High-throughput analysis unit

Abstract

The present disclosure relates to a screening system configured to identify biological agents, biological variances, pathogens, and / or genetic variances. The screening system may include an incubation zone having an incubation station for incubating multiple samples and a detector for detecting electromagnetic radiation emitted simultaneously or quasi-simultaneously from the multiple samples. The screening system may also include an optional, replaceable incubator unit housed within the incubation station. The incubation station may also include an optically based datum system used as a reference point for orienting an image of the incubation station captured by the detector and, optionally, for assisting in synchronizing the capture of spectral images corresponding to the output of a test for a pathogen or genetic variance.

Description

[Technical Field]

[0001] The present disclosure relates to screening systems for identifying pathogens or genetic variations, and particularly, but not exclusively, to systems for detecting genetic variations in either DNA or RNA or gene expression profiles. [Background technology]

[0002] The COVID-19 pandemic in particular, but also other pandemics or epidemics, require the screening of large numbers of samples taken from symptomatic individuals suspected of carrying the virus, or in routine surveillance screening of asymptomatic individuals to identify carriers of the virus. While various manual screening procedures are known, screening systems that allow for higher sample throughput to enable surveillance testing of larger numbers of samples are becoming increasingly important.

[0003] To detect pathogens such as SARS-CoV2, there are multiple, highly sensitive molecular diagnostic techniques that use a range of nucleic acid amplification and detection systems, including polymerase chain reaction (PCR), isothermal amplification, and CRISPR-based methods. For an evaluation, see "Habli, Z., Saleh, S., Zaraket, H., and Khraiche, M.L., COVID-19 in-vitro Diagnostics: State-of-the-Art and Challenges for Rapid, Scalable, and High-Accuracy Screening. Frontiers in Bioengineering and Biotechnology 8, (2021)."

[0004] Those skilled in the art will recognize that the present disclosure is applicable to an emerging range of novel molecular tests using optical readout on both nucleic acid and protein targets, including but not limited to the techniques disclosed in the following documents:

[0005] Zhang, X., Zhao, Y., Zeng, Y., and Zhang, C. Evolution of the Probe-Based Loop-Mediated Isothermal Amplification (LAMP) Assays in Pathogen Detection. Diagnostics 13, 1530 (2023).

[0006] Loop-mediated isothermal amplification (LAMP) is comprehensively reviewed in "Moehling, TJ, Choi, G., Dugan, LC, Salit, M., and Meagher, RJ, LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community. Expert Rev Mol Diagn 21, 1-19 (2021)."

[0007] MD-LAMP "Becherer, L. et al. Simplified Real-Time Multiplex Detection of Loop-Mediated Isothermal Amplification Using Novel Mediator Displacement Probes with Universal Reporters. Anal Chem 90, 4741~4748 (2018)".

[0008] CRISPR

[0009] Recent progress in nucleic acid detection with CRISPR by Liu, FX, Cui, JQ, Wu, Z., and Yao, S. Lab Chip 23, 1467~1492(2023).

[0010] Pena,JM.Real-time,multiplexed SHERLOCK for in vitro diagnostics.J.Mol.Diagn.25,428~437(2023).

[0011] Nguyen,LT.Engineering highly thermostable Cas12b via de novo structural analyzes for one-pot detection of nucleic acids.Cell Rep.Med.4,101037(2023).

[0012] DETECTR「Broughton,JPらof CRISPR-Cas12-based detection of SARS-CoV-2.Nat Biotechnol 38,870~874(2020).

[0013] miSHERLOCK「Puig,H.deらのMinimally instrumented SHERLOCK(miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants.Sci Adv 7,eabh2944(2021).

[0014] Introduction to CRISPR CONAN。「Shi,K.らのA CRISPR-Cas autocatalysis-driven feedback amplification network for supersensitive DNA diagnostics.Sci.Adv.7,eabc7802」」。

[0015] Deng, F., Sang, R., Li, Y., Deng, W., and Goldys, E. The bifunctional circular DNA amplifier transforms a classic CRISPR / Cas sensor into an ultrasensitive autocatalytic sensor.

[0016] Bi-functional antibody-CRISPR / Cas12a ribonucleoprotein conjugate for improved immunoassay performance for improved immunoassay performance.Anal Chim Acta 1259,341211(2023).

[0017] SPOT., Xun, G., Lane, ST, Petrov, VA, Pepa, BE, and Zhao, H. A rapid, accurate, scalable, and portable testing system for COVID-19 diagnosis.

[0018] RTF-EXPAR「Carter,JGらのUltrarapid detection of SARS-CoV-2 RNA using a reverse transcription free exponential amplification reaction,RTF-EXPAR.Proc National Acad Sci 118,(2021).

[0019] NACT "Selective Naked-Eye Detection of SARS-CoV 2 Mediated by N Gene Targeted Antisense Oligonucleotide Capped Plasmonic Nanoparticles.Acs Nano 14,7617-7627(2020); Alafeef, M., Moitra, P., Dighe, K. and Pan, D. RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19.Nat Protoc 16,3141~3162(2021).

[0020] Isothermal PCR. “Gavrilov, M. et al. Engineered helicase replaces thermocycler in DNA amplification while retaining desired PCR characteristics. Nat Commun 13,6312 (2022).”

