Systems and methods for monitoring progress of a biological analysis

Abstract

A computer-implemented method for monitoring a biological analysis is provided. The method includes receiving image data of a first portion of a set of reaction sites and determining fluorescence from the image data. The method further includes displaying, on a user interface, a first graphical visualization of determined fluorescence in each reaction site of the first portion and receiving a selection of a subset of reaction sites from the set of reaction sites from a user. The method also includes displaying, on the user interface, in response to the selection, a graphical visualization of the subset of the set of reaction sites, where the graphical visualization of the subset includes an indication of progress of receiving image data in each reaction site of the subset and an indication of determined fluorescence of each reaction site in the subset.

Description

SYSTEMS AND METHODS FOR MONITORING PROGRESS OF A BIOLOGICAL ANALYSISCROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of priority of U.S. Provisional Patent Application No. 63 / 669,812, filed on July 11, 2024, which is incorporated herein in its entirety by reference.BACKGROUND

[0002] Often, in biological analyses, more efficient solutions are realized when a large amount of data is collected and analyzed. In analyzing genetic sequences, for example, microarrays are used to query hundreds or thousands of sequences simultaneously. Using microarrays, sample DNA with an attached fluorophore is hybridized to known genetic sequences attached to the microarray. The presence or absence of genetic sequences can be determined in the DNA samples with the presence or absence of fluorescence determined with imaging. As such, being able to investigate a large number of samples simultaneously is an advantage and can deliver an answer more quickly.

[0003] Further, to increase efficiency, case, and accuracy, automated instruments arc often used. In a genotyping instrument, for example, an automated biological analysis instrument integrates hybridization, washing, and imaging into a single instrument enabling high throughput and productivity. Processing of samples can be done without constant user intervention. However, with such a large amount of data, it is often challenging to manage, interpret, and analyze the data. It is also difficult for the user to easily confirm reliable processing of the sample as the instrument runs. Moreover, troubleshooting any errors could become overwhelming and time consuming.

[0004] As such, an instrument that allows a user to identify biological analysis status and progress is needed.SUMMARY

[0005] In one exemplary embodiment, a computer-implemented method for monitoring a biological analysis is provided. The method includes receiving image data of a first portion of a set of reaction sites and determining fluorescence from the image data. The method further includes displaying, on a user interface, a first graphical visualization of determined fluorescence in each reaction site of the first portion and receiving a selection of a subset of reaction sites from the set of reaction sites from a user. The method also includes displaying, on the user interface, in response to the selection, a graphical visualization of the subset of the set of reaction sites, where the graphical visualization of the subset includes an indication of progress of receiving image data in each reaction site of the subset and an indication of determined fluorescence of each reaction site in the subset.

[0006] In another exemplary embodiment, a system for monitoring progress of a biological analysis is provided. The system includes a detector configured to receive image data from each reaction site of a set of reaction sites and a memory configured to store the image data. The system further includes a processor configured to receive image data of a first portion of the set of reaction sites, determine fluorescence from the image data, and display, on a user interface, a first graphical visualization of determined fluorescence in each reaction site of the first portion. The processor is further configured to receive a selection of a subset of reaction sites from the set of reaction sites from a user, and display, on the user interface, in response to the selection, a graphical visualization of the subset of reaction sites, where the graphical visualization of the subset includes an indication of progress of receiving image data in each reaction site of the subset and an indication of determined fluorescence of each reaction site in the subset.

[0007] In yet another exemplary embodiment, a computer-readable medium encoded with computer-readable instructions is provided. The computer-readable instructions, which when executed by a processor of a computer, causes the computer to carry out method for monitoring a biological analysis. The method includes receiving image data of a first portion of a set of reaction sites and determining fluorescence from the image data. The method further includes displaying, on a user interface, a first graphical visualization of determined fluorescence in each reaction site of the first portion and receiving a selection of a subset of reaction sites from the setof reaction sites from a user. The method also includes displaying, on the user interface, in response to the selection, a graphical visualization of the subset of reaction sites, where the graphical visualization of the subset includes an indication of progress of receiving image data in each reaction site of the subset and an indication of determined fluorescence of each reaction site in the subset.DESCRIPTION OF THE FIGURES

[0008] FIG. 1 illustrates a flowchart showing a method of reducing spectral crosstalk in a multiplexed assay according to various embodiments described herein.

[0009] FIG. 2 is a block diagram that illustrates a genotyping instrument upon which embodiments of the present teachings may be implemented.

[0010] FIG. 3 depicts an exemplary optical system that may be used for imaging according to embodiments described herein.

[0011] FIG. 4 illustrates an exemplary computing system for implementing various embodiments described herein.

[0012] FIG. 5 illustrates an exemplary distributed network system according to various embodiments described herein.

[0013] FIG. 6 illustrates an example of a user interface for monitoring the progress of a genotyping analysis according to embodiments described herein.

[0014] FIG. 7 illustrates another example of a user interface for monitoring the progress of a genotyping analysis according to embodiments described herein.

[0015] FIG. 8 illustrates an example of a user interface for monitoring the progress of a genotyping analysis with controls to zoom into a portion of the analysis according to embodiments described herein.

[0016] FIG. 9 illustrates an example of a user interface displaying a zoomed view of a portion of a biological analysis according to embodiments described herein.

[0017] FIG. 10 illustrates an example user interface displaying another zoomed view of a portion of a biological analysis according to embodiments described herein.

[0018] FIG. 11 illustrates an example of a user interface displaying yet another zoomed view of a portion of a biological analysis according to embodiments described herein.

[0019] FIG. 12 illustrates an example of a user interface displaying yet another zoomed view of a portion of a biological analysis according to embodiments described herein.

[0020] FIG. 13 illustrates an example of a user interface for monitoring progress of each stage of a genotyping analysis according to embodiments described herein.

