Measurement system with multiple detection modes, detection method and mode switching method thereof

Abstract

The invention discloses an assay system with multiple detection modes and a related method. The measurement system with multiple detection modes comprises a sample stage; the optical module is used for scanning a sample to be detected and at least has a sequencing mode and a fluorescent staining mode; a driving circuit selectively coupled to mode parameters corresponding to an operation mode of the optical module, the mode parameters including at least a first mode control parameter corresponding to the sequencing mode and a second mode control parameter corresponding to the fluorescent staining mode; the mode switching circuit is coupled to the driving circuit so as to control the driving circuit based on the sample to be detected; and the mode switching circuit associates different mode parameters to the driving circuit based on the type of the sample to be detected. According to the invention, multi-mode switching of the detection system is realized, and multiple detection functions are realized on the same platform.

Description

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] This application is based on the Chinese patent application with application number 2024104784632 and application date of April 19, 2024, and claims the priority of the Chinese patent application. The entire content of the Chinese patent application is hereby introduced into this application as a reference. Technical Field

[0003] The present disclosure relates to the field of bioanalysis technology, and in particular to a measurement system with multiple detection modes, a detection method, and a mode switching method thereof. Background Art

[0004] Microscopy is a key technology in the life sciences, and all relevant detection technologies in this field use microscopes as a key means of observing biomacromolecules. However, current microscopy equipment is limited in functionality and cannot perform complex, multifunctional detection tasks such as sequencing and multiplex staining and imaging on the same platform. This consumes significant manpower and material resources, and increases equipment costs. Therefore, a device that can achieve multifunctional detection at a lower cost is urgently needed. Summary of the Invention

[0005] The present disclosure addresses the drawbacks of the prior art and the above-mentioned problems, and provides a measurement system integrating multiple detection modes.

[0006] A first aspect of the present disclosure provides a measurement system integrating multiple detection modes, the system comprising:

[0007] A carrier, the carrier being used to carry a sample to be tested;

[0008] An optical system, wherein the optical system is at least selected from a combination of a light source, a lens group, and an objective lens;

[0009] a detection system for detecting optical signals;

[0010] a fluid system for providing a plurality of reagents for a detection reaction;

[0011] A control system is used to control the switching of multiple detection modes, and / or to control the optical system, fluid system and detection system according to a predetermined program in one detection mode to complete the detection of the sample to be detected.

[0012] In one embodiment, the measurement system further comprises an analysis system, which is used to receive information from the detection system, analyze the detection information, and output a detection result.

[0013] In one embodiment, the detection system is selected from a camera, a photodiode, an optical sensor, and the like.

[0014] In one embodiment, the multiple detection modes are selected from nucleic acid sequencing mode, tissue sample staining mode, DNA or RNA in situ detection mode, cell or microbial analysis mode, etc.

[0015] Another aspect of the present disclosure provides an assay system integrating multiple detection modes, wherein the assay system comprises:

[0016] One or more carriers, each carrier being used to carry the same or different samples to be tested;

[0017] One or more optical systems, wherein the optical systems are at least selected from a combination of a light source and a lens group;

[0018] one or more detection systems for detecting optical signals;

[0019] One or more fluid systems for providing a plurality of reagents for a detection reaction;

[0020] One or more control systems, wherein the control system is used to control the switching of multiple detection modes or to detect multiple samples to be detected in parallel using multiple detection modes.

[0021] In one embodiment, the control system further comprises:

[0022] a driving circuit coupled to the detection system to collect signal data generated by the sample to be detected, the driving circuit being selectively coupled to mode parameters corresponding to an operating mode of the detection system, the mode parameters including at least a first mode control parameter corresponding to the sequencing mode and a second mode control parameter corresponding to the tissue sample dyeing mode; and

[0023] Optionally, a mode switching circuit is coupled to the driving circuit to control the driving circuit based on the sample to be detected: when the sample carrier is a sequencing chip, the mode switching circuit associates a first set of mode parameters to the driving circuit, and when the sample carrier is a tissue sample carrier, the mode switching circuit associates a second set of mode control parameters to the driving circuit.

[0024] In one embodiment, the control system further comprises:

[0025] a plurality of independent driving circuits, each of which is coupled to the detection system to collect signal data generated by the sample to be detected, the plurality of driving circuits being independently selectable to be coupled to mode parameters corresponding to the operating mode of the detection system, the mode parameters including at least a first mode control parameter corresponding to the sequencing mode, a second mode control parameter corresponding to the tissue sample staining mode, a third mode control parameter corresponding to the DNA or RNA in situ detection mode, and a fourth mode control parameter corresponding to the cell or microorganism analysis mode; and

[0026] Optionally, multiple mode switching circuits are coupled to the driving circuit to control the driving circuit based on the sample to be detected: when the sample carrier is a sequencing chip, the mode switching circuit associates a first set of mode parameters to the driving circuit, and when the sample carrier is a tissue sample carrier, the mode switching circuit associates a second set of mode control parameters to the driving circuit.

[0027] In one embodiment, the optical system further comprises a bright field light source and an excitation light source.

[0028] In one embodiment, the sample to be detected includes a nucleic acid sequencing library, a biological tissue sample, a biological fluid sample, a microbial sample or a cell sample fixed on the sample slide.

[0029] In one embodiment, the optical system includes an objective lens; in the sequencing mode, the optical system scans the nucleic acid sequencing library through the objective lens and generates sequence information corresponding to the nucleic acid sequencing library; in the tissue sample staining mode, the optical system scans the biological tissue sample through the objective lens and generates an image corresponding to the biological tissue sample.

[0030] In one embodiment, the optical system includes an objective lens; in the DNA or RNA in situ detection mode, the optical system scans the biological sample through the objective lens and generates a DNA or RNA in situ image corresponding to the biological sample; in the cell or microorganism analysis mode, the optical system scans the cell or microorganism sample through the objective lens and generates image information corresponding to the cell or microorganism sample.

[0031] Another aspect of the present disclosure discloses a method for measuring multiple detection modes, characterized in that the method comprises the following steps:

[0032] Fix the sample to be tested on the stage;

[0033] The detection mode is selected by the control system, including:

[0034] Selecting a first detection mode, activating a first fluid system corresponding to the first detection mode, and controlling the sample to be detected to undergo a first detection reaction to generate a detectable first optical signal; and / or selecting a second detection mode, activating a second fluid system identical to the second detection mode, and controlling the sample to be detected to undergo a second detection reaction to generate a detectable second optical signal;

[0035] detecting the first optical signal and / or the second optical signal and transmitting the signals to an analysis system; and

[0036] The first optical signal and / or the second optical signal are analyzed to generate detection information and output a detection result.

[0037] In one embodiment, the first detection mode and the second detection mode are the same detection mode, or the first detection mode and the second detection mode are different detection modes.

[0038] In one embodiment, when the first detection mode and the second detection mode are different detection modes, the first detection reaction and the second detection reaction are different detection reactions.

[0039] In one embodiment, the multiple detection modes are selected from nucleic acid sequence determination mode, tissue sample staining mode, DNA or RNA in situ detection mode, cell or microbial analysis mode, etc.

[0040] In one embodiment, the multiple detection modes can be performed in parallel.

[0041] In one embodiment, the detection reaction corresponding to the sequencing mode is a sequencing reaction, wherein the sequencing reaction is selected from a synthesis sequencing reaction, a ligation sequencing reaction, a single molecule sequencing reaction, etc.;

[0042] In one embodiment, the detection reaction corresponding to the tissue sample staining mode is selected from affinity reactions, wherein the affinity reactions are selected from antigen-antibody, protein-aptamer, biotin-streptavidin, nucleotide-coupled antibody-fluorescent probe, etc.;

[0043] In one embodiment, the detection reaction corresponding to the DNA or RNA in situ detection mode is selected from a probe capture reaction, wherein the probe capture reaction is selected from probe-coupled fluorescence, probe ligation, probe amplification, etc.;

[0044] In one embodiment, the detection reaction corresponding to the cell or microorganism analysis mode is selected from surface antigen detection, biological marker detection, positive cell detection analysis, cell transcriptome or epigenetic analysis, etc.

[0045] In one embodiment, the control system includes at least one processor and an interaction unit, wherein the processor and the interaction unit are coupled to the carrier and the fluid system.

[0046] Input a first instruction, the first instruction including: initial information, the initial information including at least one of the type of sample to be tested, sequencing scheme, staining scheme, kit number, and confirmation information;

[0047] controlling the fluid system to perform a first detection reaction according to the initial information;

[0048] generating a first detection result based on the detection reaction;

[0049] Control the interaction unit to feed back the first detection result.

[0050] In one embodiment, fixing the sample to be detected on the carrier includes: mounting a plurality of slides on a plurality of carriers includes:

[0051] Mounting a first slide on the first stage;

[0052] Mounting a second slide on the second stage;

[0053] Optionally, the first carrier plate and the second carrier plate are fixed with different sample types, or the first carrier plate and the second carrier plate are fixed with the same sample type.

[0054] In one embodiment, an optical system and a detection system are used to collect optical signals, wherein the optical system includes a first optical link and a second optical link, and the determination method includes:

[0055] The relative position between the optical system and the stage is adjusted to align either the first carrier or the second carrier with either the first optical link or the second optical link.

[0056] Another aspect of the present disclosure discloses a mode switching method for a system for measuring multiple detection modes, wherein the mode switching method comprises:

[0057] Identify the type of sample to be tested;

[0058] determining, based on the type of the sample to be detected, mode parameters selected to be coupled to the driving circuit;

[0059] When the sample to be detected is a nucleic acid sequencing library, the mode switching circuit associates the first set of mode parameters with the driving circuit, and the driving circuit drives the optical module to enter the sequencing mode; when the sample to be detected is a biological tissue sample, a microbial sample or a cell sample, the mode switching circuit associates the second set of mode control parameters with the driving circuit, and the driving circuit drives the optical module to enter the fluorescence dyeing mode or a third mode different from the fluorescence dyeing mode and the measurement mode.

[0060] In one embodiment, it is characterized in that the third mode is a bright field imaging mode. In one embodiment, the optical system includes an excitation light source and a bright field light source;

[0061] In one embodiment, in the sequencing mode or the fluorescent staining mode, the excitation light source excites the sample to be detected to generate a fluorescent signal;

[0062] In the bright field imaging mode, the bright field light source illuminates the sample to be detected to generate a bright field signal.

[0063] In one embodiment, the assay system with multiple detection modes includes a control module, which is programmable and configured to control the fluid path module to introduce or discharge reagents into or out of the sample chamber, and control the imaging module to image the sample to be detected.

[0064] In some embodiments, the system further includes an identification circuit coupled to the mode switching circuit having an interface for identifying the sample slide type and / or the operating mode.

[0065] In some embodiments, the interface includes a user input port for receiving input of slide type information and / or the operating mode.

[0066] In some embodiments, the sample slide has an identifiable type identification; and the interface includes a scanning mechanism for identifying the type of the sample slide based on the type identification.

[0067] In some embodiments, the sample to be detected includes a nucleic acid sequencing library, a biological tissue sample, a biological fluid sample, an environmental sample, a microbial sample, or a cell sample fixed on the sample slide.

[0068] In some embodiments, the optical module includes an objective lens; in the sequencing mode, the optical module scans the nucleic acid sequencing library through the objective lens and generates sequence information corresponding to the nucleic acid sequencing library; in the fluorescence staining mode, the optical module scans the biological tissue sample through the objective lens and outputs an image corresponding to the biological tissue sample, microbial sample or cell sample.