[0021] Those skilled in the art will appreciate that the above list of nucleic acid amplification (NAAT) techniques is not exhaustive and does not explicitly mention other applicable techniques, including RPA, RCA, SPA, and NASBA. See Wang, M. et al., Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review. Biosensors 13, 160 (2023).

[0022] Those skilled in the art will recognize that the products of the above molecular diagnostic tests (whether based on nucleic acid amplification tests, CRISPR, or protein or nanoparticle-based biosensors) can be detected via changes in color, luminescence, phosphorescence, or fluorescence (detected by differences in absorption, reflectance, or transmittance of irradiated light). For example, the following review articles describe a range of nucleic acid aptamer, protein, and nanoparticle biosensors with optical outputs: "Singh, AK, Mittal, S., Das, M., Saharia, A. and Tiwari, M. Optical biosensors: a decade in review. Alex. Eng. J. 67, 673~691 (2023). Xu, R., Ouyang, L., Chen, H., Zhang, G. and Zhe, J. Recent Advances in Biomolecular Detection Based on Aptamers and Nanoparticles. Biosensors 13, 474 (2023). Futane, A., Narayanamurthy, V., Jadhav, P. and Srinivasan, A. Aptamer-based rapid diagnosis for point-of-care application. Microfluid. Nanofluidics 27, 15 (2023).

[0023] Those skilled in the art will appreciate the application of this disclosure to a range of homogeneous isothermal tests for nucleic acid, protein, or small molecule-based targets. For illustrative examples of applicable tests, see, respectively, Dekaliuk, M., Busson, P., and Hildebrandt, N., Isothermal Rolling Circle Amplification and Lanthanide-Based FRET for Femtomolar Quantification of MicroRNA. Anal. Sens. 2, (2022); and Fu, H.-J. et al., Rapid and Wash-Free Time-Gated FRET Histamine Assays Using Antibodies and Aptamers. ACS Sens. 7, 1113-1121 (2022). Li, Y., Liu, L., Qiao, L., and Deng, F., Universal CRISPR / Cas12a-associated aptasensor Suitable for rapid detection of small proteins with a plate. reader.Front.Bioeng.Biotechnol.11,1201175(2023)" and "Kadam,US, Cho,Y., Park,TY and Hong,JC, Aptamer-based CRISPR-Cas powered diagnosis of diverse biomarkers and small molecular targets.Appl Biol Chem 66,13(2023)".

[0024] One promising technique used to screen for molecular signatures in samples is the so-called "loop-mediated isothermal amplification" (LAMP) technique. This screening process involves collecting a biological sample (e.g., but not limited to, saliva, sputum, anterior nasal swab, middle turbinate swab, or nasopharyngeal swab, and throat swab) and placing the sample in a test tube with chemicals used for the LAMP process. The sample is then cultured, and the results of the screening process can be determined using colorimetric or fluorometric detection techniques. LAMP has the advantage that this culture and detection process takes only 20–30 minutes. Screening systems may be used for parallel processing and screening of samples, thereby increasing throughput compared to the manual LAMP procedure.

[0025] However, to date, the molecular diagnostic methods disclosed above have been implemented in low-throughput point-of-care formats or intermediate formats, with no feasible or economical means for operation at ultra-high throughput scales. This means that the standard approaches to molecular diagnostics disclosed above are not applicable to ultra-high throughput screening methods, specifically methods that support continuous operation at thousands of tests per hour. For example, even expensive, high-throughput molecular diagnostic instruments such as the Roche Cobas 6800, Abbott Alinity, Quiagen QIAstat-Dx, NeuMoDx, or Hologic Panther, some of which support more continuous flow-loading modes, are not configured in a manner that allows for economical scaling to continuous ultra-high throughput operation due to inherent design constraints.

[0026] Small molecular testing devices and / or smartphone-linked point-of-care solutions also have their own limitations in terms of identity verifiability, integration, and affordability for implementation at a population scale or in biosecurity surveillance applications.

[0027] Therefore, the ability to rapidly screen huge numbers of samples relevant to a pandemic, or to economically screen for genetic or phenotypic changes at the population level in the shortest possible timeframe, requires not only ultra-high-throughput parallel processing of samples, but also further technological solutions to increase throughput and versatility, such as, but not limited to, scalable random access, continuous-flow loading, etc., to flexibly adapt to variations in test volumes.

[0028] Where a prior art document is referred to in this specification, it should be understood that such reference does not constitute an admission that the document forms part of the common general knowledge in the art in Australia or any other country. [Prior art documents] [Patent documents]

[0029] [Patent Document 1] PCT / AU2022 / 051036 [Patent Document 2] PCT / AU2021 / 051209 [Non-patent literature]