[0021] FIG. 14 illustrates another example of a user interface for monitoring progress of each stage of a genotyping analysis according to various embodiments described herein.

[0022] FIG. 15 illustrates another example of a user interface for monitoring progress of each stage of a genotyping analysis according to various embodiments described herein.

[0023] FIG. 16 illustrates an example of a user interface for monitoring multiple runs of a biological analysis according to various embodiments described herein.

[0024] FIG. 17 illustrates another example of a user interface for monitoring multiple runs according to various embodiments described herein.

[0025] FIGS. 18A-18C illustrate examples of a user interface showing different alerts of a biological analysis according to various embodiments described herein.DETAILED DESCRIPTION

[0026] To provide a more thorough understanding of the present invention, the following description sets forth numerous specific details, such as specific configurations, parameters, examples, and the like. It should be recognized, however, that such description is not intended as a limitation on the scope of the present invention but is intended to provide a better description of the exemplary embodiments.BIOLOGICAL ANALYSIS INSTRUMENTS

[0027] The present disclosure is directed to biological analysis instruments such as, for example, an automated genotyping instrument, and computer systems and computer software relating to systems and methods for increasing efficiency and usability of these biological analysis devices.

[0028] Previously, manual biological analyses were completed with a user completing every step. For genotyping, for example, a user would manually complete the hybridization step, and the washing steps. The user would then move the plates to another instrument to scan and image the plate to detect for fluorescence.

[0029] More recently, automated instruments integrating the processing steps have been used. Moreover, the throughput on the instruments have increased to collect even more data easily and efficiently. However, the user interface on these instruments did not provide clear indications of the status of a microarray plate while being processed leading to a user spending more time navigating to the right status screen and interpreting the data, especially if multiple microarray plates are being processed substantially simultaneously. Further, real-time troubleshooting was not as easily accomplished or even possible.

[0030] Thus, a user interface displaying indications for a user to easily identify status and progress during an automated analysis is needed.

[0031] FIG. 1 illustrates a flowchart showing a method of monitoring progress of a biological analysis. The method includes receiving image data of a first portion of a set of reaction sites in step 102. As described below, in accordance with various embodiments described herein, reaction sites may include, but are not limited to, wells, through-holes, indentations, spots, cavities, sample retainment regions, and reaction chambers, for example. A set of reaction sites may include one reaction site or a plurality of reaction sites.

[0032] In one embodiment, each reaction site has a known genetic sequence and a sample DNA may be hybridized to the known genetic sequence. According to various embodiments, an optical detector scans each reaction site capturing an image of each reaction site.

[0033] The method includes determining fluorescence from the image data in step 104. The presence of fluorescence in the image captured by the optical detector indicates the sample DNA hybridized to a known genetic sequence.

[0034] According to various embodiments of the present teachings, the method further includes displaying, on a user interface, a first graphical visualization of determined fluorescence in each reaction site of the first portion of the set of reaction sites in step 106. The first graphical visualization, according to various embodiments, shows a representation of the microarray plate, for example. If fluorescence is detected, an indication of successful detection is shown in the first graphical visualization. The indication may be a color or symbol or a combination of both a color and symbol. In this way, a user can easily identify the status of a reaction site.

[0035] The method further includes receiving, from a user, a selection of a subset of reaction sites from the set of reaction sites in step 108. Since there may be a lot of reaction sites, it may be difficult to view the progress and status of image scanning of individual reaction sites. Thus, a user may want to zoom into a certain portion, or subset, of reaction sites so they can view the subset of reaction sites in a larger view.

[0036] After the selection is received, the method includes displaying, on the user interface, in response to the selection, a graphical representation of the subset of the plurality of reaction sites, wherein the graphical visualization of the subset includes an indication of progress of receiving image data in reaction site of the subset in step 110. Step 110 also includes displaying an indication of determined fluorescence of each reaction site of each reaction site in the subset.SEQUENCING INSTRUMENTS

[0037] In various embodiments, nucleic acid sequence data can be generated using various techniques, platforms or technologies, including, but not limited to: hybridization-based systems, capillary electrophoresis, microarrays, ligation-based systems, polymerase-based systems, direct or indirect nucleotide identification systems, pyrosequencing, ion- or pH-based detection systems, electronic signature-based systems, fluorescent-based detection systems, single molecule methods, etc.

[0038] Various embodiments of genotyping platforms, such as a nucleic acid sequencer, can include components as displayed in the block diagram of FIG. 2. Various embodiments of biological analysis instrument 200 can provide for automated sequencing that can be used to gather sequence information from a plurality of sequences in parallel, such as substantially simultaneously. In various embodiments, biological analysis instrument 200 can determine the sequence of a nucleic acid, such as a polynucleotide or an oligonucleotide. The nucleic acid can include DNA or RNA, and can be single stranded, such as ssDNA and RNA, or double stranded, such as dsDNA or a RNA / cDNA pair. In various embodiments, the nucleic acid can include or be derived from a fragment library, a mate pair library, a ChIP fragment, or the like. In particular embodiments, biological analysis instrument 200 can obtain the sequence information from a single nucleic acid molecule or from a group of substantially identical nucleic acid molecules.

[0039] According to various embodiments, biological analysis instrument 200 can include a control system 202. Control system 202 controls fluidic delivery from fluidic systems 208 to samples 204. Fluidic systems 208 may include a reagent reservoir for storing reagents. The reagents can include RNA-based primers, forward / reverse DNA primers, oligonucleotide mixtures for ligation sequencing, nucleotide mixtures for sequencing-by- synthesis, optional ECC oligonucleotide mixtures, buffers, wash reagents, blocking reagent, stripping reagents, and the like. Fluidic systems 208 are used for hybridization and wash sequences. Further, heating and cooling elements 206 are used in the hybridization step of samples 204 according to various embodiments.