[0069] In some embodiments, the optical module includes an image sensor and an image processing unit operably connected to the image sensor, and the image processing unit is called by the second mode control parameter to receive multiple images corresponding to multiple FOVs generated by the image sensor and integrate and stitch the multiple images.

[0070] In some embodiments, the optical module includes a first optical link and a second optical link that are independent of each other, the first optical link includes a first objective lens, the second optical link includes a second objective lens, and when the first optical link is in the sequencing mode, the second optical link is in the same or different mode as the first optical link.

[0071] In some embodiments, the optical module also has a third operating mode different from the sequencing mode and the fluorescent staining mode, and the optical module also includes a third optical link. The first optical link, the second optical link, and the third optical link are in any one of the sequencing mode, the fluorescent staining mode, and the third operating mode at the same time.

[0072] In some embodiments, the sample stage includes at least two detection positions for receiving a plurality of the sample slides.

[0073] In some embodiments, the assay system for multiple detection modes includes a fluidic system arranged in a one-to-one correspondence with the detection sites.

[0074] In another aspect, the present disclosure further provides a detection method of a measurement system with multiple detection modes, comprising:

[0075] Mount the slide on the sample stage;

[0076] The mode switching circuit determines a mode parameter that is selectively coupled to the driving circuit, wherein the mode parameter corresponds to an operation mode of the optical module and includes at least a first mode control parameter corresponding to the sequencing mode and a second mode control parameter corresponding to the fluorescence staining mode;

[0077] The driving circuit applies the mode parameters determined by the mode switching circuit to the optical module to enable the optical module to switch between at least the sequencing mode and the fluorescence staining mode.

[0078] In some embodiments, before or after installing the first slide to the first detection position of the sample stage, the detection method further includes: loading a first sample to be detected onto the first slide, wherein the first sample to be detected includes a nucleic acid sequencing library, a biological tissue sample, a microbial sample, or a cell sample.

[0079] In some embodiments, before or after installing the second slide to the second detection position of the sample stage, the detection method further includes: loading a second sample to be detected onto the second slide, wherein the second sample to be detected includes a nucleic acid sequencing library, a biological tissue sample, a microbial sample or a cell sample.

[0080] In some embodiments, the first sample to be tested is different from the second sample to be tested.

[0081] In some embodiments, the third operating mode is a bright field imaging mode.

[0082] The technical solution disclosed in the present invention realizes multiple automated detection functions, has simple operation steps, more effectively utilizes resources, and saves equipment costs. BRIEF DESCRIPTION OF THE DRAWINGS

[0083] The above and / or additional aspects and advantages of the present disclosure will become apparent and readily understood from the description of the embodiments in conjunction with the following drawings, in which:

[0084] Non-limiting and non-exhaustive embodiments of the present disclosure are described, by way of example, with reference to the following drawings, in which:

[0085] Figure 1 is a simplified schematic diagram of a measurement system for multiple detection modes provided by an embodiment of the present disclosure;

[0086] Figure 2 is a schematic diagram of an optical module and a sample stage of a measurement system with multiple detection modes according to an embodiment of the present disclosure;

[0087] Figure 3 is a schematic diagram of an optical module and a controller of a measurement system with multiple detection modes according to an embodiment of the present disclosure;

[0088] Figure 4 is a partial schematic diagram of an optical module of a measurement system with multiple detection modes provided by an embodiment of the present disclosure;

[0089] Figure 5A is another schematic diagram of a measurement system with multiple detection modes provided by an embodiment of the present disclosure;

[0090] Figure 5B A schematic diagram of the optical path of a measurement system with multiple detection modes provided by an embodiment of the present disclosure in a fluorescence staining mode;

[0091] Figure 5C A schematic diagram of a detection system with multiple detection modes in a sequencing mode provided by an embodiment of the present disclosure;

[0092] Figure 6 1 is a flow chart of a detection method of a measurement system with multiple detection modes provided by an embodiment of the present disclosure;

[0093] Figure 7 1 is a flow chart of a method for switching modes of a measurement system with multiple detection modes provided by an embodiment of the present disclosure.

[0094] Figure 8 A schematic diagram of the specific structure of a multifunctional biochemical detection system according to an exemplary embodiment of the present disclosure is shown.

[0095] Figures 9A-9B shows a schematic diagram of a sample slide according to an exemplary embodiment of the present disclosure, Figure 9A Represents the sample slide assembly diagram, Figure 9B Shows an exploded view of the sample slide assembly.

[0096] Figures 10A-10D A schematic diagram showing the process of adhering tissue sections to sample slides is shown. Figure 10A The process of adhering tissue sections to slides is shown; Figure 10B The diagram shows the state after the tissue section has been adhered to the slide; Figure 10C The double-sided tape is shown attached to the slide; Figure 10D The assembly of the specimen slide is shown with the cover slip placed on the frame.

[0097] Figure 11 A schematic diagram of the sample carrier adapter fixing fixture is shown. The chip is placed in the chip fixing position of the base, and downward pressure is applied to the pressing block to press the chip.

[0098] Figure 12 A schematic diagram of a liquid circuit module of a measurement system with multiple detection modes according to an exemplary embodiment of the present disclosure is shown, wherein: 1. Reagent chamber; 2. Sample slide; 3. Selection valve; 4. Injection pump; 5. Waste liquid barrel.

[0099] Figure 13 This is an exemplary embodiment of the present disclosure in which a measurement system with multiple detection modes according to an embodiment of the present disclosure photographs a mouse brain slice tissue in a fluorescent staining mode.

[0100] Figure 14 The figure is a schematic diagram of the structure of a computer terminal that implements software selectability in an exemplary embodiment of the present disclosure.

[0101] Figure 15 This is a diagram of the in situ mRNA detection results obtained using RNA in situ hybridization sequencing technology in one embodiment of the present disclosure.

[0102] Figure 16 This is a flowchart of a multi-mode detection result analysis module in one embodiment of the present disclosure.

[0103] Figure 17This is the result of detecting single-cell transcriptome in one embodiment of the present disclosure. DETAILED DESCRIPTION

[0104] The embodiments of the present disclosure are described in detail below. The embodiments described below are exemplary and are only used to explain the present disclosure, and should not be understood as limiting the present disclosure.

[0105] It should be noted that the terms "first" and "second" are used for descriptive purposes only and should not be understood to indicate or imply relative importance or implicitly specify the number of the technical features indicated. Therefore, features defined as "first" or "second" may explicitly or implicitly include one or more of the features. Furthermore, in the description of this disclosure, unless otherwise specified, "plurality" means two or more.

[0106] The endpoints of the ranges and any values ​​disclosed herein are not limited to the precise ranges or values, and these ranges or values ​​should be understood to include values ​​close to these ranges or values. For numerical ranges, the endpoints of each range, the endpoints of each range and individual point values, and the individual point values ​​can be combined with each other to obtain one or more new numerical ranges, which should be considered to be specifically disclosed herein.

[0107] In this document, the terms “include” or “comprising” are open expressions, that is, including the contents specified in the present disclosure, but not excluding other contents.

[0108] In this document, the terms "longitudinal", "transverse", "up", "down", "vertical", "horizontal", "top", "bottom", "inside", "outside", etc., indicating orientations or positional relationships, are based on the orientations or positional relationships shown in the accompanying drawings, and are only for the convenience of describing the present disclosure and simplifying the description, and do not indicate or imply that the device or element referred to must have a specific orientation, be constructed and operate in a specific orientation, and therefore cannot be understood as a limitation on the present disclosure.

[0109] In this document, unless otherwise specified or limited, terms such as "connected," "connect," and "fixed" should be understood in a broad sense. For example, they can refer to fixed connections, detachable connections, or integration; mechanical connections or electrical connections; direct connections or indirect connections through an intermediate medium; and internal communication between two elements or interaction between two elements, unless otherwise specified. Those skilled in the art will understand the specific meanings of the above terms in this disclosure based on specific circumstances.

[0110] In the present disclosure, unless otherwise expressly specified or limited, when a first feature is "above" or "below" a second feature, it may mean that the first and second features are in direct contact, or the first and second features are in indirect contact through an intermediate medium. Furthermore, when a first feature is "above," "above," or "above" a second feature, it may mean that the first feature is directly above or diagonally above the second feature, or simply means that the first feature is at a higher level than the second feature. When a first feature is "below," "below," or "below" a second feature, it may mean that the first feature is directly below or diagonally below the second feature, or simply means that the first feature is at a lower level than the second feature.

[0111] In this document, unless otherwise specified or limited, terms such as "system," "module," and "device" should be interpreted broadly and have essentially the same meaning and can be used interchangeably. For example, a fluidic system is equivalent to a fluidic module, an optical module is equivalent to an optical device, a carrier is equivalent to a sample stage, and a slide is equivalent to a chip, etc., all of which are similar concepts known to those skilled in the art.

[0112] Omics analysis refers to the application of a range of high-throughput, large-scale, and multidimensional technologies to study the collection of diverse molecules within an organism and their interactions. The term "omics" derives from concepts in biology such as the genome, proteome, transcriptome, and metabolome. Each "omics" represents the complete set of molecules of a specific type within an organism.

[0113] Genome generally refers to genomic information from a subject, which can be, for example, at least a portion or all of the subject's genetic information. A genome can be encoded in DNA or RNA. A genome can include coding regions that encode proteins as well as non-coding regions. A genome can include the sequences of all chromosomes in an organism. For example, the human genome has a total of 46 chromosomes. All of these sequences together may constitute the human genome.

[0114] Cytomics refers to the comprehensive study of all components within a cell, including its structure, function, behavior, and interactions. Cytomics encompasses all levels, from individual cells to cell populations, aiming to reveal the complexity and diversity of cells.

[0115] Transcriptome: The study of the collection of RNA molecules, particularly mRNA, that represent the expression of genes at a specific time and under specific conditions. Transcriptome analysis helps understand how genes are regulated and their roles in biological processes.

[0116] The proteome refers to the comprehensive study of the expression, function, interaction, and dynamic changes of all proteins in an organism, cell, or tissue. The goal of proteomics is to establish a complete protein catalog, including protein identification, quantification, modification, and functional analysis.

[0117] Metabolome studies the collection of all small molecule metabolites in an organism. Metabolome analysis can reveal changes in metabolic pathways and the roles of metabolites in biological processes.

[0118] Epigenome studies the epigenetic regulatory mechanisms of gene expression, such as DNA methylation and histone modification. These regulatory mechanisms do not change the DNA sequence itself but can affect gene activity.

[0119] Sample, also known as sample, refers to biological samples of different sources. A biological sample can be a nucleic acid sample, a cell sample, a microbial sample, or a protein sample. A biological sample can be derived from another sample. A sample can be a tissue sample, such as a biopsy, a core biopsy, a needle aspiration, or a fine needle aspiration. A sample can be a fluid sample, such as a blood sample, a urine sample, or a saliva sample. A sample can be a skin sample. A sample can be a cheek swab. A sample can be a plasma or serum sample. A sample can be cell-free or acellular. A cell-free sample can include extracellular polynucleotides. Extracellular polynucleotides can be isolated from body samples, and body samples can be selected from blood, plasma, serum, urine, saliva, mucosal excretions, sputum, feces, and tears. It can also be a microbial sample such as a virus or bacteria. Different sources mean that biological samples can come from human, animal, plant, microbial community, environmental samples, and even space samples.

[0120] Slides are a common experimental tool in biological and omics research, used to fix biological samples (such as cells, tissue slices, or other biological materials) on a flat surface for observation, analysis, and various biological experiments. Slides can be made of different materials, such as glass, silicon, resin, polymer, metal, metal oxide, etc. They can also be differentiated according to their use. For example, they can include sequencing chips, closed or open sequencing chips, semiconductor chips, nanopore chips, microscope slides, tissue microarrays (TMAs), cell arrays, protein arrays, biochips, microarrays, flow cytometry slides, tissue slices, etc.