[0030] [Non-Patent Document 1] Habli, Z., Saleh, S., Zaraket, H., and Khraiche, ML. COVID-19 in-vitro Diagnostics: State-of-the-Art and Challenges for Rapid, Scalable, and High-Accuracy Screening. Frontiers in Bioengineering and Biotechnology8, (2021) [Non-patent document 2] Zhang, X., Zhao, Y., Zeng, Y., and Zhang, C. Evolution of the Probe-Based Loop-Mediated Isothermal Amplification (LAMP) Assays in Pathogen Detection. Diagnostics 13, 1530 (2023) [Non-patent document 3] Moehling, TJ, Choi, G., Dugan, LC, Salit, M. and Meagher, RJ, LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community.Expert Rev Mol Diagn 21,1~19(2021) [Non-patent document 4] Becherer, L. et al., Simplified Real-Time Multiplex Detection of Loop-Mediated Isothermal Amplification Using Novel Mediator Displacement Probes with Universal Reporters. Anal Chem 90, 4741~4748 (2018) [Non-patent document 5] Liu, FX, Cui, JQ, Wu, Z. and Yao, S. Recent progress in nucleic acid detection with CRISPR, Lab Chip 23, 1467-1492 (2023) [Non-patent document 6] Pena, JM et al. Real-time, multiplexed SHERLOCK for in vitro diagnostics. J. Mol. Diagn. 25, 428~437 (2023) [Non-Patent Document 7] Nguyen, LT et al. Engineering highly thermostable Cas12b via de novo structural analyzes for one-pot detection of nucleic acids.Cell Rep.Med.4,101037(2023) [Non-patent document 8] Broughton, JP et al. CRISPR-Cas12-based detection of SARS-CoV-2.Nat Biotechnol 38,870~874(2020) [Non-Patent Document 9] Puig, H. de et al., Minimally instrumented SHERLOCK(miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants.Sci Adv 7, eabh2944(2021) [Non-Patent Document 10] Shi, K. et al. A CRISPR-Cas autocatalysis-driven feedback amplification network for supersensitive DNA diagnostics.Sci.Adv.7, eabc7802 [Non-Patent Document 11] Deng, F., Sang, R., Li, Y., Deng, W. and Goldys, E. Bifunctional circular DNA amplifier transforms a classic CRISPR / Cas sensor into an ultrasensitive autocatalytic sensor. (2023)doi:10.21203 / rs.3.rs-2626952 / v1 [Non-Patent Document 12] Deng, F., Li, Y., Hall, T., Vesey, G. and Goldys, EM, Bi-functional antibody-CRISPR / Cas12a ribonucleoprotein conjugate for improved immunoassay performance. Anal Chim Acta 1259,341211(2023) [Non-Patent Document 13] Xun, G., Lane, ST, Petrov, VA, Pepa, BE and Zhao, H. A rapid, accurate, scalable, and portable testing system for COVID-19 diagnosis.Nat Commun 12,2905(2021) [Non-Patent Document 14] Carter, JG et al. Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription free exponential amplification reaction,RTF-EXPAR.Proc National Acad Sci 118,(2021) [Non-Patent Document 15] Moitra, P., Alafeef, M, Dighe, K., Frieman, MB and Pan, D. Selective Naked-Eye Detection of SARS-CoV 2 Mediated by N Gene Targeted Antisense Oligonucleotide Capped Plasmonic Nanoparticles.Acs Nano 14,7617-7627(2020) [Non-Patent Document 16] Alafeef, M., Moitra, P., Dighe, K. and Pan, D. RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19. Nat Protoc 16, 3141~3162 (2021) [Non-Patent Document 17] Gavrilov, M. et al., Engineered helicase replaces thermocycler in DNA amplification while retaining desired PCR characteristics.Nat Commun 13,6312(2022) [Non-Patent Document 18] Wang, M. et al., Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis:A Review.Biosensors 13,160(2023) [Non-Patent Document 19] Singh, AK, Mittal, S., Das, M., Saharia, A. and Tiwari, M. Optical biosensors: a decade in review. Alex. Eng. J. 67, 673~691 (2023) [Non-Patent Document 20] Xu, R., Ouyang, L., Chen, H., Zhang, G. and Zhe, J. Recent Advances in Biomolecular Detection Based on Aptamers and Nanoparticles.Biosensors 13,474(2023) [Non-Patent Document 21] Futane, A., Narayanamurthy, V., Jadhav, P., and Srinivasan, A. Aptamer-based rapid diagnosis for point-of-care application. Microfluid. Nanofluidics 27, 15 (2023) [Non-Patent Document 22] Dekaliuk, M., Busson, P. and Hildebrandt, N. Isothermal Rolling Circle Amplification and Lanthanide-Based FRET for Femtomolar Quantification of MicroRNA.Anal.Sens.2, (2022) [Non-Patent Document 23] Fu, H.-J. et al. Rapid and Wash-Free Time-Gated FRET Histamine Assays Using Antibodies and Aptamers. ACS Sens. 7, 1113~1121 (2022) [Non-Patent Document 24] Li, Y., Liu, L., Qiao, L. and Deng. F. Universal CRISPR / Cas12a-associated aptasensor Suitable for rapid Detection of small protein with a plate reader.Front.Bioeng.Biotechnol.11,1201175(2023) [Non-Patent Document 25] Kadam, US, Cho, Y., Park, TY and Hong, JC Aptamer-based CRISPR-Cas powered diagnosis of diverse biomarkers and small molecular targets. Appl Biol Chem 66,13(2023) Summary of the Invention

[0031] Each embodiment is directed to a screening system configured to identify biological agents, biological variances, pathogens, and / or genetic variances at a continuous screening throughput rate of at least 2000 samples per hour. Such systems are sometimes referred to as continuous "ultra-high throughput" screening systems.