[0040] In various embodiments, samples 204 may be in reactions sites within a sample holder. A sample holder may be, according to various embodiments described herein, an array plate, a microarray, a flow cell, a substrate, a multi-well tray, such as a standard microtiter 96- well, a 384-well plate, a 24-well plate, or a microcard, or a substantially planar support, such as a glass or plastic slide or a silicon chip, or the like. Further, according to various embodiments described herein, reaction sites may include, but are not limited to, wells, through-holes, indentations, spots, cavities, sample retainment regions, and reaction chambers, for example. Samples 204 may be included in multiple lanes, multiple channels, multiple wells, or other means of processing multiple sample sets substantially simultaneously.

[0041] Optical system 210 scans each reaction site to generate an image that is analyzed for fluorescence. Optical system 210 includes an optical sensor, such as an imaging or detection sensor. For example, the imaging or detection sensor can include a CCD, a CMOS, an ion sensor, such as an ion sensitive layer overlying a CMOS, a current detector, or the like. Optical system 210 is further described below with reference to FIG. 3.

[0042] According to various embodiments, control system 202 controls various elements of biological analysis instrument 200. For example, control system 202 controls heat / cool elements 206 in conjunction with fluidic systems 208 to perform some processing steps of the biological analysis. Further, control system 202 controls optical system 210. Control system 202 may be accessible to an end user through user interface 212 of biological analysis instrument 200.According to various embodiments, control system 202 includes a computer system, as depicted in FIG. 4, which provides the control the function biological analysis instrument 200, as well as the user interface 212. Control system 202 may provide data processing, display and report preparation functions. All such instrument control functions may be dedicated locally to the biological analysis instrument 200, or control system 202 may be pail of a more remote distributed system as depicted in FIG. 5 in various embodiments.

[0043] As mentioned above, user interface 212 may provide user access to control system 202. Further, user interface 212 displays data collected in useful and in an easily to digest manner according to embodiments of the present teachings. User interface 212 may be local to biological analysis instrument 200 in some embodiments. In other embodiments, user interface 212 may be remote to biological analysis instrument 200 and be connected to a distributed network.OPTICAL SYSTEM FOR IMAGING

[0044] FIG. 3 illustrates a block diagram of an inverted general fluorescent optical system configuration. An inverted system is favorable for some sample types, such as large and thick samples.

[0045] Reaction site on sample holder 302 is being imaged for fluorescent emission light. Light from light source 304 includes a plurality of wavelengths of light. Light from light source 304 passes through excitation filter 306, which is designed to transmit a certain bandwidth oflight for excitation of a fluorescent dye. The transmitted light is reflected upward by dichroic filter 308. The reflected light then passes through objective lens 310 to direct the reflected light to sample holder 302. A plurality of reaction sites may be included in sample holder 302. Sample holder 302 may be immersed in a fluid (not shown). In accordance with various embodiments described herein, reaction sites may include, but are not limited to, through-holes, wells, indentations, spots, cavities, sample retainment regions, and reaction chambers, for example.

[0046] Any fluorescent emission light from sample holder 302 then passes through objective lens 310 and dichroic filter 308. Emission filter 312 is designed to transmit the expected fluorescent emission bandwidth through tube lens 314 and reflected by mirror 318 to optical detector 316. Optical detector 316 generates an image of a reaction site on sample holder 302 and fluorescent emission intensity can be determined.

[0047] The following descriptions of various implementations of the present teachings have been presented for purposes of illustration and description. It is not exhaustive and does not limit the present teachings to the precise form disclosed. Modifications and variations are possible in light of the above teachings or may be acquired from practicing of the present teachings.COMPUTING SYSTEM

[0048] Additionally, the described implementation includes software, but the present teachings may be implemented as a combination of hardware and software or in hardware alone. The present teachings may be implemented with both object-oriented and non-object-oriented programming systems.

[0049] FIG. 4 is a block diagram that illustrates a computer system 400 that may be employed to carry out processing functionality, according to various embodiments. Instruments to perform experiments may be connected to the exemplary computing system 400. Computing system 400 can include one or more processors, such as a processor 404. Processor 404 can be implemented using a general or special purpose processing engine such as, for example, amicroprocessor, controller or other control logic. In this example, processor 404 is connected to a bus 402 or other communication medium.

[0050] Further, it should be appreciated that computing system 400 of FIG. 4 may be embodied in any of a number of forms, such as a rack-mounted computer, mainframe, supercomputer, server, client, a desktop computer, a laptop computer, a tablet computer, handheld computing device (e.g., PDA, cell phone, smart phone, palmtop, etc.), cluster grid, netbook, embedded systems, or any other type of special or general purpose computing device as may be desirable or appropriate for a given application or environment. Additionally, computing system 400 can include a conventional network system including a client / server environment and one or more database servers, or integration with LIS / LIMS infrastructure. A number of conventional network systems, including a local area network (LAN) or a wide area network (WAN), and including wireless and / or wired components, are known in the art. Additionally, client / server environments, database servers, and networks arc well documented in the art. According to various embodiments described herein, computing system 400 may be configured to connect to one or more servers in a distributed network. Computing system 400 may receive information or updates from the distributed network. Computing system 400 may also transmit information to be stored within the distributed network that may be accessed by other clients connected to the distributed network.

[0051] Computing system 400 may include bus 402 or other communication mechanism for communicating information, and processor 404 coupled with bus 402 for processing information.

[0052] Computing system 400 also includes a memory 406, which can be a random access memory (RAM) or other dynamic memory, coupled to bus 402 for storing instructions to be executed by processor 404. Memory 406 also may be used for storing temporary variables or other intermediate information during execution of instructions to be executed by processor 404. Computing system 400 further includes a read only memory (ROM) 408 or other static storage device coupled to bus 402 for storing static information and instructions for processor 404.