[0121] Sequencing is a new type of genetic testing technology that can analyze and determine the full sequence of gene bases from blood or saliva, thereby predicting the possibility of suffering from various diseases, individual behavioral characteristics and behavioral rationality. Sequencing generally refers to methods and techniques for determining the nucleotide base sequence in one or more polynucleotides. Polynucleotides can be, for example, deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), including variants or derivatives thereof (e.g., single-stranded DNA). Sequencing can be performed by various currently available systems, such as, but not limited to, sequencing systems from MGI, Sequencing, Illumina, Pacific Biosciences, Oxford Nanopore or Life Technologies (Ion Torrent). Alternatively, nucleic acid amplification, polymerase chain reaction (PCR) (e.g., digital PCR, quantitative PCR or real-time PCR) or isothermal amplification can be used for sequencing. Such devices can provide multiple raw genetic data corresponding to the genetic information of a subject (e.g., human), as generated by the device from a sample provided by the subject.

[0122] Sequencers, generally referring to those used to determine the sequence of the genetic material of a sample, can function in a variety of ways and based on a variety of technologies, including sequencing by primer extension using labeled or unlabeled nucleotides, such as sequencing-by-ligation or pyrosequencing, for example, using any of the Sanger dideoxy sequencing methods, nanopore sequencing, or "NexGen" sequencing methods known in the art (e.g., using the sequencing platform of MGI, the ROCHE 454 sequencing platform, the ILLUMINA™ SOLEXA™ sequencing platform, the SOLID™ sequencing platform of LIFE TECHNOLOGIES / APPLIED BIOSYSTEMS, the SMRT™ sequencing platform of PACIFIC BIOSCIENCES, the POLLONATOR Polony sequencing platform, the COMPLETEGENOMICS sequencing platform, the INTELLIGENT BIOSYSTEMS sequencing platform, the HELICOS sequencing platform, or any other sequencer and system known in the art).

[0123] Multiple staining imaging can be multiple immunofluorescence staining (mIF) technology. Through multiple rounds of staining cycles, mIF can achieve in situ multi-target staining of tissues or cells, thereby comprehensively studying cell composition, cell function and cell-to-cell interactions. This method not only improves the sensitivity of detection, but also allows for analysis of the spatial distribution of multiple biomarkers in the sample. It can also be multiple fluorescent protein immunoblotting (multiple fluorescent Western Blot), which uses different fluorescent markers to detect multiple target proteins in a protein sample. This method reduces background fluorescence and avoids signal leakage by optimizing the sample load and selecting appropriate fluorescent markers, thereby achieving simultaneous detection of multiple proteins. It can also be other methods such as multiple ion beam imaging technology (MIBI), which can quantify proteins in single cells or even subcellular structures.

[0124] Iterative indirect immunofluorescence imaging (4i) is an imaging technique developed by Professor Lucas Pelkmans at the University of Zurich that can use fluorescence microscopy to visualize dozens of proteins in thin tissue sections at high resolution.

[0125] A workstation is a high-performance computer system designed to meet the needs of professional users or specific industries. It typically features powerful processing capabilities, high-quality graphics, and extensive scalability, enabling it to handle complex computing tasks, data analysis, graphics rendering, and engineering design.

[0126] A sample analyzer is a device used to analyze and evaluate biological, chemical, or physical samples. It can be at least one of an optical microscope, electron microscope, fluorescence microscope, UV-Vis spectrophotometer, infrared spectrometer, nuclear magnetic resonance spectrometer, liquid chromatograph (HPLC), gas chromatograph (GC), mass spectrometer (MS), flow cytometer, gene sequencer, mass spectrometer, biochemical analyzer, cell counter, thermal cycler, electrophoresis equipment, biosafety cabinet, and freeze dryer.

[0127] In order to make the above and other features and advantages of the present disclosure more clear, the present disclosure is further described below in conjunction with the accompanying drawings. The accompanying drawings constitute a part of this disclosure and are used together with the embodiments of the present disclosure to illustrate the present disclosure. For the purpose of clarity and simplicity, detailed descriptions of known functions and structures of the devices described herein will be omitted when they may obscure the subject matter of the present disclosure. It should be understood that the specific embodiments given herein are for the purpose of explaining to those skilled in the art and are merely illustrative and non-restrictive.

[0128] The embodiments disclosed in the present disclosure provide a measurement system for multiple detection modes including an optical scanning device and related methods. The measurement system for multiple detection modes is particularly used for biochemical sample detection, and includes a sample stage for holding a sample slide and an optical module for scanning the sample to be detected. The optical module has a variable operating mode, and its operating mode is related to the type of sample to be detected. Different operating modes of the optical module involve calling different mode control parameters. It should be understood that in some specific applications, the optical module and the sample stage can be arranged to move relative to each other, and the operations of the optical module, such as the liquid circuit part that supplies fluid to the slide, the motion control module that controls the relative movement between the optical module and the sample stage, etc., which cooperate with the optical module, may also be adaptively adjusted in different operating modes of the optical module, such as the timing adjustment of the liquid supply and discharge speed of the liquid circuit part, the change of the driving parameters of the motion control part, etc.

[0129] In some embodiments, the parameter groups corresponding to the different operating modes of the optical module can be predetermined and stored in the memory, for example, the optical module has any combination of a first operating mode (e.g., sequencing mode), a second operating mode (e.g., fluorescence staining mode), and a third operating mode (e.g., bright field imaging mode). Accordingly, the first mode control parameters corresponding to the sequencing mode, the second mode control parameters corresponding to the fluorescence staining mode, and the third mode control parameters corresponding to the bright field imaging mode are pre-stored in the memory for selective call during actual operation. The first mode control parameters include laser power parameters, real-time focus parameters, slide motion control parameters, fluid timing parameters, etc., wherein the real-time focus parameters include, for example, the real-time focus module SNR parameters of the sequencing chip supported by the adaptive algorithm. The second mode control parameters include laser power parameters (e.g., 150mW and 300mW laser power), focus parameters (e.g., chip real-time focus SNR parameters based on tissue autofluorescence), and fluid timing parameters corresponding to the second mode (e.g., corresponding to immunofluorescence staining fluid timing), as well as splicing parameters, etc., which are different from the first mode control parameters. The third mode control parameters include, for example, laser power parameters for 100mW and 200mW lasers, adaptive focus parameters for image scoring based on cell / microorganism fluorescence intensity, and image sensor parameters corresponding to cell / microorganism fluorescence. These control parameters are selectively invoked based on the type of sample being tested on the sample slide. Therefore, the system can dynamically invoke different mode control parameters based on changes in the sample being tested, switching the operating mode of the optical module in real time, and enabling multiple biochemical tests on biological samples without the need for additional equipment.

[0130] like Figure 1-2 As shown, in a measurement system with multiple detection modes according to an embodiment of the present disclosure, the sample slide 120 is used to carry the sample to be detected, and the sample slide 120 can be positioned on the sample stage 110, which is located below the objective lens of the optical module 110. For example, the sample slide can be fixed by vacuum adsorption or the like. The optical module 100 and the sample stage 110 are relatively movably arranged. The optical module 100 has at least a sequencing mode and a fluorescent staining mode. It should be understood that the optical module 100 can also have a third operating mode different from the sequencing mode and the fluorescent staining mode, such as a bright field imaging mode. The operating mode of the optical module 100 is related to the type of sample to be detected. The sample to be detected includes but is not limited to a nucleic acid sequencing library, a biological tissue sample, a microbial sample or a cell sample, etc.

[0131] In the sequencing mode, the optical module 100 scans the nucleic acid sequencing library via the objective lens and generates sequence information corresponding to the nucleic acid sequencing library. In the fluorescence staining mode, the optical module 100 scans the biological tissue sample via the objective lens and outputs an image corresponding to the biological tissue sample, microbial sample, or cell sample. In the brightfield imaging mode, the optical module 100 captures and outputs a brightfield image of the sample to be tested. The optical module 100 includes an image sensor and an image processing unit operably connected to the image sensor. In the fluorescence staining mode, the image processing unit receives multiple images corresponding to multiple FOVs generated by the image sensor and integrates and stitches the multiple images.

[0132] like Figure 5A The optical module 100 shown may include a first optical link 100a and a second optical link 100b that are independent of each other, and the sample stage 110 correspondingly includes at least two detection positions for receiving a plurality of the sample slides. The first optical link 100a includes a first objective lens, and the second optical link 100b includes a second objective lens. When the first optical link is in the sequencing mode, the second optical link is in the same or different mode as the first optical link. The operating mode control of the two optical links can be independent of each other. It should be understood that the optical module 100 may also include a third optical link, and the first optical link, the second optical link, and the third optical link are in any one of the sequencing mode, the fluorescent staining mode, and the third operating mode at the same time.

[0133] Specifically, the optical module's light source module includes multiple light source elements, such as an excitation light source L1 and a brightfield light source L2. These light sources are selectively connected to, for example, a multiplexer MUX. The multiplexer MUX is controlled by a controller 200 and selectively outputs light signals matching the operating mode of the optical module 100 to the sample to be tested. Illuminated by the light signal, the sample to be tested generates a corresponding detectable light signal. For example, in sequencing mode or fluorescence staining mode, the sample is excited by laser light to generate a fluorescence signal; in brightfield imaging mode, the sample receives brightfield light to generate a brightfield signal. This detectable light signal is transmitted through an objective lens and captured by an associated optical sensor. In sequencing mode, the optical sensor is connected to a corresponding base recognition device, which ultimately converts the detectable light signal into sequence information and outputs it. In fluorescence staining mode or brightfield imaging mode, the optical sensor is connected to an image processing device, which outputs the detectable signal as an image. Specifically, the optical module includes an image sensor and an image processing unit operably connected to the image sensor. The image processing unit receives multiple images corresponding to multiple FOVs generated by the image sensor in the fluorescence staining mode and integrates and stitches these images.

[0134] The sample stage 110 is movable relative to the objective lens to facilitate scanning of the objective lens at multiple detection locations of the sample to be detected. Phase shift between the sample stage 110 and the objective lens can be achieved by moving the sample stage itself, the objective lens, the entire optical table, or any combination thereof.

[0135] like Figure 3 As shown, the controller 200 includes a driver circuit 210 and a mode switching circuit 220, which are coupled to the optical module 100 to control the optical module 100 to collect data from the sample to be detected. The driver circuit 210 is selectively coupled to mode parameters corresponding to the operating mode of the optical module 100, which include at least first mode control parameters corresponding to the sequencing mode and second mode control parameters corresponding to the fluorescence staining mode. The mode switching circuit 220 is coupled to the driver circuit 210 to control the driver circuit based on the sample to be detected: when the sample slide is a sequencing chip, the mode switching circuit 220 associates a first set of mode parameters with the driver circuit 210, and when the sample slide is a tissue slide, the mode switching circuit 220 associates a second set of mode control parameters with the driver circuit 210. After the type of the sample to be detected is determined, the mode switching circuit 220 selects the mode control parameters corresponding to the detected sample type. Exemplarily, the mode control parameters can be stored in a memory or other similar storage device. The driver circuit 210 calls the mode switching circuit 220 to match the mode control parameters and loads them into the corresponding circuits of the optical module 100. The host computer control software integrates the startup parameters corresponding to different modes. When the first set of mode parameters is activated, the host computer can automatically switch to / start the sequencing mode; when the second set of mode parameters is activated, the host computer can automatically switch to / start the fluorescence staining mode.