[0032] One embodiment is a screening system for identifying a pathogen or genetic variation, comprising: an incubation zone having incubation stations for incubating a plurality of samples; a source of electromagnetic radiation for irradiating a plurality of samples; a detector for detecting electromagnetic radiation emitted from the plurality of samples; a reference system for measuring the position of the detector relative to the incubation station; A screening system comprising:

[0033] The reference system may include an optical-based datum system. The reference system may include optical, acoustic, and / or magnetic detectors configured to measure distance. This distance may be used to calculate the relative position of the detector and the incubation station. The optical and / or acoustic detectors may include ultrasonic detectors and / or laser light. The magnetic detector may include a detector capable of detecting a change in magnetic state. For example, a change in magnetic state may occur at the location of the incubation station. The magnetic detector may also include a linear encoder that uses magnetic coding over the entire travel distance.

[0034] One embodiment is a screening system for identifying a pathogen or genetic variation, comprising: an incubation zone having incubation stations for incubating a plurality of samples; an incubator unit that can be housed in the incubation station and is replaceable; a heating element or temperature regulator having a plurality of containers each capable of containing a sample, the heating element or temperature regulator being configured to heat or cool the plurality of containers; and an incubator unit comprising an electromagnetic radiation source for irradiating one or more containers; a detector for detecting electromagnetic radiation emitted from the plurality of samples; A screening system comprising:

[0035] In one embodiment, the screening system may include multiple incubation stations, each capable of housing an incubator unit. Each incubator unit may be operable independently of the others, allowing the system to simultaneously analyze samples requiring different incubation conditions. The temperature regulator may be located above or form the upper portion of the incubator unit during use. The electromagnetic radiation source may be located below or form the lower portion of the incubator unit during use. In one embodiment, each vessel is optically connected to the electromagnetic radiation source via a fiber optic cable. However, the present disclosure is not limited to the use of fiber optic cables, and alternative embodiments may be used to allow the electromagnetic radiation source to pass into the vessel.

[0036] The incubator unit may include an identifier that can be read by the incubation station when the incubator unit is placed in the incubation station, and this identifier may be used to identify the predetermined operating conditions of the incubator unit.

[0037] The incubator unit may include an optically-based datum system capable of generating light used as a reference point for orienting an image of the incubation station captured by the detector. The optically-based datum system may include a laser light source and an optical detector. The laser light may be detected by the optical detector to generate a signal and capture images of the plurality of samples.

[0038] One embodiment is a screening system configured to identify a biological agent, biological variance, pathogen, and / or genetic variance, comprising: an incubation zone having an incubation station for incubating a plurality of samples, the incubation station having an optical-based datum system; a source of electromagnetic radiation for irradiating a plurality of samples; a detector for detecting electromagnetic radiation emitted from the plurality of samples; Equipped with An optically based datum system serves as the screening system, used as a reference point to orient the image of the incubation station captured by the detector.

[0039] The light-based datum system may be considered to form a position system that serves to indicate the position of the incubation station. Light emitted from the light-based datum system may be detected by a detector. The screening system may include multiple incubation stations. The incubation station may include an incubator unit having a heating element or a temperature regulator, such as a magnetic induction system or a piezoelectric system, for heating or cooling the multiple samples. The incubator system may be replaceable. The light-based datum system may be disposed on the temperature regulator. The incubator unit may include an electromagnetic radiation source for irradiating the multiple samples.

[0040] In one embodiment, the electromagnetic radiation source is configured to illuminate the plurality of samples in a first wavelength range, and the detector is configured to detect electromagnetic radiation emitted from the plurality of samples in a second wavelength range, which may be different from the first wavelength range. The optical-based datum system may be visible in the second wavelength range.

[0041] The optical-based datum system may include two optical-based datums disposed in the incubation station. The optical-based datum system may include a laser light source that triggers an optical detector disposed in the incubation station. Triggering the optical detector may provide a signal to the detector to capture electromagnetic radiation emitted from the multiple samples. This trigger may help ensure that the detector is in the same position for each image capture.

[0042] The system may be configured to simultaneously detect electromagnetic radiation emitted from multiple samples and light from the optical-based datum position system, for example, by a multispectral detector and / or via a split beam or prism linked to multiple detectors. The system may be configured to at least quasi-simultaneously detect electromagnetic radiation emitted from multiple samples, such as by filter wheel multiplexing and / or narrow band filter-based imaging devices / cameras, using synchronous detection of light emitted from the optical-based datum position system.

[0043] The optical-based datum system may include a light source disposed in the incubation station. In one embodiment of the screening system, the detector and the incubation station may be movable relative to one another. In one embodiment of the screening system, the screening system may further include a movement mechanism configured to move the detector throughout the incubation zone. The screening system may be configured such that the detector moves continuously throughout the incubation zone during use of the system. The detector may move continuously back and forth throughout the incubation zone. In one embodiment, the system may be configured such that the at least quasi-simultaneous detection of electromagnetic radiation emitted from the multiple samples includes detecting light from the optical-based datum system either at a predetermined time interval immediately before or after the detection of the electromagnetic radiation emitted from the multiple samples, followed by a time resolution that allows the positions of the multiple samples to be calculated from the optical-based datum system by interpolating a trajectory of relative movement between the detector and the incubation zone.