[0053] Computing system 400 may also include a storage device 410, such as a magnetic disk, optical disk, or solid state drive (SSD) is provided and coupled to bus 402 for storing information and instructions. Storage device 410 may include a media drive and a removablestorage interface. A media drive may include a drive or other mechanism to support fixed or removable storage media, such as a hard disk drive, a floppy disk drive, a magnetic tape drive, an optical disk drive, a CD or DVD drive (R or RW), flash drive, or other removable or fixed media drive. As these examples illustrate, the storage media may include a computer-readable storage medium having stored therein particular computer software, instructions, or data.

[0054] In alternative embodiments, storage device 410 may include other similar instrumentalities for allowing computer programs or other instructions or data to be loaded into computing system 400. Such instrumentalities may include, for example, a removable storage unit and an interface, such as a program cartridge and cartridge interface, a removable memory (for example, a flash memory or other removable memory module) and memory slot, and other removable storage units and interfaces that allow software and data to be transferred from the storage device 410 to computing system 400.

[0055] Computing system 400 can also include a communications interface 418. Communications interface 418 can be used to allow software and data to be transferred between computing system 400 and external devices. Examples of communications interface 418 can include a modem, a network interface (such as an Ethernet or other NIC card), a communications port (such as for example, a USB port, a RS-232C serial port), a PCMCIA slot and card, Bluetooth, etc. Software and data transferred via communications interface 418 are in the form of signals which can be electronic, electromagnetic, optical or other signals capable of being received by communications interface 418. These signals may be transmitted and received by communications interface 418 via a channel such as a wireless medium, wire or cable, fiber optics, or other communications medium. Some examples of a channel include a phone line, a cellular phone link, an RF link, a network interface, a local or wide area network, and other communications channels.

[0056] Computing system 400 may be coupled via bus 402 to a display 412, such as a cathode ray tube (CRT) or liquid crystal display (LCD), for displaying information to a computer user. An input device 414, including alphanumeric and other keys, is coupled to bus 402 for communicating information and command selections to processor 404, for example. An input device may also be a display, such as an LCD display, configured with touchscreen inputcapabilities. Another type of user input device is cursor control 416, such as a mouse, a trackball or cursor direction keys for communicating direction information and command selections to processor 404 and for controlling cursor movement on display 412. This input device typically has two degrees of freedom in two axes, a first axis (e.g., x) and a second axis (e.g., y), that allows the device to specify positions in a plane. Computing system 400 provides data processing and provides a level of confidence for such data. Consistent with certain implementations of embodiments of the present teachings, data processing and confidence values are provided by computing system 400 in response to processor 404 executing one or more sequences of one or more instructions contained in memory 406. Such instructions may be read into memory 406 from another computer-readable medium, such as storage device 410. Execution of the sequences of instructions contained in memory 406 causes processor 404 to perform the process states described herein. Alternatively, hard-wired circuitry may be used in place of or in combination with software instructions to implement embodiments of the present teachings. Thus, implementations of embodiments of the present teachings are not limited to any specific combination of hardware circuitry and software.

[0057] The term "computer-readable medium" and “computer program product” as used herein generally refers to any media that is involved in providing one or more sequences or one or more instructions to processor 404 for execution. Such instructions, generally referred to as “computer program code” (which may be grouped in the form of computer programs or other groupings), when executed, enable the computing system 400 to perform features or functions of embodiments of the present invention. These and other forms of non-transitory computer- readable media may take many forms, including but not limited to, non-volatile media, volatile media, and transmission media. Non-volatile media includes, for example, solid state, optical or magnetic disks, such as storage device 410. Volatile media includes dynamic memory, such as memory 406. Transmission media includes coaxial cables, copper wire, and fiber optics, including the wires that comprise bus 402.

[0058] Common forms of computer-readable media include, for example, a floppy disk, a flexible disk, hard disk, magnetic tape, or any other magnetic medium, a CD-ROM, any other optical medium, punch cards, paper tape, any other physical medium with patterns of holes, aRAM, PROM, and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave as described hereinafter, or any other medium from which a computer can read.

[0059] Various forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to processor 404 for execution. For example, the instructions may initially be carried on magnetic disk of a remote computer. The remote computer can load the instructions into its dynamic memory and send the instructions over a telephone line using a modem. A modem local to computing system 400 can receive the data on the telephone line and use an infra-red transmitter to convert the data to an infra-red signal. An infra-red detector coupled to bus 402 can receive the data carried in the infra-red signal and place the data on bus 402. Bus 402 carries the data to memory 406, from which processor 404 retrieves and executes the instructions. The instructions received by memory 406 may optionally be stored on storage device 410 either before or after execution by processor 404.

[0060] It will be appreciated that, for clarity purposes, the above description has described embodiments of the invention with reference to different functional units and processors.However, it will be apparent that any suitable distribution of functionality between different functional units, processors or domains may be used without detracting from the invention. For example, functionality illustrated to be performed by separate processors or controllers may be performed by the same processor or controller. Hence, references to specific functional units are only to be seen as references to suitable means for providing the described functionality, rather than indicative of a strict logical or physical structure or organization.DISTRIBUTED SYSTEM

[0061] Some of the elements of a typical Internet network configuration 500 are shown in FIG. 5, where a number of client machines 502 possibly in a remote local office, are shown connected to a gateway / hub / tunnel-server / etc. 510 which is itself connected to the internet 508 via some internet service provider (ISP) connection 510. Also shown are other possible clients 512 similarly connected to the internet 508 via an ISP connection 514, with these units communicating to possibly a central lab or office, for example, via an ISP connection 516 to a gateway / tunnel-server 518 which is connected 520 to various enterprise application servers 522 which could be connected through another hub / router 526 to various local clients 530. Any ofthese servers 522 could function as a development server for the analysis of potential content management and delivery design solutions as described in the present invention, as more fully described below.USER INTERFACE FOR MONITORING IMAGING PROGRESS