[0136] In some embodiments, the controller 200 further includes an identification circuit coupled to the mode switching circuit 220, and in particular, includes an interface for identifying the sample slide type and / or the operating mode. The interface, for example, includes a user input port for receiving input slide type information and / or the operating mode. The sample slide has a recognizable type identifier, such as a barcode or QR code; the interface includes a scanning mechanism (e.g., a barcode scanner) for identifying the type of the sample slide based on the type identifier and transmitting the scanned information to the mode switching circuit 220.

[0137] like Figure 6As shown, the present disclosure discloses a detection method for the above-mentioned measurement system with multiple detection modes. In step S11, a slide 120 is mounted on the sample stage 110. In conjunction with FIG5 , when multiple slides are involved in the detection, the measurement system with multiple detection modes is configured with multiple sample stages and optical links. In this case, the first slide is mounted to the first detection position of the sample stage; the second slide is mounted to the second detection position of the sample stage.

[0138] Before or after the first slide is installed on the first detection position of the sample stage, the detection method further includes: loading a first sample to be detected onto the first slide, the first sample to be detected includes a nucleic acid sequencing library, a biological tissue sample, a microbial sample or a cell sample. Before or after the second slide is installed on the second detection position of the sample stage, the detection method further includes: loading a second sample to be detected onto the second slide, the second sample to be detected includes a nucleic acid sequencing library, a biological tissue sample, a microbial sample or a cell sample. The types of samples to be detected on the first slide and the second slide may be different or the same. The optical module includes a first optical link and a second optical link, and the detection method includes: adjusting the relative position between the optical module and the sample stage so that either the first slide or the second slide is aligned with either the first optical link or the second optical link.

[0139] Furthermore, in step S12, the mode switching circuit determines the mode parameters selected for coupling to the driver circuit. As described above, the mode parameters correspond to the operating mode of the optical module and include at least a first mode control parameter corresponding to the sequencing mode and a second mode control mode parameter corresponding to the fluorescence staining mode. In further embodiments, the mode parameters may further include, for example, a third mode control mode parameter corresponding to a brightfield imaging mode.

[0140] In step S13 , the driving circuit applies the mode parameters determined by the mode switching circuit to the optical module so that the optical module switches at least between the sequencing mode and the fluorescence staining mode.

[0141] like Figure 7 As shown, embodiments of the present disclosure further provide a method for mode switching of a measurement system with multiple detection modes. The method includes: S21, identifying the type of sample to be detected, especially when a slide at a detection site on a sample stage is replaced. For example, the measurement system with multiple detection modes is provided with a sensor for real-time monitoring of the slide status at the detection site or monitors the slide status through scanning imaging and machine vision. When a slide at the detection site is replaced, the identification circuit is driven to execute the above step S21.

[0142] In step S22 , based on the type of the sample to be detected, steps S231 - 232 determine the mode parameters that are selected to be coupled to the driving circuit.

[0143] Step S24, when the sample to be detected is a nucleic acid sequencing library, the mode switching circuit associates the first set of mode parameters with the driving circuit, and the driving circuit drives the optical module to enter the sequencing mode; when the sample to be detected is a biological tissue sample, a microbial sample or a cell sample, the mode switching circuit associates the second set of mode control parameters with the driving circuit, and the driving circuit drives the optical module to enter the fluorescence staining mode or a third operating mode different from the fluorescence staining mode and the sequencing mode. The third operating mode is the bright field imaging mode. When the types of samples to be detected are different, the real-time change of the sample type can be detected by the above-mentioned recognition circuit, and the new operating mode parameters are selected and called into the corresponding control loop of the optical module. In some applications, the calling of the operating mode parameters can occur in real time (but may still depend on system delays or other delays), so that the operating mode of the optical system can be changed dynamically.

[0144] like Figure 8 As shown, in a measurement system with multiple detection modes according to an embodiment of the present disclosure, a sample slide includes a sample cavity for placing a sample to be detected, the sample cavity is a closed cavity provided with an exchange hole, the exchange hole is used to pass fluid into the sample cavity or discharge fluid from the sample cavity, a liquid path module for passing fluid into or discharging fluid from the sample cavity, includes a reagent cavity and a pipeline connecting the reagent cavity with the sample cavity; and an imaging module for imaging the sample to be detected.

[0145] In the present disclosure, the sample cavity can be a detachable component to facilitate loading of the sample to be tested therein, and it can be loaded before use. For example, the sample cavity is a detachable sample slide. The exchange hole includes a liquid inlet and a liquid outlet, and there can be one or more liquid inlet and liquid outlet, and more than one can be selected. When the fluid is introduced, the fluid enters the sample cavity through the liquid inlet, and the air is discharged from the sample cavity through the liquid outlet; when the fluid is discharged, the fluid is discharged from the sample cavity through the liquid outlet, and a new fluid (liquid or gas) replaces the original fluid and enters the sample cavity. The entry and discharge of the fluid can be carried out by a pump, such as a micro pump.

[0146] In the present disclosure, there may be multiple reagent chambers for accommodating multiple reagents, which may be the same or different. Each of the multiple reagent chambers is connected to the sample chamber via a respective pipeline, and each pipeline is provided with a selection valve for introducing different reagents into the sample chamber as needed. A control module may be used to control the sequential introduction of multiple reagents from the multiple reagent chambers into the sample chamber and the discharge of the multiple reagents from the sample chamber.

[0147] In the present disclosure, a temperature control module can be used to control the temperature of the fluids in the sample chamber and the reagent chamber, with the goal of ensuring that the incubation of the sample to be tested is carried out at a set temperature. Any method can be used to maintain the temperature of the fluids in the sample chamber and the reagent chamber, such as using an electric heater and a temperature-sensitive sensor to adjust the on and off of the electric heater. It should be understood that the temperature control parameters of the temperature control module may vary depending on the sample to be tested.

[0148] In the fluorescence staining mode, the optical path diagram of the optical module 100 is as follows: Figure 5B As shown, the optical module 100 includes an objective lens 1001, an eyepiece 1006, fluorescence imaging cameras 1007-1008, and spectroscopic / filtering components. Specifically, the objective lens 1001 is positioned opposite the sample slide 120 to collect optical signals from the sample slide 120. The fluorescence signal contained in the optical signal is transmitted by the filter assembly 1003. In the fluorescence staining mode, the light source module includes an epi-illumination light source L2a and a transillumination light source L2b, which can be selectively activated by the user according to actual needs. The epi-illumination light source L2a is, for example, an epi-illumination LED light source. After collimation, the light passes through the filter assembly 1003 and enters the objective lens 1001, uniformly illuminating the tissue slice area of ​​the sample slide 120 within the field of view of the objective lens 1001. The fluorescent material in the sample slide 120 is stimulated to emit fluorescence. The objective lens 1001 collects the fluorescence and collimates the output. After being filtered by the filter assembly 1003, the fluorescence enters the tube lens, which magnifies the fluorescence and forms an image on the eyepiece 1006 or the sensor chip of the fluorescence imaging camera 1007-1008. A binocular beam splitter is also provided between the eyepiece 1006 and the filter assembly 1003. During the camera exposure process, the sample slide 120 moves linearly at a constant speed, and the objective lens 1001 scans the imaging area of ​​the biological tissue slice. To ensure that excessive defocus is not introduced when the imaging area changes, an additional focus detector can be provided to monitor the defocus of the biological tissue slice in real time. A focusing mechanism is used to ensure that the tissue slice remains within the allowable defocus range. Furthermore, the epi-illumination light source L2a can selectively emit epi-fluorescence and epi-bright field light, so Figure 5B The optical path shown is also applicable to bright field imaging mode. In epi-bright field imaging, any of the cameras 1007-1008 needs to be switched to a color camera, and the filter block 1003 needs to be switched to a bright field filter block. Figure 5B As shown, the bright field imaging mode can also use transmitted illumination: the transmitted illumination LED light source L2b emits illumination light, which is collimated and output, and then enters the condenser after passing through the reflector. The condenser focuses the light on the sample in the sample carrier 120 to obtain strong light illumination. The bright field light signal of the sample carrier 120 is magnified by the objective lens 1001 and the like, and the image is displayed on the eyepiece 1006 or the sensor chip of the camera 1007-1008 (in this case, any of the cameras 1007-1008 can be replaced by a color camera).

[0149] like Figure 5C As shown, in sequencing mode, the sample slide 120 includes multiple sample receiving sites 1201. A DNA sample is placed at a sample site 1201, where it emits a fluorescent signal. A light source (not shown) in the optical system emits a light signal toward the sample site, stimulating the sample to produce a fluorescent signal. A light-transmitting layer (equivalent to a microlens) corresponding to each sample site transmits the fluorescent signal from the sample site 1201 to a corresponding photosensor 1005. The photosensor 1005 collects the fluorescent signal and generates an analog electrical signal. A control circuit electrically connected to the photosensor 1005 then processes the analog electrical signal to determine the type and / or sequence of bases contained in the sample.

[0150] Figure 8 A schematic structural diagram of a measurement system with multiple detection modes according to an exemplary embodiment of the present disclosure is shown. Figure 8The multiple detection mode measurement system can include sequencing and fluorescence staining modes, further expanding the functionality of the sequencer and achieving multifunctionality. As shown in the figure, the multiple detection mode measurement system includes a slide for placing the sample to be tested, an optical module for optically scanning the sample to be tested, a fluidic module for introducing and removing liquid reagents from the sample to be imaged, a temperature control module for controlling the temperature of the fluids in the sample and reagent chambers, and a control module for controlling the rectification system. The sample chamber of the slide can be a sealed cavity with an exchange port for introducing fluid into or removing fluid from the sample chamber. Therefore, the exchange port includes an inlet and an outlet. In some embodiments, the sample chamber is a detachable component, for example, a detachable sample slide can be used as the sample chamber. The optical module optionally includes a light source module, an optical detector, motion control, and autofocus mechanisms to implement optical scanning. Scanning a sample with a known focal length can ensure a clear image of at least one layer by capturing images from several layers above and several layers below. The fluidic module includes a reagent chamber and a pipeline connecting the reagent chamber to the sample chamber. There can be multiple reagent chambers for accommodating various reagents, each connected to the sample chamber via a pipeline. Optionally, a selector valve can be provided on the pipeline to selectively connect the reagent chamber to the sample chamber. Supplying multiple reagents sequentially to the sample chamber allows for multiple incubations of multiple samples to be tested, with optional washing between incubations with different reagents. Washing can be performed using water or a buffer solution. Incubation and washing can be programmed. Based on a pre-set program, a control module automatically selects and drives fluids, allowing the various reagents to be sequentially introduced into and removed from the sample chamber from the multiple reagent chambers. A temperature control module can separately control the temperatures of the sample and reagent chambers, allowing them to be the same or different. In the case of multiple reagent chambers, the temperatures of the multiple reagent chambers can be controlled separately, allowing the temperatures of the different reagent chambers to be the same or different. Automated temperature control can be achieved using the control module. The temperature control module can employ a PID control method to regulate temperature increase and decrease, with temperature changes achieved using Peltier elements built into the sample stage. The control module can be run by a software system executed by a main control computer and is responsible for controlling the operation of the assay system in various detection modes. The control module is used to control the liquid circuit module to exchange reagents on the sample slide, and to control the microscope imaging module to image the sample slide, so that the incubation and imaging of the sample slide are carried out in the required order. The editable configuration file allows the settings of the control module to be modified, and the customizable protocol file specifies the fluid processing, temperature setting and imaging steps in sequence. In addition, the position of the sample chamber can be moved by a mobile platform (for example, by an x, y, z three-axis mobile platform) to accurately position and move the sample on the chip to ensure the superposition and image stitching of multiple images.