[0044] In one embodiment of the screening system, the detector is a fixed detector and has a field of view that captures at least one incubation station. One embodiment of the screening system may include multiple detectors. One embodiment of the screening system may include multiple incubation stations. Each detector of the multiple fixed detectors may be configured to record radiation emitted from a portion of the multiple incubation stations, such that the multiple fixed detectors collectively record radiation emitted from the multiple incubation stations. Each detector of the multiple detectors may be configured to record radiation emitted from the multiple samples at a predetermined wavelength or at one or more predetermined wavelengths that are different from the wavelengths of the other detectors of the multiple detectors. In one embodiment, at least one of the multiple detectors is configured to record radiation emitted from the multiple samples at a predetermined wavelength that is different from the wavelengths of at least one detector of the multiple detectors, and at least one detector of the multiple detectors is configured to record radiation at the same wavelength as the other detectors but is distinguished by time-resolved detection of asynchronous radiation in response to an excitation pulse provided by the electromagnetic radiation source.

[0045] One embodiment is a screening system for identifying a pathogen or genetic variation, comprising: an incubation zone having incubation stations for incubating a plurality of samples; an incubator unit that can be housed in the incubation station and is replaceable; a temperature regulator having a plurality of vessels for containing samples, the temperature regulator being configured to heat or cool the plurality of vessels; an electromagnetic radiation source optically coupled to the container for irradiating the plurality of samples; and an incubator unit equipped with an optically based datum system; a detector for detecting electromagnetic radiation emitted from multiple samples, and light from an optical-based datum system; Equipped with An optically based datum system serves as the screening system, used as a reference point to orient the image of the incubation station captured by the detector.

[0046] An embodiment of the screening system may further include a liquid handling system for transferring liquid reagents to the plurality of samples. The liquid handling system may include a pipette for transferring the liquid and may receive and dispense pipette tips from a pipette tip rack during use. An embodiment may further include a detector for visually detecting the presence or absence of one or more pipette tips in the pipette tip rack.

[0047] An embodiment of the screening system may further comprise an airflow system. The airflow system may have an inlet arranged to draw air from an environment outside the screening system, a filter, and an outlet arranged within the chamber housing the liquid handling system. The airflow system may be configured to draw air through the inlet and filter to form purified air and then blow the purified air into the chamber housing the liquid handling system. The airflow system may be configured to maintain the chamber housing the liquid handling system at an elevated pressure compared to an environment outside the chamber housing the liquid handling system. The airflow system may comprise a duct to direct the purified air to an upper portion of the chamber housing the liquid handling system.

[0048] An embodiment of the screening system may further include a robotic system for loading and unloading samples. A system for screening for pathogens or genetic differences may be configured to identify whether and when screening and / or processing for individual samples or groups of samples in an incubation zone is complete. In one embodiment, the robotic system may be configured to remove individual samples or groups of samples from an incubator, leaving behind an empty sample holder or group of sample holders. The sample or group of samples may be removed from a location surrounded by or adjacent to a sample or group of samples for which screening and / or processing has not been completed. The robotic system may be configured to retrieve an unused sample or group of samples and then fill an empty location in the incubator with the unused sample. The system may be suitable for continuous throughput of samples. For example, an embodiment of the screening system may be configured for continuous operation in which incubated samples are continuously removed and replaced with new samples.

[0049] An embodiment of the screening system may include an ultrasonic detector for detecting one or more physical states of the system. The one or more physical states of the system may include the presence or absence of a sample at a predetermined location in the incubation zone. For example, the sample may be a microplate containing multiple samples. An embodiment may further include a bin or waste container configured to contain waste generated by the screening system. The ultrasonic detector may be configured to measure the fill level of the bin or waste container.

[0050] One embodiment is a screening system configured to identify a biological agent, biological variance, pathogen, and / or genetic variance, comprising: an incubation zone having an incubation station for incubating a plurality of samples, wherein an incubator unit is accommodated in the incubation station and is replaceable, the incubator unit comprising: an incubation zone including a temperature controller having a plurality of containers, each container being capable of containing a sample, the temperature controller being configured to heat or cool the plurality of containers; a source of electromagnetic radiation for irradiating one or more containers; a source of electromagnetic radiation for irradiating a plurality of samples; a detector for detecting electromagnetic radiation emitted from the plurality of samples; a chamber housing a liquid handling system for transferring liquid reagents to a plurality of samples; an airflow system having an inlet positioned to draw air from an environment external to the screening system, a filter, and an outlet positioned within the chamber; drawing air through the inlet and filter to form purified air, and then blowing the purified air into the chamber; an airflow system configured to maintain the chamber at an elevated pressure relative to an environment outside the chamber; A screening system comprising:

[0051] The incubation station may have an optically based datum system that may be used as a reference point for orienting an image of the incubation station captured by the detector. The detector may be in a fixed relationship with respect to the incubation zone. The detector may be movable with respect to the incubation zone.