[0062] As mentioned above, a user interface may allow a user to control the biological analysis instrument, and also display data collected from the analysis. According to various embodiments, data may be displayed in a clear and simple manner to allow the user to interpret and infer information. According to various embodiments described herein, different visual indications, such as different colors, patterns, symbols, icons, and the like, may be used on a user interface to convey information quickly and easily to a user. Navigating results for a large number of reaction sites makes it difficult to digest information quickly. Further, real-time interpretation of some results and being able to continually monitor a run may increase efficiency. For example, if errors on a microarray are noticed earlier, during a run, a user may be able to stop a run and troubleshoot the problem, saving time and resources.

[0063] FIG. 6 illustrates an exemplary user interface 600 showing the progress of an imaging scan in a genotyping analysis according to various embodiments described herein. Various embodiments may include other platforms or technologies, including, but not limited to: hybridization-based systems, capillary electrophoresis, microarrays, ligation-based systems, polymerase-based systems, direct or indirect nucleotide identification systems, pyro sequencing, ion- or pH-based detection systems, electronic signature-based systems, fluorescent-based detection systems, single molecule methods, for example.

[0064] In this example, a set of reaction sites is depicted in a graphical visualization of a grid of squares. Each square represents a reaction site. In accordance with various embodiments described herein, reaction sites may include, but are not limited to, wells, through-holes, indentations, spots, cavities, sample retainment regions, and reaction chambers, and the like.

[0065] Imaging progress for each reaction site may be easily viewed by a user. As an optical detector scans each reaction site and the processor determines whether an image is successfully generated, the results are displayed on the user interface according to variousembodiments of the present teachings. According to various embodiments described herein, color and / or symbols arc used so a user may easily decipher an imaging result of a reaction site. In this way, a user is able to see the progress of the imaging scan. Some statuses that may be indicated on the graphic visualization of the reaction sites are: scan scheduled, in progress, successful, failed, and no scan, for example.

[0066] In this example, reaction sites where an image has been completed is shown with a green color and a check mark symbol, such as reaction site 604. Other colors and / or symbols may also be used to indicate a successful scan and detection according to various embodiments described herein.

[0067] In the same example, a reaction site where an image has not been completed is shown in an orange color and with a warning symbol, indicating a failed result, such as reaction site 606. Further, progress of image scanning can be determined from user interface 600. A subset 602 of reaction sites are indicated as complete since the color and symbols differ than reaction sites where the image scan is still scheduled to be completed, such as reaction site 612. Moreover, the reaction site where image scanning is currently being done is also indicated by a different color and symbol, such as reaction site 610. An estimated time for completion 614 is also shown on user interface 600. As mentioned previously, the status of a reaction site may be shown by a single visual indication, or a combination of two or more visual indications.

[0068] In other embodiments, successful fluorescent detection determined from a computing system from an image may be displayed on a user interface so that the result is easily viewed by a user. After an optical detector scans each reaction site, the images are analyzed, and fluorescent emissions are detected by a processor. Fluorescent detection results may be displayed on a user interface on a graphical visualization of the reaction sites with a visual indication such as color and / or symbols. For example, if fluorescent detection is detected, the reaction site on a graphical visualization may be shown in a green color. Similarly, if fluorescent detection is not detected, the reaction site on the graphical visualization may be shown in an orange color. It should be appreciated that any combination of a visual indicator, such as colors and symbols, may be used.

[0069] FIG. 7 illustrates another example of a user interface 700 according to various embodiments of the present teachings. A graphical visualization of the set of reaction sites shows more reaction sites as than the example from FIG. 6. Similar to FIG. 6, successfully scanned reaction sites, such as reaction site 704, failed scanned reaction sites, such as reaction site 706, and a reaction that is currently being scanned, such as reaction 710, is displayed on user interface 700. Moreover, an estimated time remaining, and the scan end time is also displayed. A user will be able to ascertain the quality of this run as well as understand how long the entire biological analysis run will take.

[0070] With a large number of reaction sites, such as shown in user interface 700, a zoomed view of a portion of the reaction sites would be useful. FIG. 8 illustrates an example of a user interface for monitoring the progress of a genotyping analysis with controls to zoom into a portion of the analysis according to embodiments described herein. According to various embodiments, user interface 700 may also be displayed on a touchscreen. As such, other methods of zooming via the touchscreen may also be used to evaluate a smaller portion of the set of reaction sites included in the run. Finger gestures, zoom in and zoom out buttons, a zooming scrollbar, a zooming dial, selection a predetermined subset of reaction sites, manual selection of a subset of reaction sites, and the like, may be implemented on a touchscreen display in some embodiments. In other embodiments, methods of zooming included those listed above, may be implemented on a non-touchscreen display. The graphical representation may change in response to a selection of a subset of reaction sites according to various embodiments described herein.

[0071] In exemplary user interface 800, a user may use the navigator zoom control 816. A user may choose the subset of reaction sites to view using navigator zoom control 816. Another graphical visualization of the set of reaction sites is viewed. After viewing the large number of reaction sites, a user may select the desired subset of reaction sites they would like to zoom into.

[0072] In this embodiment, predetermined subsets of the reaction sites are available selections. The predetermined subsets are fourths of the set of reaction sites. In other embodiments, a user may manually select which portions of the reaction sites are displayed. The user may select which subset of reaction sites by being able to select the area of the graphicalvisualization of set of reaction sites they would like to view. In this example, a user selected to view the whole set of reaction sites by selecting the whole set option 820.