[0151] The scheme using the disclosed system combines the automation of microscopy and sample processing to visualize tens of thousands of features in millions of pixels of the sample. The present disclosure can realize a simple and effective multiplexed, sensitive in situ protein detection method with programmable signal amplification. The present disclosure can enable higher throughput imaging analysis from super-resolution studies to centimeter-scale tissue mapping work. These omics methods require precise control of temperature, reagent application and image acquisition parameters during iterative chemistry and imaging cycles of days or weeks. Automated execution of these methods enables robust and reproducible data generation.

[0152] In a measurement system that integrates multiple detection modes such as sequencing and fluorescent staining, the sample slide can be a sequencing slide for fixing a nucleic acid detection library, or it can be other slides for supporting, for example, biological tissue samples, and the sample slide is fixed on a sample stage. Figures 9A-9B shows a schematic diagram of a sample slide according to an exemplary embodiment of the present disclosure, Figure 9A Represents the sample slide assembly diagram, Figure 9B Shows an exploded view of the sample slide assembly. Figures 10A-10D The schematic diagram of attaching tissue slices to a sample slide of an exemplary embodiment is shown, which fixes the tissue slices to facilitate subsequent incubation and prevents the tissue slices from moving in the liquid during incubation and washing. Figure 10A The process of adhering tissue sections to slides is shown; Figure 10B The diagram shows the state after the tissue section has been adhered to the slide; Figure 10C The double-sided tape is shown attached to the slide; Figure 10D It is shown that the sample slide assembly is completed by covering the cover glass with a frame. The sample slide is fixed on the chip operating table. The present disclosure is suitable for double-layer slide flow channel design of tissue slices in the form of paraffin tissue slices, frozen tissue slices, etc. In one embodiment, the tissue slices are transferred to the slide after pre-treatment and fixed to the slide. Thereafter, the flow channel cut with double-sided tape is adhered to the slide, and finally the cover slide is covered on top (or the double-sided tape can be adhered to the cover slide first, and then adhered to the slide). Through the above method, a three-layer flow channel chip is formed. The sample slide can be fixed on the fixture base. Figure 11 A schematic diagram of the sample slide adapter fixture is shown. A chip is placed in the chip-holding position of the base, and downward pressure is applied to the compression block to compress the chip. In this embodiment, the base is made of engineering plastic, which has a certain degree of hardness; the compression block is made of silicone, and together with the base, it compresses the chip without damaging it.

[0153] As mentioned above, the measurement system of multiple detection modes disclosed in the present invention integrates multi-mode detection schemes such as sequencing mode and fluorescent staining mode to form a multifunctional platform for staining, imaging and sequencing. The measurement system of multiple detection modes can expand the application of sequencers, realize the integration of different applications, and improve the use value of the instrument. By introducing the measurement system of multiple detection modes disclosed in the present invention, the present invention transforms the sequencer into a multifunctional platform that is compatible with protein tissue staining and imaging in addition to gene sequencing functions. Through the fluorescent staining operation formulated for the instrument, the experimental design includes synchronous 4-channel image acquisition, temperature control, reagent exchange, stable positioning and sample integrity of the extended experiment. Similar to existing sequencers, this solution can realize the cyclic indirect immunofluorescence imaging (4i) function of complex multi-day continuous workflows in an unattended manner. At present, the system disclosed in the present invention can perform highly automated 4i methods during the fluorescent staining imaging process, and is compatible with the vast majority of readily available antibodies on the market. After multiple cycles of staining, imaging and antibody elution, a highly multiplexed map of cell types and pathological characteristics of animals or plants is finally constructed. In addition to indirect immunofluorescence imaging, the scheme of the present disclosure is also applicable to Vectra multispectral imaging, Lunaphore microfluidic liquid exchange system, CellDive platform, CyCif platform, ZellScannerONEinstrument platform, Immuno-Saber platform, PhenoCycler platform, InSituPlex technology. In the present disclosure, the optical system is modified to realize a multiplexing scheme of more than multiple (for example, 6) labels per round through multispectral imaging. With the development of imaging and spectroscopy, it is possible to unmix images. Different biomolecules are labeled with multiple dyes. Even if there is very obvious spectral overlap, each optical signal can be separated from each other by spectral unmixing.

[0154] The disclosed scheme can be applied to immunofluorescence imaging, nucleotide-coupled antibody fluorescence imaging, RNA in situ hybridization fluorescence imaging (corresponding to RNAScope hybridization signal), and supports in situ sequencing of nucleotide extension on tissue samples. The disclosed multiplex biochemical detection is compatible with a variety of antibody fluorescence staining reagent schemes, including 4i based on fluorescently labeled secondary antibody amplification, TSA signal amplification, fluorescently labeled nucleotide-coupled antibody CODEX (co-detection through indEXing), etc. Among them:

[0155] Fluorescent labeling amplification technology: Cyclic indirect immunofluorescence imaging (4i) is the first imaging technology that can provide a multiplexed perspective from tissue to organelle. In the same experiment, correlated multiplexed information at the tissue, cellular and subcellular levels can be obtained. Immunofluorescence (IF) uses antibodies to visualize and locate proteins in biological samples. Standard IF can usually only label 2-3 proteins. 4i uses ready-made antibodies and conventional fluorescence microscopes. By repeatedly removing antibodies and hybridizing, it can visualize 10 times the number of proteins of IF.

[0156] The TSA (Tyramide Signal Amplification) multi-labeling solution for tissue sections utilizes horseradish peroxidase (HRP) for high-density in situ labeling of target proteins or nucleic acids, enhancing detection sensitivity and significantly improving the signal-to-noise ratio by over a thousand-fold. It can use primary antibodies from the same animal source to perform fluorescent multi-labeling of multiple markers on the same tissue section. Its excellent signal amplification performance can boost signal intensity by 10-100 times, significantly improving detection sensitivity for weak signals and difficult-to-label proteins.

[0157] The CODEX platform combines oligonucleotide labeling (barcode) and microfluidic automated staining technology to enable the detection and in-depth analysis of more than 50 protein markers in the same sample, and can provide high-resolution images at the single-cell level. The core design principle of CODEX is to label each antibody with a specific oligonucleotide "barcode tag" (barcode), rather than directly labeling it with a fluorescent dye. The fluorescent dye required for imaging is specifically bound to the oligonucleotide sequence complementary to the barcode, allowing CODEX to break the limitation of the number of visible spectrum fluorescence imaging channels and easily achieve the simultaneous detection and analysis of 50 or more protein indicators.

[0158] The disclosed approach is also applicable to RNA and DNA targets, complementing single-cell RNA sequencing analysis with functional information on protein expression, and will prove to have a wide range of potential applications, including tissue atlases, tumor and disease atlases, in situ single-cell validation of large-scale assays such as flow cytometry or mass cytometry, and CITE-Seq (single-cell sequencing of cell surface proteins and RNA simultaneously), as well as digital pathology and biomarker screening and discovery.

[0159] The disclosed method is also applicable to using DNA or RNA probes to detect the location of the complementary strand in bacteria or other eukaryotic cells.

[0160] RNA in situ nucleic acid hybridization, also known as RNA in situ hybridization histochemistry or RNA in situ hybridization, is an in situ hybridization technique that uses probes such as cRNA or oligonucleotides to detect RNA expression in cells and tissues. The basic principle is that, under conditions where the cell or tissue structure remains unchanged, labeled RNA nucleotide fragments are used to bind (hybridize) to corresponding gene fragments in the cells or tissues being tested, following the base pairing principle of nucleic acid hybridization. The resulting hybrids undergo a colorimetric reaction, and the corresponding mRNA, rRNA, and tRNA molecules within the cells are visualized under an optical or electron microscope. With continuous improvements, RNA in situ hybridization has expanded its application beyond DNA in situ hybridization. It is particularly effective in genetic analysis and diagnosis, enabling qualitative, localized, and quantitative analysis, making it a highly effective molecular pathology technique. It has also become a significant area of ​​molecular biology for analyzing low-abundance and rare mRNA expression. Detection of nucleic acid targets can be achieved through probe hybridization, where oligonucleotide probes reversibly hybridize to the target nucleic acid, undergoing extension and ligation reactions. In the detection reaction, when the probe is combined with the target in the correct direction, they can extend and ligate, thereby produce the oligonucleotide product connected.Then the existence of the target of interest can be determined by measuring the existence or quantity of the oligonucleotide product connected.Wherein, oligonucleic acid probes can directly connect detectable labels, such as fluorescent labels, electrochemical labels, magnetic beads, nanoparticles, biotin, etc., for quantitative or detection of the oligonucleotide product connected.Or, oligonucleic acid probes can also not connect detectable signals, and oligonucleic acid probes are specific to the target of interest, and produce connection products at each target site, can carry out the amplification reaction of signal amplification, produce multiple copies of connection products, utilize signal probe hybridization amplification products, thereby amplify detectable signals.In some cases, nucleic acid target is RNA target, and RNA target can be reverse transcribed to produce cDNA.Then cDNA can be amplified or can be contacted with probe (for example, padlock probe).Probe can hybridize with cDNA.In some cases, nucleic acid target is DNA target, and DNA target can be made to undergo amplification or can be contacted with probe (for example, padlock probe).For example, DNA target can be directly amplified by amplification primers. For example, a padlock probe can be contacted with a DNA target and hybridized to the DNA target. The padlock probe can then be cyclized and amplified. The amplified product or amplicon can be directly bound to a signal probe for in situ signal detection. Figure 15 The figure shows the in situ mRNA detection data obtained using RNA in situ hybridization sequencing technology.

[0161] In some embodiments, the signaling probe can be a sequence-specific oligonucleotide probe that is optically active when hybridized to a nucleic acid target or a derivative thereof (e.g., an amplification product). The probe can be linked to any optically active (e.g., dye) described herein and can further include a quencher that blocks the optical activity of the associated dye. Non-limiting examples of probes that can be used as reporters include TaqMan probes, TaqMan Tamara probes, TaqMan MGB probes, or Lion probes.

[0162] Figure 12A schematic diagram of a liquid circuit module of a measurement system for multiple detection modes according to an embodiment of the present disclosure is shown. As shown in the figure, the measurement system for multiple detection modes includes multiple groups of reagent chambers 1 for storing multiple reagents. The reagent chamber 1 is connected to a sample slide 2 serving as a sample cavity through a pipeline, and a selection valve 3 is provided on the pipeline for selecting the reagents in different reagent chambers 1. The sample slide 2 is also connected to a waste liquid barrel 5 through a pipeline for discharging the reagents from the sample slide 2. An injection pump 4 is installed on the recovery line connected to the waste liquid barrel 5. The injection pump 4 provides power, and the reagent is drawn out from the reagent chamber 1, enters the chip 2 through a precision fluid system, acts on the tissue in the chip 2, and is then drawn out from the chip 2 and finally enters the waste liquid barrel 5. The microfluidic system can ensure rapid reaction between the target and the reagent and highly stable repeatability. In one example of the present disclosure, for multiplex biochemical testing in a fluorescent staining mode, sample preparation may include the following steps: a) setting a glass slide so that the sample is firmly bonded to the slide; b) after the sample is mounted, it can be pre-treated by traditional methods before being loaded onto the machine; c) after loading onto the machine, it can be heated by a temperature control system and antigen repair can be performed under strong acid or strong base conditions as needed. The purpose of antigen repair is to fully expose the antigens cross-linked with paraffin so that the antibody can bind to the relevant antigen. The acid, base, heat or pressure used is adjusted according to the specific antibody; d) the sample is incubated and punched with 0.5% TritonX-100 for 15 minutes. The purpose of punching the cell membrane in the tissue is to allow the antibody to enter the cell and bind to the relevant antigen. In the present disclosure, the entire sample preparation process can be reduced from 300 minutes to about 180 minutes. After loading, the sample can be pre-treated for multiple fluorescent staining as follows: a) Fluidity washing with PBS (time: 100 seconds, flow rate: 1200 microliters per minute); b) Blocking treatment with a blocking reagent (such as 10% BSA, 5% Goat Serum or 10% skim milk, etc.) for 30 minutes; c) Fluidity washing with PBS (time: 100 seconds, flow rate: 1200 microliters per minute); d) Add imaging buffer (Trolox, N-acetylcysteine, DTT and other antioxidant reagent solutions); e) Perform full-slice scanning to obtain autofluorescence background for correction. The method disclosed in the present invention can reduce the time to 5.3 hours or even shorter, while the traditional fluorescent staining process takes up to 8 hours or even longer. Moreover, most of the operations of the method disclosed in the present invention are completely automatically operated by the machine and do not require human participation.