[0052] One embodiment is a screening system configured to identify a biological agent, biological variance, pathogen, and / or genetic variance, comprising: an incubation zone having incubation stations for incubating a plurality of samples; a source of electromagnetic radiation for irradiating a plurality of samples; a detector for detecting electromagnetic radiation emitted from the plurality of samples; a chamber housing a liquid handling system for transferring liquid reagents to a plurality of samples; an airflow system having an inlet positioned to draw air from an environment outside the screening system, a filter, and an outlet positioned within the chamber, the airflow system configured to draw air through the inlet and filter to form purified air, and then blow the purified air into the chamber and maintain the chamber at an elevated pressure relative to the environment outside the chamber; A screening system comprising:

[0053] The incubation station may include an optically based datum system, which may be used as a reference point for orienting an image of the incubation station captured by the detector. The screening system may further include an incubator unit that is housed in and replaceable with the incubation station. The incubator unit may include a temperature regulator having a plurality of containers, each capable of containing a sample, the temperature regulator configured to heat or cool the plurality of containers, and an electromagnetic radiation source for irradiating one or more containers.

[0054] One embodiment is a screening system configured to identify a biological agent, biological variance, pathogen, and / or genetic variance, comprising: an incubation zone having incubation stations for incubating a plurality of samples; a source of electromagnetic radiation for irradiating a plurality of samples; a detector for detecting electromagnetic radiation emitted from the plurality of samples; Equipped with The incubation station and detector may be movable or in a fixed relationship relative to one another to provide a screening system.

[0055] One or more embodiments of the screening system may be configured to serially identify biological agents, biological variances, pathogens, and / or genetic variances.

[0056] Embodiments will now be described, by way of example only, with reference to the accompanying non-limiting drawings in which: [Brief explanation of the drawings]

[0057] [Figure 1] FIG. 1 is a perspective view of one embodiment of a screening system. [Figure 2] FIG. 2 is a close-up perspective view of area A in FIG. [Figure 3] FIG. 1 is a schematic diagram of an image captured by a detector at a first time point during incubation. [Figure 4] FIG. 10 is a schematic diagram of an image captured by the detector at a second time point during the culture. [Figure 5] FIG. 1 is a diagram of one embodiment of an optically based datum system. [Figure 6] FIG. 1 is a diagram of one embodiment of an optically based datum system. [Figure 7] FIG. 1 is a diagram of one embodiment of an optically based datum system. [Figure 8] FIG. 1 is a top perspective view of one embodiment of an incubator unit. [Figure 9] FIG. 1 is a bottom perspective view of one embodiment of an incubator unit. [Figure 10] FIG. 1 is a perspective view of one embodiment of a screening system. [Figure 11] FIG. 11 is a cross-sectional view taken along line BB in FIG. [Figure 12] FIG. 1 is an end view of one embodiment of a screening system. [Figure 13] FIG. 10 is an end view of another embodiment of a screening system. DETAILED DESCRIPTION OF THE INVENTION

[0058] Each embodiment is directed to a screening system configured to identify biological agents, biological variations, pathogens, and / or genetic variations. The screening system may have a continuous screening throughput rate of at least 2,000 samples per hour. Such systems are sometimes referred to as continuous "ultra-high throughput" screening systems. Biological agents may include molecules used, formed, and / or metabolized in biological systems, including small molecules such as drugs, hormones, and steroids, and macromolecules such as biopolymers, including proteins and carbohydrates, biological substrates, and metabolites. Biological variations may include analyzing one or more markers of a biological system to assess or determine changes in the biological system.

[0059] 1, a screening system 10 includes a structure 12 that supports an incubation zone 14. The incubation zone 14 includes multiple incubation stations 16, each used to incubate multiple samples. Only the top portion of the screening system 10 is shown in each figure, with features such as legs omitted solely for clarity and as will be readily apparent to one skilled in the art.

[0060] In the embodiment shown in Figure 1, twelve incubation stations are configured in three rows of four incubation stations 16 spanning the entire width of the incubation zone 14. Although twelve incubation stations 16 are shown in Figure 1, any number of incubation stations may be used. For example, the incubation zone 14 may have one incubation station 16, or two or more incubation stations 16. In one embodiment, the number of incubation stations 16 is nX, where n is the number of rows of incubation stations 16 in the incubation zone 14 and X is the number of incubation stations 16 in each row.

[0061] In use, the incubation stations 16 receive samples, which are then incubated for a predetermined period of time to induce changes in the fluorometric and / or optical properties of the sample in response to the characteristics of the pathogen or genetic differences of the analytes within the sample. Each sample will typically have a fluorometric and / or colorimetric agent that will alter the characteristics of fluorescent and / or penetrating electromagnetic radiation. In one embodiment, each incubation station 16 can receive well inserts, such as a 96-well insert.

[0062] The screening system 10 includes a source of electromagnetic radiation in the form of light (not shown in FIG. 1) for illuminating the plurality of samples. The electromagnetic radiation source may include one or more of UV, visible, IR, near-IR, and far-IR light sources. While the electromagnetic radiation source is associated with the incubation zone 14 in FIG. 1, its actual location may vary depending on the illumination and / or excitation parameters required to analyze the analytes in each sample and the type of incubation station 16.