[0073] With reference to FIG. 9, a user has selected the upper left quadrant of the set of reaction sites in subset option 920. The subset selected in subset option 920 is also shown in the navigator zoom view as subset 916. In this way, a user is able to more easily see if the selected subset includes the reaction sites the user is interested in seeing.

[0074] The graphical visualization of the selected subset of reaction sites 902 is now displayed on user interface 900.

[0075] Similar to the view in FIG. 9, FIG. 10 shows a user has selected option 1020 to view the upper right quadrant of the set of reaction sites. The subset selection 1016 is viewed in the navigator zoom control. Further, in response to the user selection of the subset of reaction sites 1020, graphical visualization 1002 dynamically changes to the upper right quadrant of the set of reaction sites included in the biological analysis run.

[0076] In FIG. 11, user interface 1100 shows a zoomed subset of the set of reaction sites that have not been imaged yet 1102. A user selected the lower left quadrant option 1120 to view a portion of the reaction sites that have not been imaged. The lower left quadrant subset 11 16 is also viewed in the navigator zoom control.

[0077] Similarly, in FIG. 12, lower right quadrant option 1220 is selected to view a portion of reaction sites that have not been imaged. Graphical visualization 1202 illustrates the selected subset of reaction sites. The selected subset 1216 is also viewed in the navigator zoom control.USER INTERFACE FOR MONITORING RUN

[0078] A user may also want to easily view overall progress of a whole analysis. FIGS. 13- 15 show user interfaces for monitoring progress of each stage of a genotyping analysis according to embodiments described herein.

[0079] FIG. 13 illustrates another example of a user interface for monitoring progress of each stage of a genotyping analysis according to various embodiments described herein. FIG. 13 illustrates time dial 1302. Time dial 1302 is a visual indication of time progressing. Progressring 1310 of time dial 1302 shows the elapsed time and gives an indication of the percentage of completion of a biological analysis run according to embodiments described herein. Progress ring 1310 may show the level of completion with a color or other visual indicator. Further, spinning ring 1312 of time dial 1302 indicates that the run is in progress. Time dial 1302 uses visual indicators such as text, color, icons, and animation, for example, to show progress and amount of progress of a biological analysis run, according to various embodiments of the present teachings.

[0080] Time dial 1302 also includes the time left in the run and temperature of the samples. The time may be displayed as a timer with hours and minutes or hours, minutes, and seconds, for example. Icons 1304, 1306, and 1308 represent stages of analysis and progress of each stage. Icon 1304 represents hybridization stage and the progress is illustrated with a colored progress ring. In this example, the wash stage and scan stage have not started. Hybridization icon 1304 indicates 25% of the hybridization stage is complete.

[0081] FIG. 14 illustrates another example of a run progress user interface 1400. Time dial 1402 indicates the run is complete. Time dial 1402 shows completion by changing a color and no longer displaying a completion time. Progress ring 1410 shows a fully completed ring, indicating the run is fully completed. Spinning ring 1412 may also show a solid non-spinning animation to indicate a ran is no longer in progress. Further, icons 1404, 1406, and 1408, representing the hybridization stage, the wash stage, and the scan stage, respectively, indicate completion with colored progress rings. The progress rings of each icon, 1404, 1406, and 1408, are completed in a color indicating the hybridization stage, wash stage, and scan stage are 100% complete.

[0082] FIG. 15 depicts time dial 1502 indicating to a user that it is time to unload the sample plate. Similar to FIG 14, progress ring 1510 shows the run is 100% completed, and spinning ring 1512 is a solid color to show there is no active scanning of the reaction sites. Further, icons 1504, 1506, and 1508, representing the hybridization stage, the wash stage, and the scan stage, respectively, indicate completion with colored progress rings. The progress rings are completed in a color indicating the hybridization stage, wash stage, and scan stage are 100% complete.

[0083] As mentioned above, multiple runs may also be run for one analysis. According to various embodiments described herein, a user interface that displays progress information for each biological analysis run in a multiple biological run analysis allows for a user to quickly understand the progress of each run.

[0084] The multiple runs may be run at a later time or substantially simultaneously. A user is able to easily navigate between information for different runs in user interface 1600.Furthermore, user interface 1600 shows the progress of each run in one place. User interface 1600 may also show the instrument status. In the example depicted in FIG. 16, a first run 1702 is shown and the progress of the run is shown in icons 1604, 1606, and 1608, representing the hybridization stage, the wash stage, and the scan stage, respectively. By looking at icon 1604, a user is able to quickly determine that the hybridization stage is not fully complete. Icon 1606 and icon 1608 both indicate that those stages have not started. From user interface 1600, a user may also see that second run 1610 also has not started.

[0085] FIG. 17 illustrates another solution for a user interface to monitor multiple runs according to various embodiments described herein. It is easily seen run 1702 has not started. Runs 1706 and 1708 are complete. The colored progress rings are all fully completed indicating each stage has been completed. Run 1704 shows hybridization and wash stages are not complete.

[0086] In various embodiments described herein, users may need to be aware of high-priority alerts to make important time-sensitive actions. Various user interfaces may present these alerts in a prominent manner so that the alert is noticed by a user. A user interface, according to various embodiments, provides the relevant information to the user and may indicate any potential problem or loss of information associated with the problem or potential action taken by the user. Different types of alerts may be displayed differently to a user. For example, important alerts, note alerts, and tip alerts, may be displayed with different visual indications, such as color or symbols, for a user to easily determine the importance of an alert.

[0087] Additionally, in some embodiments, the color of the user interface may also coordinate to the color of a LED indicator light on the biological analysis instrument. In this way, a user may be able to easily notice the LED indicator light and understand the type of alertbefore looking more closely at the user interface. Tn some embodiments, the LED indicator light is integrated near the user interface. This is another way a user is able to quickly identify an issue.

