined distance from the tissue, wherein:

the predetermined distance may be configured such that tissue is not obscured by the pixel grid;

the predetermined distance may be between about 0.01 and 5 mm;

the predetermined distance may be between about 0.50 and 2.5 mm;

the predetermined distance may be between about 0.75 and 2.25 mm; or

The predetermined distance may be between about 1 and 2 mm; and/or

The predetermined distance may be configured to at least provide clear visibility of the tissue, or to minimize diffusion of UV light;

the photomask apparatus may be configured to provide at least one of: illumination resolution between about 50 and 300 nm, about 1-12.5 cm²Or 5-12.5 cm²A field of view in between, and/or a magnification of between about 1-5x or 1-3 x;

at least one of the housing, the chamber and the slot is configured such that the slide is movable relative thereto, wherein:

the relative movement of the slides may be configured for tissue imaging;

at least one of the housing, the chamber and the slot is configured to receive and/or retrieve at least one solution, wherein the receiving and/or retrieving of the at least one solution may be via fluid transport, wherein the fluid transport may comprise at least one of pipetting and capillary action, and the pipetting may be manual or automated via a robotic device;

the housing may contain or comprise at least one, in some embodiments a plurality and in some embodiments all of the following: a plurality of mounts, a PMD frame, at least one objective frame, at least one slide frame, a photomask frame, at least one light gathering frame, and at least one thermal management device;

the thermal management means may comprise at least one of a heat sink, a heat pump, a fan, a liquid cooling system and a Peltier (Peltier) device;

the housing may be configured to removably receive a single objective frame of a plurality of objective frames, wherein each objective frame has a different objective lens and corresponding magnification, wherein:

each objective frame may be configured so as to provide a different pitch from the camera sensor; and/or

At least the thermal management device may include a plurality of heat dissipation clips;

-further may comprise a PMD;

PMD may include at least one, and in some embodiments, a plurality, and in some embodiments, all of the following: a PMD processor, a display, a camera sensor for imaging tissue disposed on a slide, and a first wireless communication device for transmitting information to a remote device, either directly or via a network, and optionally including a second wireless communication device for communicating with a local device; and/or

The second wireless communication device may include at least one of bluetooth, Wi-Fi, or infrared;

a software application, which may be configured to operate on the processor, may be configured to cause the mobile device to display a Graphical User Interface (GUI), which may be configured to receive user input to select a region of interest (ROI) of a tissue image obtained via a camera sensor of the tissue slide and presented on a display of the PMD;

the system may further be configured for at least one of dark field microscopy, bright field microscopy, phase contrast microscopy, fluorescence microscopy and microscopy with uv surface excitation;

-a pump system configured to provide a flow of solution to the slide, wherein the solution may be a buffer and/or a tissue stain;

-a temperature sensor which may be configured to determine a temperature in at least one of the housing and the chamber;

the processor may be configured to:

receiving input from a temperature sensor corresponding to a sensed temperature, and/or

At least one of the following: when the sensed temperature is greater than the predetermined temperature, turning off the UVS; and providing at least one of a visual and audible warning when the sensed temperature is greater than a predetermined amount;

-a sealing device, which may be configured to maintain a liquid environment over the tissue; and

-a manual fluid collection guide which can:

the arrangement is made in the vicinity of the tissue,

is configured to enable pipetting of solution from tissue, and

o comprises a mesh barrier, wherein the mesh barrier may be configured in or near the sealing means, or may be configured as or with a flow cell, and/or the mesh barrier may be arranged in or near the chamber.

In some embodiments, the manual fluid collection guide may include a microarray, wherein the microarray may be configured as or have a flow cell, and/or the microarray may be disposed within or near the chamber.

In some embodiments, a digital spatial profiling system is provided and includes at least one, and in some embodiments, a plurality, and in some embodiments all, of the following: a Personal Mobile Device (PMD) having a processor, a display, a camera sensor for imaging tissue disposed on a slide, and a communication apparatus for communicating information to a remote device, either directly or via a network, a software application operating on the processor and configured to cause the mobile device to display a Graphical User Interface (GUI) configured to receive user input to select a region of interest (ROI) of a tissue image obtained via the camera sensor of the tissue slide and presented on the display, and a housing or other structure for containing at least one component of the DSP system, which may include at least one, and in some embodiments, a plurality, and in some embodiments, all of the following: a UV Source (UVs), a Visible Light Source (VLS) for bright field imaging, a photomask device configured to selectively illuminate tissue with UV light from the UV source or visible light from the visible light source, a slot configured to receive a slide, and a chamber having at least a portion of tissue thereon configured to receive the slide via the slot. The chamber may be configured with an aqueous environment for the tissue. The system may further include an optical device configured to at least one of: the UVS and/or VLS is directed and/or focused onto at least one of a tissue, a chamber, a photomask device, and a camera sensor. The housing, slot, and/or cavity may be configured to be removably attached to the PMD such that the camera sensor may image the tissue, and the communication device may be a wireless communication device.

In some embodiments, a Digital Spatial Profiling (DSP) method is provided and includes at least one, and in some embodiments, a plurality, and in some embodiments, all of the following: optionally, a system, apparatus and/or device according to one of such disclosed systems, apparatuses and devices is provided, initiating a software application on a Personal Mobile Device (PMD), inserting a slide with a tissue sample, the tissue having been previously conjugated with an antibody solution and, prior to insertion, overlaid in a buffer solution such that it is received by a chamber for imaging and alignment with a photomask, providing illumination light to the tissue, imaging the tissue sample with a camera sensor of the PMD and displaying the image via a PMD display, selecting a plurality of indicia of the photomask displayed via the GUI, such selection forming an outline of a rectangular ROI, selecting the PMD via the GUI, wirelessly connecting the DSP system to the DSP system, stopping the illumination light, exposing the tissue to UV illumination for a predetermined period of time sufficient to cut oligomers in the tissue, and collecting the solution from the tissue containing the cut oligomers.

Such embodiments may additionally include at least one or more (in some embodiments, a plurality of, in further embodiments, all) of the following features, structures, functions, steps and/or descriptions, resulting in yet further embodiments:

-imaging the photomask before inserting the slide in order to calibrate the photomask, an

-changing the size of the rectangle outlined by the selected marker, wherein the changed size may correspond to one of a plurality of specified sizes.

In some embodiments, a non-transitory computer-readable medium is provided having stored thereon instructions for enabling one or more computer processors to perform one or more steps of any method embodiment presented by the present disclosure.

In some embodiments, the first wireless communication means for transmitting information to a remote device, either directly or via a network, allows remote selection of an ROI and/or delivery of healthcare services such as health assessment or consultation through the telecommunications infrastructure.

These and other embodiments of the present disclosure will become more apparent with reference to the drawings, a brief description of which is provided below, along with additional details of at least some embodiments of the present disclosure.