[0063] The screening system 10 includes a detector 18 for detecting electromagnetic radiation emitted from or passed through the samples. For example, if a fluorometric agent is used in the samples, the detector can detect the emission of the fluorometric agent after excitation from an electromagnetic radiation source.

[0064] The detector 18 and the incubation station 16 may be movable relative to one another. For example, in one embodiment, the detector 18 is mounted to a gantry 22. The gantry 22 is coupled to rails 24 and 26 such that the gantry 22 can move back and forth in the direction D along the length of the structure 12 across at least the entire incubation zone 14. In one embodiment, the gantry 22 is coupled to the rails 24 and 26 by linear bearings. In one embodiment, the gantry 22 is provided with wheels that run along the rails 24 and 26. In one embodiment, the detector 18 can move along the gantry 22 between the rails 24 and 26.

[0065] In one embodiment, the detector 18 has a fixed relationship (not shown) with respect to the incubation stations 16 and / or the incubation zone 14. For example, the gantry 22 may be fixed to the rails 24 and 26. In such an embodiment, the fixed detector 18 has a field of view that captures at least one incubation station 16. If the fixed detector 18 can capture only a portion of the incubation station 16, multiple fixed detectors 18 may be used, with each fixed detector 18 configured to record radiation emitted from a portion of multiple incubation stations 16, such that the multiple fixed detectors 18 jointly image multiple incubation stations. For example, the screening system 10 may include two fixed detectors, where a first detector can detect electromagnetic radiation from a first half of the incubation zone 14 and a second detector can detect electromagnetic radiation from a second half of the incubation zone 14. Data, such as images, collected by the first and second detectors can be combined so that the first and second detectors can record radiation emitted from every incubation station 16 in the incubation zone. The use of two detectors 18 is merely an example, and the screening system may use any number of fixed detectors 18. When the detectors 18 are fixed relative to the incubation stations 16 and / or incubation zones 14, the detectors 18 may be provided with optics to mitigate optical issues, such as parallax towards the edges of the detector's 18 field of view.

[0066] In the embodiment shown in FIG. 1 , detector 18 comprises multiple detectors. In one embodiment, multiple detectors comprise cameras 20a-20d. In one embodiment, the number of cameras 20 equals the number of incubation stations 16 in each row of incubation stations 16 in incubation zone 14. In this manner, each camera 20a, 20b, 20c, and 20d is responsible for detection along a "detection channel" extending along the direction of structure 12, i.e., direction D. When detector 18 comprises one or more cameras, this detection may be in the form of images that are processed by a processing unit to analyze colorimetric and / or fluorometric properties of the samples captured in the images. However, a single camera may image two or more rows. For example, a first camera may image the first and second rows, and a second camera may image the third and fourth rows.

[0067] In one embodiment, camera 20 may be one or more color and / or IR cameras. The one or more cameras may be monochromatic or polychromatic. Camera 20 may be a multispectral camera. Camera 20 may be a mechanical multispectral camera. The cameras and fluorophores used in the screening system may be as outlined in PCT / AU2022 / 051036.

[0068] The screening system 10 may use multiple cameras, each of which detects light (i.e., electromagnetic radiation) at a certain wavelength or wavelengths. For example, a first detector may detect at wavelengths between 400 nm and 500 nm, and a second detector may detect at wavelengths between 500 nm and 600 nm. In one embodiment, a control included in each sample of the multiple samples may emit at a wavelength that is removed from or orthogonal to other wavelengths or channels used to detect biological agents, biological variations, pathogens, and / or genetic variations in the multiple samples. For example, the control may be triggered by an electromagnetic radiation source at the beginning or end of an incubation period, where the emission from the control is within a wavelength range that is considered noisy or undesirable for probes, such as those used to detect biological agents, biological variations, pathogens, and / or genetic variations. In such instances, the electromagnetic radiation source used to activate or excite this control may be activated at the beginning or end of the culture, while the electromagnetic radiation used to activate or excite the probe used to detect differences in biological agents, biological differences, pathogens, and / or genetic differences is deactivated or suppressed. Such a configuration may eliminate the need for a dedicated channel to monitor the control that would otherwise be required to detect electromagnetic radiation emitted from the probe.

[0069] A robotic system 28 is used to load and unload samples to and from the incubation zone 14. The structure 12 typically includes side walls and a hood to prevent unwanted light and foreign objects from interfering with the samples. The front side wall and hood are omitted from FIG. 1 to better visualize the components of the screening system 10. Samples enter the structure 12 through a window 30 by an actuator 32, and the robotic system 28 can move the samples from the pickup zone 31 to the free incubation station 16. The actuator 32 may include a slidable plate, such as a microplate or pipette tips, that can accommodate multiple samples.

[0070] The screening system 10 includes a liquid handling system. The liquid handling system is shown in FIG. 1 as a pipetting system 34 used to pipette a reagent, such as a fluorescent analyzer, into a sample. The pipetting system 34 includes a pipette 35 (see FIG. 12 or 13) and pipette tips 42 arranged in a pipette tip rack 44. The pipette tip rack 44 may be provided as a cassette of pipette tips 42, or the pipette tips 42 may be mounted on an actuator 32 and moved through a window along with the sample. In use, the pipette 35 can receive and dispense a pipette tip 42 from the pipette tip rack 44.