[0088] In some embodiments, if a certain color is used to indicate success of a process, both the LED indicator light on the biological analysis instrument and the color of the visible user interface may be that certain color to quickly indicate to a user success of the process. Similarly, in some examples, another color may indicate failure, or another color may indicate user attention is needed. The LED indicator light and the user interface may be presented in those previously determined colors so a user is able to easily recognize the issue.

[0089] For example, with reference to FIGS. 18A-18C, user interface 1800 is a green color. A LED indicator light may also be green. Similarly, user interface 1810 is a blue color and may have a blue LED indicator light on the biological analysis instrument. The orange color of user interface 1820 may also cause an LED indicator light to be orange.

[0090] FIG. 18A illustrates an exemplary user interface 1800 for an important alert related to the biological analysis instrument. Further, user interface 1800 may also include action buttons for a user to easily select an action based on the important alert. Visual indications such as colors and symbols are used to help a user quickly see and understand the alert.

[0091] In the example of FIG. 18 A, user interface 1800 with a green color indicates the plate is securely clamped in a biological analysis instrument. A corresponding green LED indicator light may also visible on the biological analysis instrument to indicate this message. Further, on user interface 1800, an action button 1802 for a user to indicate acknowledgement of the message is displayed. After a user selects action button 1802, the biological analysis instrument may continue the run.

[0092] Similarly, in the example depicted in FIG. 18B, user interface 1810 indicates an important message that a USB drive needs to be inserted. User interface 1810 includes action button 1804 to cancel the alert, and action button 1806 to try again to determine if a USB drive is inserted. In this example, user interface 1910 displays a blue color. A corresponding blue LED indicator light may be included on the biological analysis instrument so a user may easilyunderstand what the status is of the biological analysis instrument and may also notice the alert more quickly.

[0093] FIG. 18C shows a warning alert on user interface 1820. A warning may indicate that there is an issue that must be corrected before the run can continue or that there is a problem with the run. Actions associated with the warning alert are also displayed for a user to easily make a decision on the subsequent actions that a user can take.

[0094] As an example, FIG. 18C depicts user interface 1820 indicating a warning that the system was not shut down properly. Action button 1808 is also displayed on user interface 1820 for a user to select for acknowledging the warning. Further, an orange color is used on user interface 1820. Similar to the examples shown in FIG. 18A and FIG. 18B, an orange LED indicator light may be visible to a user on biological analysis instrument so a user may quickly notice the warning alert. The color also can give an indication of what the status is of the biological analysis instrument.

[0095] As an example, an error message displayed on a user interface and a corresponding LED indicator light may indicate an error. In various embodiments according to the present teachings, an orange color user interface and an orange LED indicator light may indicate an error. Examples of other indicators on the user interface and LED indicator light may include: a white color to indicate no plates arc in the biological analysis instrument, a blue light to indicate plates are in the biological analysis instrument, and an amber color to indicate an error that must be corrected to continue the analysis. LED indicator lights may be a solid or flashing light for different indications.Examples

[0096] The following numbered examples are embodiments:1. A computer-implemented method for monitoring a biological analysis, the method comprising: receiving image data of a first portion of a set of reaction sites; determining fluorescence from the image data;displaying, on a user interface, a first graphical visualization of determined fluorescence in each reaction site of the first portion; receiving a selection of a subset of reaction sites from the set of reaction sites from a user; and displaying, on the user interface, in response to the selection, a graphical visualization of the subset of the set of reaction sites, wherein the graphical visualization of the subset includes an indication of progress of receiving image data in each reaction site of the subset and an indication of determined fluorescence of each reaction site in the subset.2. The computer-implemented method of example 1, further comprising: receiving image data, during the image scan time, of a second portion of the first set of reaction sites; determining fluorescence from the image data; and displaying, on a user interface, an updated graphical visualization of determined fluorescence in each reaction site of the first portion and the second portion.3. The computer- implemented method of any one of the examples 1 to 2, further comprising: receiving a second set of image data from each reaction site of a second set of reaction sites; and displaying, on the user interface, a second graphical visualization of determined fluorescence in each reaction site of the second set.4. The computer-implemented method of any one of the examples 1 to 3, wherein the indication of progress is a color.5. The computer- implemented method of any one of the examples 1 to 4, wherein the indication of determination of fluorescence is a symbol.6. The computer-implemented method of any one of the examples 1 to 5, wherein the indication of determination of fluorescence indicates hybridization success.7. The computer-implemented method of any one of the examples 1 to 6, further comprising: calculating an estimated time of completion of receiving image data for the set of reaction sites in the first set; and displaying the estimated time of completion on the user interface.8. The computer-implemented method of any one of the examples 1 to 7, further comprising: receiving biological analysis parameters for a set of reaction sites at a processor; and displaying the progress of completion of the biological analysis parameters on the user interface.9. The computer-implemented method of example 8, wherein the biological analysis parameters include hybridization time, wash time, and scan time.10. A system for monitoring progress of a biological analysis, the system comprising: a detector configured to receive image data from each reaction site of a set of reaction sites; a memory configured to store the image data; and a processor configured to: receive image data of a first portion of the set of reaction sites; determine fluorescence from the image data; display, on a user interface, a first graphical visualization of determined fluorescence in each reaction site of the first portion;receive a selection of a subset of reaction sites from the set of reaction sites from a user; and display, on the user interface, in response to the selection, a graphical visualization of the subset of the reaction sites, wherein the graphical visualization of the subset includes an indication of progress of receiving image data in each reaction site of the subset and an indication of determined fluorescence of each reaction site in the subset.11. The system of example 10, wherein the processor is further configured to: receive image data, during the image scan time, of a second portion of the first set of reaction sites; determine fluorescence from the image data; and display, on a user interface, an updated graphical visualization of determined fluorescence in each reaction site of the first portion and the second portion.12. The system of any one of the examples 10 to 11, wherein the processor is further configured to: receive a second set of image data from each reaction site of a second set of reaction sites; and display, on the user interface, a second graphical visualization of determined fluorescence in each reaction site of the second set.13. The system of any one of the examples 10 to 12, wherein the indication of progress is a color.14. The system of any one of the examples 10 to 13, wherein the indication of determination of fluorescence is a symbol.15. The system of any one of the examples 10 to 14, wherein the indication of determination of fluorescence indicates hybridization success.16. The system of any one of the examples 10 to 15, wherein the processor is further configured to: calculate an estimated time of completion of receiving image data for the reaction sites included in the set of reaction sites; and display the estimated time of completion on the user interface.17. The system of any one of the examples 10 to 16, wherein the processor is further configured to: receive biological analysis parameters for the set of reaction sites at a processor; and display the progress of completion of the biological analysis parameters on the user interface.18. The system of example 17, wherein the biological analysis parameters include hybridization time, wash time, and scan time.19. A computer-readable medium encoded with computer-readable instructions, which when executed by a processor of a computer, causes the computer to carry out the method of any one of the examples 1 to 9.20. A system comprising a processor, and a storage medium storing instruction, which when executed by a processor, causes the system to carry out the method of any one of examples 1 to 9.