[0163] Three different examples of multiplex fluorescent staining are given below.

[0164] Example 1

[0165] 1) Select the fluorescence dyeing mode in the multi-mode detection instrument and perform fluorescence dyeing detection.

[0166] Immunofluorescence detection is a secondary antibody amplification method:

[0167] i. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0168] ii. Add primary antibody diluted in 1% BSA solution (1:10-1:400) and incubate at 37 degrees Celsius for 15-45 minutes;

[0169] iii. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0170] iv. Add fluorescently labeled secondary antibody diluted in 1% BSA solution (1:10-1:400) and incubate at 37 degrees Celsius for 10-30 minutes;

[0171] v. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0172] vi. Add imaging buffer (Trolox, N-acetyl cysteine, DTT and other antioxidant reagent solutions);

[0173] vii. Scan the entire slide using a fluorescently labeled secondary antibody at a specific wavelength;

[0174] viii. Antibody elution was performed using an antibody elution buffer (weakly acidic 2ME + SDS + TrisHCl solution, acidic glycine + SDS solution, or acidic glycine + urea + GC + TCEP solution) at a temperature controlled temperature (25-56 degrees Celsius);

[0175] ix. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0176] x. Block the cells again with a blocking reagent (e.g., 10% BSA, 5% Goat Serum, or 10% skim milk) for 30 minutes.

[0177] xi. Repeat steps i. to x. for multiple rounds of dyeing.

[0178] Example 2

[0179] 2) Select the fluorescence dyeing mode in the multi-mode detection instrument and perform fluorescence dyeing detection.

[0180] Immunofluorescence staining is performed using fluorescently labeled primary antibodies:

[0181] i. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0182] ii. Add fluorescently labeled primary antibody diluted in 1% BSA solution (1:10-1:400) and incubate at 37 degrees Celsius for 15-45 minutes;

[0183] iii. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0184] iv. Add imaging buffer (Trolox, N-acetyl cysteine, DTT and other antioxidant reagent solutions);

[0185] v. Scan the entire slide with a fluorescently labeled primary antibody at a specific wavelength;

[0186] vi. Elute the antibody using an antibody elution buffer (weakly acidic 2ME + SDS + TrisHCl solution, acidic glycine + SDS solution, or acidic glycine + urea + GC + TCEP solution) at a temperature of 25-56 degrees Celsius for 30 minutes. Alternatively, use a quencher (0.1 M sodium bicarbonate + 3% hydrogen peroxide, sodium borohydride, 24 mM sodium hydroxide + 4.5% hydrogen peroxide, etc.) to quench the fluorescence.

[0187] vii. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0188] viii. Block the cells again with a blocking reagent (such as 10% BSA, 5% Goat Serum, or 10% skim milk) for 30 minutes;

[0189] ix. Repeat cycles i. to viii. for multiple rounds of staining and photography.

[0190] Example 3

[0191] 3) Select the fluorescence dyeing mode in the multi-mode detection instrument and perform fluorescence dyeing detection.

[0192] Immunofluorescence staining is nucleotide-coupled fluorescence:

[0193] i. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0194] ii. Add nucleotide-conjugated primary antibody diluted in 1% BSA solution (1:10-1:400) and incubate at 37 degrees Celsius for 15-45 minutes;

[0195] iii. Add PFA or other amine-based fixatives to fix the antibody and sample;

[0196] iv. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0197] v. The nucleotides coupled to the primary antibody can be amplified by RCA, PER (primer replacement method) and other amplification methods;

[0198] vi. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0199] vii. Add the corresponding fluorescently labeled nucleotide duplex to a solution (PBS, TBS, etc.), add the sample, and incubate for 30 minutes. The temperature can be gradually lowered to enhance specificity.

[0200] viii. Wash with PBS for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0201] ix. Add imaging buffer (Trolox, N-acetyl cysteine, DTT and other antioxidant reagent solutions);

[0202] x. Perform full-slide scanning at a specific fluorescence wavelength;

[0203] xi. Double-stranded DNA can be eluted by high-temperature unwinding, degradation by double-stranded DNA degrading enzyme, unwinding and eluting by DNA helicase, etc. to elute the fluorescently labeled nucleotide duplex;

[0204] xii. Repeat vi. to xi. for multiple rounds of staining and photography.

[0205] In a multiplex fluorescent staining protocol, the present disclosure can add a reducing agent to the reagent to free the antibodies from cross-linking caused by photography, making them easier to elute.

[0206] Select the sequencing mode in the multi-mode detection instrument to perform nucleic acid sequence detection.

[0207] The multi-mode measurement mode is to perform staining and photography mode, and then the instrument can switch to sequencing mode to sequence the prepared nucleic acid library. The specific steps are as follows:

[0208] i. Deep cleaning of multi-mode detection instruments;

[0209] Sequencing was performed using the DNBSEQ-G400 PE150 sequencing kit. Table 1 shows the sequencing report for the nucleic acid libraries in the four lanes of the chip after the staining and photography mode.

[0210] Lane 1 Lane2 Lane3 Lane4 CycleNumber 310 310 310 310 Chip Productivity (%) 85.53 85.37 86.35 85.09 ImageArea 432 432 432 432 TotalReads(M) 516.08 515.03 520.98 513.35 Q30(％) 94.38 94.16 94.25 93.97 SplitRate(%) 99.19 99.18 99.19 99.18 Runon1(%) 0.03 0.03 0.03 0.03 Runon2(%) 0.04 0.04 0.04 0.05 Lag1(%) 0.1 0.1 0.1 0.1 Lag2(%) 0.14 0.14 0.14 0.14 ESR (%) 85.53 85.37 86.35 85.09 MaxOffsetX 17.25 18.26 20.16 22.49 MaxOffsetY -30.29 -33.56 -36.22 -37.84 InitialOffsetX 8.58 8.81 9.99 12.11 InitialOffsetY -16.85 -19.62 -21.85 -23.13 RecoverValue(A) 2.06 2.04 2.03 2.03 RecoverValue(C) 2.64 2.64 2.6 2.56 RecoverValue(G) 2.83 2.83 2.79 2.75 RecoverValue(T) 2.23 2.22 2.2 2.21 RecoverValue(AVG) 2.44 2.43 2.41 2.39

[0211] Table 1

[0212] The results of staining and photography are as follows Figure 13Figure 2 shows the results of multiple fluorescent staining of mouse brain slices captured using the multi-mode detector imaging platform. Green areas are stained with GFAP antibodies, and red areas are stained with fibronectin antibodies. Imaging parameters: laser intensity: red—300mW, green—150mW; exposure time: 40ms.

[0213] Example 4

[0214] The multi-mode detection instrument can perform mRNA in situ hybridization detection. An example of a protocol based on mRNA in situ hybridization is given below.

[0215] Select the fluorescence staining mode in the multi-mode detection instrument and perform fluorescence staining detection.

[0216] The in situ detection method is mRNA in situ hybridization detection.

[0217] 1) Primary probe binding:

[0218] i. Wash with 2XSSC buffer for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0219] ii. Add the Primary probe (9 nM) diluted in a solution containing 10-40% Formamide and 0-10% dextran sulfate and incubate at 37 degrees Celsius for 3 hours;

[0220] iii. Wash with 2XSSC buffer for fluidity (time: 100 seconds, flow rate: 1200 μl per minute);

[0221] iv. Add a secondary probe (20 nM) diluted in a solution containing 10-40% Formamide and 0-10% dextran sulfate and incubate at 37 degrees Celsius for 1 hour;

[0222] v. Wash with 2XSSC buffer (time: 100 seconds, flow rate: 1200 μl per minute);

[0223] vi. Add Tertiary probe (20 nM) diluted with 10-40% Formamide and 0-10% dextran sulfate solution and incubate at 37 degrees Celsius for 1 hour;

[0224] vii. Repeat steps iii-vi for signal amplification;

[0225] viii. Wash with 2XSSC buffer for mobility (time: 100 seconds, flow rate: 1200 μl per minute);

[0226] ix. Add a Readout probe (10 nM) diluted in a solution containing 10-40% Formamide and 0-10% dextran sulfate and incubate at 37 degrees Celsius for 15 minutes;

[0227] x. Wash with 2XSSC buffer (time: 100 seconds, flow rate: 1200 μl per minute);

[0228] xi. Add imaging buffer and proceed to imaging.

[0229] The results are as follows Figure 15 The following image shows the results of multiple fluorescent staining of mouse tumor model tissue sections purchased from Wuhan Sevier, captured using a multi-mode detector imaging platform. Green areas represent Cd8 mRNA, and red areas represent Ki67 mRNA. Imaging settings: Laser intensity: Red—300mW, Green—150mW; Exposure time: 40ms.

[0230] The system and method disclosed in the present invention liberate manpower by realizing a highly automated staining + photography process that can be unattended; compared with the dye-shooting separation instruments in the prior art, the dye-shooting functions can be integrated into the instrument; the scheme disclosed in the present invention can accurately control the amount of reagents used, thereby generating stable data for multiple rounds of quantitative analysis; the scheme disclosed in the present invention supports multiple immunofluorescence staining of a single slice and is compatible with a variety of biochemical staining schemes; the scheme disclosed in the present invention can greatly optimize the reagent reaction time.

[0231] In one example of the present disclosure, for analysis and detection in cell or microbial mode, chip preparation may include the following steps: a) setting up a sequencing chip, fixing capture probes on the chip surface; b) loading a cell suspension onto the chip surface, fixing it and scanning and photographing it (fluorescence photography or bright field photography may be optional as needed); c) permeabilizing the cells so that the mRNA in the cells can pass through the cell membrane and be captured by the capture probes on the chip surface; d) performing reverse transcription and sequencing library construction on the chip surface; e) switching the multi-mode detector to sequencing mode, sequencing to obtain transcriptome data; f) integrating and analyzing the transcriptome data and cell photographic data to obtain single-cell transcriptome data. The method disclosed herein is automatically operated by the multi-mode detector and does not require human participation.

[0232] In one example of the present disclosure, for analysis and detection in a cell or microorganism mode, chip preparation may include the following steps: a) setting up a sequencing chip, fixing capture probes on the chip surface; b) extracting the nuclei of cells or tissues; c) adding transposition complexes and incubating the nuclei for transposition reaction; d) loading the nucleus suspension onto the chip surface, fixing it and scanning and photographing it (fluorescence photography or bright field photography can be selected as needed); e) lysing the nuclei, and the genomic fragments interrupted by the transposition complex are captured by the capture probes on the chip surface; f) amplification and extension and sequencing library construction are performed on the chip surface; g) switching the multi-mode detector to sequencing mode, sequencing to obtain epigenetic group data; h) integrating and analyzing the epigenetic group data and the nucleus photograph data to obtain single-cell epigenetic group data. According to the purpose of the experiment, the single-cell transcriptome data and epigenetic data can be integrated and analyzed to obtain single-cell multi-omics analysis data.