[0097] Although the present invention has been described with respect to certain exemplary embodiments, examples, and applications, it will be apparent to those skilled in the art that various modifications and changes may be made without departing from the invention.

Claims

CLAIMSWhat is claimed is:

1. A computer-implemented method for monitoring a biological analysis, the method comprising: receiving image data of a first portion of a set of reaction sites; determining fluorescence from the image data; displaying, on a user interface, a first graphical visualization of determined fluorescence in each reaction site of the first portion; receiving a selection of a subset of reaction sites from the set of reaction sites from a user; and displaying, on the user interface, in response to the selection, a graphical visualization of the subset of the set of reaction sites, wherein the graphical visualization of the subset includes an indication of progress of receiving image data in each reaction site of the subset and an indication of determined fluorescence of each reaction site in the subset.

2. The computer-implemented method of claim 1, further comprising: receiving image data, during the image scan time, of a second portion of the first set of reaction sites; determining fluorescence from the image data; and displaying, on a user interface, an updated graphical visualization of determined fluorescence in each reaction site of the first portion and the second portion.

3. The computer- implemented method of any one of the claims 1 to 2, further comprising: receiving a second set of image data from each reaction site of a second set of reaction sites; and displaying, on the user interface, a second graphical visualization of determined fluorescence in each reaction site of the second set.

4. The computer-implemented method of any one of the claims 1 to 3, wherein the indication of progress is a color.

5. The computer-implemented method of any one of the claims 1 to 4, wherein the indication of determination of fluorescence is a symbol.

6. The computer- implemented method of any one of the claims 1 to 5, wherein the indication of determination of fluorescence indicates hybridization success.

7. The computer- implemented method of any one of the claims 1 to 6, further comprising: calculating an estimated time of completion of receiving image data for the set of reaction sites in the first set; and displaying the estimated time of completion on the user interface.

8. The computer- implemented method of any one of the claims 1 to 7, further comprising: receiving biological analysis parameters for a set of reaction sites at a processor; and displaying the progress of completion of the biological analysis parameters on the user interface.

9. The computer-implemented method of claim 8, wherein the biological analysis parameters include hybridization time, wash time, and scan time.

10. A system for monitoring progress of a biological analysis, the system comprising: a detector configured to receive image data from each reaction site of a set of reaction sites; a memory configured to store the image data; and a processor configured to: receive image data of a first portion of the set of reaction sites; determine fluorescence from the image data;display, on a user interface, a first graphical visualization of determined fluorescence in each reaction site of the first portion; receive a selection of a subset of reaction sites from the set of reaction sites from a user; and display, on the user interface, in response to the selection, a graphical visualization of the subset of the reaction sites, wherein the graphical visualization of the subset includes an indication of progress of receiving image data in each reaction site of the subset and an indication of determined fluorescence of each reaction site in the subset.

11. The system of claim 10, wherein the processor is further configured to: receive image data, during the image scan time, of a second portion of the first set of reaction sites; determine fluorescence from the image data; and display, on a user interface, an updated graphical visualization of determined fluorescence in each reaction site of the first portion and the second portion.

12. The system of any one of the claims 10 to 11, wherein the processor is further configured to: receive a second set of image data from each reaction site of a second set of reaction sites; and display, on the user interface, a second graphical visualization of determined fluorescence in each reaction site of the second set.

13. The system of any one of the claims 10 to 12, wherein the indication of progress is a color.

14. The system of any one of the claims 10 to 13, wherein the indication of determination of fluorescence is a symbol.

15. The system of any one of the claims 10 to 14, wherein the indication of determination of fluorescence indicates hybridization success.

16. The system of any one of the claims 10 to 15, wherein the processor is further configured to: calculate an estimated time of completion of receiving image data for the reaction sites included in the set of reaction sites; and display the estimated time of completion on the user interface.

17. The system of any one of the claims 10 to 16, wherein the processor is further configured to: receive biological analysis parameters for the set of reaction sites at a processor; and display the progress of completion of the biological analysis parameters on the user interface.

18. The system of claim 17, wherein the biological analysis parameters include hybridization time, wash time, and scan time.

19. A computer-readable medium encoded with computer-readable instructions, which when executed by a processor of a computer, causes the computer to carry out the method of any one of the claims 1 to 9.

20. A system comprising a processor, and a storage medium storing instruction, which when executed by a processor, causes the system to carry out the method of any one of claims 1 to 9.

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