[0233] The following are examples of cell or microbial analysis and detection protocols, such as Figure 16 As shown, the analysis process of the cell or microbial analysis detection results and sequencing results includes: S31, scanning the cell chip and taking a photo to obtain a scanned image; S32 obtaining the sample nucleic acid sequence information in the sequencing mode; S33, analyzing and integrating the sequencing data and cell images; S34, performing cluster analysis on the cell transcriptome data to obtain single-cell transcriptome data.

[0234] Example 5

[0235] Start the multimode assay analyzer and select the cell or microbial analysis mode.

[0236] 1. Prepare the sample phase suspension: Pipette 10,000 cell nuclei for cell phase preparation, and the preparation system is (100 μL system); 2. Sample loading: Fix the sequencing chip on the carrier and load the cell suspension onto the chip;

[0237] 3. Fixation: Load pre-cooled methanol and incubate at low temperature for 20 minutes to fix the cells on the chip surface, and scan and take pictures;

[0238] 4. Permeabilization: Dilute 0.01M HCl 10-fold to obtain the working solution concentration (working solution volume is 100 μL / chip), load onto the chip surface and incubate at 37°C for 0-30 minutes;

[0239] 5. Reverse transcription: The capture probes fixed on the chip surface hybridize with the mRNA in the cells and then perform reverse transcription (BGI Stereo-seq Transcriptome Kit, Cat. No. 101KT114) to obtain cDNA.

[0240] 6. Library construction: Circularization and rolling circle amplification reactions, or sequencing library, are performed on the chip surface.

[0241] 7. Switch the multimode detection analyzer to sequencing mode, perform sequencing reaction, and obtain transcriptome data.

[0242] 8. Integrate and analyze the transcriptome data and the cell images collected in step 3) to obtain single-cell transcriptome data ( Figure 17 ),in Figure 17 This capture captures a portion of the chip image, showing a large number of single cells distributed across the chip. Circle one cell to see the average number of genes and UMIs captured for that cell.

[0243] Figure 14 In one embodiment of the present disclosure, a computer system for implementing the present measurement system or method. The control system is implemented by a computer system, which is programmed or otherwise configured to use the method of the present disclosure to control the optical system, fluid system, detection system and analysis system to collaboratively process the sample to be tested according to a predetermined program. The computer system can regulate various aspects of the processing of the various systems of the present disclosure, for example, processing instructions in a processor, contacting reagents or buffers with the sample to be tested, reacting on the surface of the slide, and controlling the optical system and detection system to collect signals. The computer system can be an electronic device integrated into a multi-mode measurement system or a computer system remotely located relative to the electronic device. The electronic device can be a mobile electronic device.

[0244] The computer system includes a central processing unit (CPU, also referred to herein as a "processor" and "computer processor"), which can be a single-core or multi-core processor, or multiple processors for parallel processing. The computer system also includes memory or storage location 310 (e.g., random access memory, read-only memory, flash memory), an electronic storage unit (e.g., a hard disk), a communication interface (e.g., a network adapter) for communicating with one or more other systems, and peripheral devices such as cache, other memory, data storage, and / or an electronic display adapter. The memory, storage unit, interface, and peripheral devices communicate with the CPU via a communication bus (solid line), such as a motherboard. The storage unit can be a data storage unit (or data repository) for storing data. The computer system can be operatively coupled to a computer network ("network") via a communication interface. The network can be the Internet, an Internet and / or an extranet, or an intranet and / or extranet in communication with the Internet. In some cases, the network is a telecommunications and / or data network. The network can include one or more computer servers that can implement distributed computing, such as cloud computing.

[0245] The CPU can execute a series of machine-readable instructions, which can be embodied in a program or software. The instructions can be stored in a storage location, such as a memory. The instructions can be directed to the CPU, which can then program or otherwise configure the CPU to implement the methods of the present disclosure. Examples of operations performed by the CPU can include fetching, decoding, executing, and writing back. The CPU can be part of a circuit, such as an integrated circuit.

[0246] The one or more processors 102 and / or other data processing circuits described above may generally be referred to herein as "data processing circuitry." The data processing circuitry may be embodied in whole or in part as software, hardware, firmware, or any other combination thereof. Furthermore, the data processing circuitry may be a single, independent processing module, or may be incorporated in whole or in part into any of the other components of the computer terminal 10 (or mobile device). As described in the embodiments of the present disclosure, the data processing circuitry functions as a processor control (e.g., selection of a variable resistor terminal path connected to an interface).

[0247] The memory 104 can be used to store software programs and modules of application software, such as the program instructions / data storage device corresponding to the method for detecting samples in the embodiment of the present disclosure. The processor 102 executes various functional applications and data processing by running the software programs and modules stored in the memory 104, that is, implementing the vulnerability detection method of the above-mentioned application. The memory 104 may include a high-speed random access memory, and may also include a non-volatile memory, such as one or more magnetic storage devices, flash memory, or other non-volatile solid-state memory. In some instances, the memory 104 may further include a memory remotely located relative to the processor 102, and these remote memories may be connected to the computer terminal 10 via a network. Examples of the above-mentioned network include, but are not limited to, the Internet, an intranet, a local area network, a mobile communication network, and combinations thereof.

[0248] The transmission device 106 is configured to receive or transmit data via a network. A specific example of the aforementioned network may include a wireless network provided by the communications provider of the computer terminal 10. In one embodiment, the transmission device 106 includes a network interface controller (NIC), which can be connected to other network devices via a base station to enable communication with the Internet. In another embodiment, the transmission device 106 may be a radio frequency (RF) module, which is configured to communicate with the Internet wirelessly.

[0249] The display may be, for example, a touch screen liquid crystal display (LCD) that enables a user to interact with a user interface of the computer terminal 10 (or mobile device), but is not limited thereto.

[0250] In some embodiments, the control system includes at least one interaction unit configured to obtain a first instruction from a user to select at least one of at least two omics analyses.

[0251] In some embodiments, the omics analysis selected by the user is based on the detection results of different detection modes that have been obtained, and different omics analysis contents are selected for the detection results obtained by different detection modes. For example, sequencing data can be used for genomic analysis or transcriptomics analysis, and tissue sample staining data can be used for pathological omics, proteomics or spatial omics analysis, etc.

[0252] In some embodiments, the interaction unit can be a physical computer, keyboard, mouse, touch screen, etc., or a virtual machine, with the purpose of enabling information exchange between the machine and the user, and the specific form is not limited. In some embodiments, the unit for interacting with the multi-mode detector and the user is a first interaction unit, and the unit for interacting with the workstation and the user is a second interaction unit. The multi-mode detector and the workstation can communicate via a local area network transmission method, for example, by directly connecting to a network hard disk via a network cable using the TCP / IP protocol, but is not limited thereto.

[0253] Among them, omics analysis refers to the analysis of at least one of the genome, cell group, proteome, metabolome, transcriptome, and epigenetic group. Taking genome and proteome analysis as an example, the inventive concept of one embodiment of the present disclosure is introduced.

[0254] Specifically, the first instruction can be an instruction for the user to click on the controls of different software or functions, such as files in base recognition and image conversion information analysis formats, such as Cal files, BCL files or FastQ files; it can also be an instruction to click on the controls of bright field or dark field staining software or functions.

[0255] The carrier can be a platform for realizing functions such as temperature control, chip or chip and chip frame placement, chip fluid injection or suction, and data collection in cooperation with the optical unit.

[0256] Specifically, the fluid system further includes a reaction unit for performing a biochemical reaction on the sample.

[0257] The reaction unit can realize biochemical reactions for sequencing, as well as biochemical processes such as immunohistochemistry and multiple staining imaging.

[0258] Specifically, the device further includes at least one processor coupled to the interaction unit, the carrier, and the reaction unit, and configured to:

[0259] According to the first instruction, the user is instructed to input initial information, where the user input method includes at least one of keyboard input, touch screen input, gesture input, handwriting input, mouse input, code scanning input, camera input, radio frequency identification input, voice input and brain-computer interface input, and the initial information includes at least one of chip type, sequencing scheme, staining scheme, reagent kit number and confirmation information.

[0260] Among them, the code scanning input can be completed by inputting the identification code on the carrier or chip using an external code scanning gun, or by inputting the identification code on the carrier through an optical unit, and there is no restriction here.

[0261] The sequencing scheme may be any one of Sanger sequencing, NGS sequencing, single molecule sequencing, and nanopore sequencing, but is not limited thereto.

[0262] The staining scheme refers to a staining scheme including the antibody name, wavelength and staining time or a nucleic acid probe fluorescence detection scheme.

[0263] The kit number refers to the different codes for different types of kits.

[0264] Among them, confirmation information refers to the confirmation of the information entered by the user. For example, when performing protein analysis, it confirms the input antibodies, time and other information to avoid users finding input errors and clicking to directly enter the next step, which can effectively prevent mistakes.

[0265] The processor is further configured to control the reaction unit to perform a biochemical reaction according to the initial information.

[0266] The processor is further configured to control the interaction unit to feed back the information being processed by the user.

[0267] In some embodiments, during the sequencing or staining process, users can access images in stages. For example, after a preset number of cycles have been sequenced, a sequencing image or result may be displayed, or a "Sequencing in Progress" interface may be displayed without displaying the sequencing image or result. Another example is the interactive unit displaying images after each round of brightfield or darkfield staining, or displaying the countdown to the completion of a biochemical reaction. This allows the interactive unit to provide feedback to the user regarding the information being processed.

[0268] In other embodiments, for the bright field or dark field staining technology, each round of scanning will display an image after the current round of staining. If the user determines that the staining result or staining quality does not meet expectations, the biochemical reaction process can be interrupted or terminated.

[0269] The processor is further configured to complete the biochemical reaction based on the reaction unit and generate a first processing result.

[0270] Specifically, the first processing result can be the Cal file, BCL file, FastQ file, offline report, quality control report and other contents after sequencing is completed, but is not limited to this. It can also be a highly multiplexed map of the cell types and pathological characteristics of animals or plants after multiple cycles of staining, imaging and antibody elution. It can also be the result of processing the transcriptome, metabolome, and epigenetic group, such as expression statistics, differential expression analysis, functional enrichment analysis, metabolite identification, metabolic pathway analysis, methylation level analysis, ChIP-seq analysis, function and pathway analysis and other data, information or reports.

[0271] The processor is further configured to control the interaction unit to feed back the first processing result to the user.

[0272] Specifically, the first processing result is data, information or a report, which can be fed back to the user through display screen, voice prompts and brain-computer interface output, but is not limited to these.

[0273] In some embodiments, integrated circuits, such as CMOS FETs and biosensors, are often integrated on expansion cards, such as peripheral component interconnect (PCI) cards. These expansion cards can be easily installed in computing devices, providing users with additional processing power and sensor data acquisition capabilities. Integrated circuits can also include field programmable gate arrays (FPGAs) and application-specific integrated circuits (ASICs), which are key components for achieving high-performance computing. FPGAs are known for their flexibility and reconfigurability, allowing them to adjust in real time to changing application requirements. ASIC chips are optimized for specific tasks to improve execution efficiency and reduce energy consumption.

[0274] In other implementations, with the development of cloud computing technology, local computing resources can be combined with cloud platforms to form a hybrid computing environment. Cloud platforms provide almost unlimited storage space and computing resources that can be dynamically expanded according to demand. Local computing resources are responsible for processing tasks with high real-time requirements, while cloud platforms store large amounts of data and handle large-scale computing tasks that can be processed in parallel. Through this hybrid computing model, the system can more effectively manage and distribute computing loads to ensure optimal resource utilization. For example, for large-scale data analysis and storage-intensive applications, cloud platforms can provide the necessary support. For tasks that require fast response and processing, local FPGA / ASIC chipsets and CPUs / GPUs can provide the required computing power.

[0275] In some embodiments, the at least one interaction unit further includes obtaining a second instruction input by the user.

[0276] In some embodiments, the first instruction and the second instruction input by the user can be obtained through only one interaction unit, or the first instruction and the second instruction input by the user can be obtained respectively through different interaction units. It can be set according to actual needs and depends on the hardware design, which will not be repeated here.

[0277] In some embodiments, the second instruction may be an instruction for the user to click on primary analysis, secondary analysis, or tertiary analysis, or may be a control for clicking on software or functions of cell analysis or protein analysis, but is not limited thereto.

[0278] Specifically, the processor is further configured to instruct the user to input analysis information according to the second instruction, where the analysis information includes at least one of opening a file to be analyzed, selecting an area of ​​interest, and selecting an analysis target.

[0279] Among them, the file to be analyzed can be a report from the machine after the sequencing is completed, a sequencing file, or a protein or cell image set that has undergone multiple rounds of staining. Opening the file to be analyzed can include the process of loading colors into the protein or cell image set. Selecting the region of interest can determine the scope of cell segmentation and analysis. It can be selected automatically or manually according to user needs. Selecting the analysis target can be selecting different markers to determine the number and probability of cells corresponding to the marker when the table is finally generated. It can also be a control displayed on the interface corresponding to the primary analysis of the sequencing data, the conversion of Cal files or BCL files to FastQ files, primary analysis, secondary analysis, tertiary analysis, and diagnostic analysis to determine what kind of analysis to perform subsequently.

[0280] Specifically, the processor is also used to analyze the first processing result and generate a second processing result according to a third preset method. The third preset method includes converting the Cal file or BCL file into a FastQ file, primary analysis, secondary analysis, tertiary analysis, diagnostic analysis, merging all images in the first processing result, displaying in the interactive unit, performing cell segmentation according to the region of interest, analyzing the segmented cells, and generating at least one of information including the number of cells corresponding to the marker and the positive probability.

[0281] Specifically, the processor is further used to control the interactive unit to feed back the second processing result to the user, where the second processing result includes at least one of a secondary analysis result, a tertiary analysis result, a quantitative analysis, a phenotypic analysis, a spatial analysis, and a diagnostic report.

[0282] The various technical features described above can be combined arbitrarily. Although not all possible combinations of these technical features are described, any combination of these technical features should be considered to be covered by this specification as long as such combination does not conflict.

[0283] Although the embodiments of the present disclosure have been shown and described above, it is understood that the above embodiments are illustrative and are not to be construed as limitations on the present disclosure. A person skilled in the art may change, modify, replace and vary the above embodiments within the scope of the present disclosure.

Claims

1. A measurement system integrating multiple detection modes, characterized in that: The measuring system comprises: A carrier, the carrier being used to carry a sample to be tested; An optical system, wherein the optical system is at least selected from a combination of a light source, a lens group, and an objective lens; a detection system for detecting optical signals; a fluid system for providing a plurality of reagents for a detection reaction; A control system is used to control the switching of multiple detection modes, and / or to control the optical system, fluid system and detection system according to a predetermined program in one detection mode to complete the detection of the sample to be detected.

2. The measurement system according to claim 1, wherein It further includes an analysis system, which is used to receive information from the detection system, analyze the detection information, and output detection results.

3. The measurement system according to claim 1 or 2, characterized in that The detection system is selected from a camera, a photodiode, an optical sensor, etc.

4. The measurement system according to any one of claims 1 to 3, characterized in that The multiple detection modes are selected from sequencing mode, tissue sample staining mode, DNA or RNA in situ detection mode, cell or microorganism staining detection mode, etc.

5. The measurement system according to claim 4, characterized in that One or more carriers, each carrier being used to carry the same or different samples to be tested; One or more optical systems, wherein the optical systems are at least selected from a combination of a light source and a lens group; one or more detection systems for detecting optical signals; One or more fluid systems for providing a plurality of reagents for a detection reaction; One or more control systems, wherein the control system is used to control the switching of multiple detection modes or to detect multiple samples to be detected in multiple detection modes in parallel.

6. The measurement system according to claim 5, characterized in that The control system further comprises: a driving circuit coupled to the detection system to collect signal data generated by the sample to be detected, wherein the driving circuit is selectively coupled to mode parameters corresponding to an operating mode of the detection system, the mode parameters including at least a first mode control parameter corresponding to the sequencing mode and a second mode control parameter corresponding to the tissue sample dyeing mode; A mode switching circuit is coupled to the driving circuit to control the driving circuit based on the sample to be detected: when the sample carrier is a sequencing chip, the mode switching circuit associates a first set of mode parameters with the driving circuit, and when the sample carrier is a tissue sample carrier, the mode switching circuit associates a second set of mode control parameters with the driving circuit.

7. The measurement system according to claim 5, characterized in that The control system further comprises: A plurality of independent driving circuits, each of which is coupled to the detection system to collect signal data generated by the sample to be detected, and the plurality of driving circuits can be independently selectively coupled to mode parameters corresponding to the operating mode of the detection system, the mode parameters including at least a first mode control parameter corresponding to the sequencing mode, a second mode control parameter corresponding to the tissue sample staining mode, a third mode control parameter corresponding to the DNA or RNA in situ detection mode, and a fourth mode control parameter corresponding to the cell or microbial analysis and detection; A mode switching circuit is coupled to the driving circuit to control the driving circuit based on the sample to be detected: when the sample carrier is a sequencing chip, the mode switching circuit associates a first set of mode parameters with the driving circuit, and when the sample carrier is a tissue sample carrier, the mode switching circuit associates a second set of mode control parameters with the driving circuit.

8. The measurement system according to any one of claims 1 to 7, characterized in that The optical system further includes a bright field light source and an excitation light source.

9. The measurement system according to claim 1, wherein The sample to be detected includes a nucleic acid sequencing library, a biological tissue sample, a biological fluid sample, a microbial sample or a cell sample fixed on the sample slide.

10. The measurement system according to claim 9, characterized in that The optical system includes an objective lens; in the sequencing mode, the optical system scans the nucleic acid sequencing library through the objective lens and generates sequence information corresponding to the nucleic acid sequencing library; In the tissue sample dyeing mode, the optical system scans the biological tissue sample through the objective lens and generates an image corresponding to the biological tissue sample.

11. The measurement system according to claim 7, wherein The optical system includes an objective lens; in the DNA or RNA in situ detection mode, the optical system scans the biological sample through the objective lens and generates an in situ image of the DNA or RNA corresponding to the biological sample; in the cell or microorganism analysis mode, the optical system scans the cell or microorganism sample through the objective lens and generates image information corresponding to the detection target of the cell or microorganism sample.

12. A multi-mode detector, characterized in that: The multi-mode detector comprises the measurement system according to any one of claims 1-11.

13. A method for measuring multiple detection modes, characterized in that: The determination method comprises the following steps: Fix the sample to be tested on the stage; The detection mode is selected by the control system, including: Selecting a first detection mode, activating a first fluid system corresponding to the first detection mode, and controlling the sample to be detected to undergo a first detection reaction to generate a detectable first optical signal; and / or selecting a second detection mode, activating a second fluid system identical to the second detection mode, and controlling the sample to be detected to undergo a second detection reaction to generate a detectable second optical signal; detecting the first optical signal and / or the second optical signal and transmitting the signals to an analysis system; and The first optical signal and / or the second optical signal are analyzed to generate detection information and output a detection result.

14. The measuring method according to claim 13, characterized in that The first detection mode and the second detection mode are the same detection mode, or the first detection mode and the second detection mode are different detection modes.

15. The measuring method according to claim 14, characterized in that When the first detection mode and the second detection mode are different detection modes, the first detection reaction and the second detection reaction are different detection reactions.

16. The measuring method according to any one of claims 13 to 15, characterized in that The multiple detection modes are selected from nucleic acid sequence determination mode, tissue sample staining mode, DNA or RNA in situ detection mode, cell or microbial analysis mode, etc.

17. The measuring method according to any one of claims 13 to 16, characterized in that The multiple detection modes can be performed in parallel.

18. The measuring method according to claim 16, characterized in that The detection reaction corresponding to the nucleic acid sequence determination mode is a sequencing reaction, wherein the sequencing reaction is selected from synthesis sequencing reaction, ligation sequencing reaction, single molecule sequencing reaction, etc.; The detection reaction corresponding to the tissue sample staining mode is an affinity reaction, wherein the affinity reaction is selected from antigen-antibody, protein-aptamer, biotin-streptavidin, nucleotide-coupled antibody-fluorescent probe, etc. The detection reaction corresponding to the DNA or RNA in situ detection mode is a probe capture reaction, wherein the probe capture reaction is selected from probe-coupled fluorescence, probe ligation, probe amplification, etc., wherein the DNA or RNA can be selected from one of an in situ nucleic acid sample in a tissue sample, a liquid nucleic acid sample such as blood or body fluid, or an in situ nucleic acid sample inside a cell or microorganism; The detection reactions corresponding to the cell or microorganism analysis mode are surface antigen detection, biomarker detection, positive cell number ratio analysis, transcriptome or epigenetic analysis, etc.

19. The measuring method according to any one of claims 13 to 18, characterized in that The control system includes at least one processor and an interaction unit, wherein the processor and the interaction unit are coupled to the carrier and the fluid system. Input a first instruction, the first instruction including: initial information, the initial information including at least one of the type of sample to be tested, sequencing scheme, staining scheme, kit number, and confirmation information; controlling the fluid system to perform a first detection reaction according to the initial information; generating a first detection result based on the detection reaction; Control the interaction unit to feed back the first detection result.

20. The measuring method according to any one of claims 13 to 19, characterized in that The fixing of the sample to be tested on the carrier includes: mounting a plurality of slides on a plurality of carriers, further including: Mounting a first slide on the first stage; Mounting a second slide on the second stage; The first carrier plate and the second carrier plate are fixed with different sample types, or the first carrier plate and the second carrier plate are fixed with the same sample type.

21. The assay method according to claim 20, wherein An optical signal is collected using an optical system and a detection system, wherein the optical system includes a first optical link and a second optical link, and the measurement method includes: The relative position between the optical system and the stage is adjusted to align either the first carrier or the second carrier with either the first optical link or the second optical link.

22. A method for switching modes of a multi-detection mode measurement system, characterized in that: The mode switching method includes: Identify the type of sample to be tested; determining, based on the type of the sample to be detected, mode parameters selected to be coupled to the driving circuit; When the sample to be detected is a nucleic acid sequencing library, the mode switching circuit associates the first set of mode parameters with the driving circuit, and the driving circuit drives the optical module to enter the sequencing mode; when the sample to be detected is a biological tissue sample, a microbial sample or a cell sample, the mode switching circuit associates the second set of mode control parameters with the driving circuit, and the driving circuit drives the optical module to enter the fluorescence dyeing mode or a third mode different from the fluorescence dyeing mode and the measurement mode.

23. The switching method according to claim 22, wherein: The third mode is a bright field imaging mode.

24. The switching method according to claim 23, wherein: The optical system includes an excitation light source and a bright field light source; In the sequencing mode or the fluorescence staining mode, the excitation light source excites the sample to be detected to generate a fluorescence signal; In the bright field imaging mode, the bright field light source illuminates the sample to be detected to generate a bright field signal.

Images