[0071] In use, a sample passes through window 30, then incubation reagents are added by pipetting system 34 and the sample is then transported to pickup zone 31, where robotic system 28 picks up the sample and transports it to an empty incubation station 16 where the sample is incubated. After incubation, the sample is removed from incubation station 16 and discarded, leaving a new, empty incubation station that can be filled with an unused sample. This process of loading a new sample, incubating, and discarding the incubated sample can occur continuously by randomly accessing the next available incubation station 16.

[0072] In one embodiment, the screening system 10 is provided with a waste chute 36 where waste samples, such as used microplates produced by the screening system 10, can be deposited after incubation. A bin 50 is positioned below the waste chute where the discarded samples can be collected (see FIG. 12). A side panel 38 can be attached to the waste chute 36 to direct discarded samples, such as microplates, to the waste chute. In the embodiment shown in FIG. 1, the waste chute 36 is positioned adjacent to the pickup zone 31. Typically, when a sample is discarded, a free incubation station 16 becomes available for a new sample to be picked up in the pickup zone 31.

[0073] In one embodiment, the pipetting system 34 is provided with a detector in the form of a camera 46 for visually detecting the presence or absence of one or more pipette tips 42 in the pipette tip rack 44. For example, during pipette pickup, the camera 46 can detect any lost or missing pipette tips 42 in the pipette tip rack 44 before the pipette tip 42 is placed on the pipette, and / or can detect any remaining or unpicked pipette tips 42 that may remain in the pipette tip rack 44 after pickup. The absence of a pipette tip 42 before pickup and the presence of a pipette tip 42 after pickup may indicate that one or more samples were not properly prepared, resulting in a false positive or false negative result. Using the camera 46 to detect the presence or absence of a pipette tip 42 during liquid sample transfer may trigger a system controller to alert the user of the error. If necessary, such an error can be corrected before incubation.

[0074] The screening system 10 is configured to identify whether and when screening and / or processing for an individual sample or group of samples in the incubation zone 14 is complete. For example, when incubation of a sample in one incubation station 16 is complete, the robotic system 28 can remove the sample from the incubation station 16 and provide an empty incubation station 16 that can then be filled with a new sample. This allows the screening system 10 to function for continuous throughput of samples. Each incubation station 16 can incubate a sample independently of the others, eliminating the need for batch processing.

[0075] In use, the detector 18 continuously scans the incubation stations 16 within the incubation zone 14 to monitor the incubation of multiple samples. When the detector 18 includes a camera 20, the camera captures multiple images of the incubation stations 16 throughout the defined incubation period. Because the camera moves in the direction D along the length of the structure 12 via the gantry 22, the specific position of the camera relative to the incubation stations 16 may change when an image is captured. To ensure that the images captured by the camera are processed correctly, the images should advantageously be aligned so that the position of each sample is consistent. Alignment can be achieved by using a fiducial locator or datum. However, for samples analyzed by fluorometric methods, during the initial incubation stages, the incubation zone 14 is typically dark and no light source is available to illuminate the incubation stations 16. Using a light source to illuminate the incubation stations 16 would result in reduced sensitivity, as any fluorometric responses in the samples would be drowned out by the light source used to illuminate the reference incubation stations 16.

[0076] Thus, in one embodiment, the screening system 10 includes a datum in the form of an optical-based datum system 40 disposed within the incubation zone 14. The optical-based datum system 40 uses a light source, such as an LED light, to provide a reference for aligning images along the X and Y axes. In one embodiment, as shown in FIG. 2, the optical-based datum system 40 uses two separate point light sources 38a and 38b associated with each incubation station 16. The point light sources 38a and 38b remain in fixed positions relative to the incubation stations 16. In one embodiment, the detector 18 is configured to detect light emitted from the optical-based datum system 40. For example, a camera 20 can be used to detect the light from the optical-based datum system 40. The optical-based datum system 40 may remain fixed in the incubation zone. To prevent any emitted fluorescence from being quenched or its optical properties from changing, the point light sources 38a and 38b are of low intensity, having just enough brightness to be consistently recorded in the image, and are spaced apart from the microplates contained therein when in use in the incubation station 16 to prevent light from leaking from the point light sources 38a and 38b onto the microplates.

[0077] The electromagnetic radiation source used to illuminate the samples in each incubation station 16 can have a first wavelength range. Detectors 18 (e.g., cameras 21a-21d) are collectively configured to detect electromagnetic radiation emitted from the samples in a second wavelength range. The first wavelength range is typically different from the second wavelength range. For example, the electromagnetic radiation source can be a UV light emitting light with wavelengths between 100 nm and 400 nm, and camera 20 can be fitted with a UV filter to block the UV light and detect only visible light with wavelengths >400 nm. In one embodiment, light from light-based datum system 40 is visible in the second wavelength range.

[0078] During the early stages of incubation, when no fluorometric reaction is yet present in the sample, the resulting image of incubation station 16 will be completely devoid of signal, due to filters or the like that would prevent any light from the electromagnetic radiation source used to excite the fluorometric agent in the sample from reaching detector 18. However, as shown in Figure 3, point light sources 38a and 38b provide optical signals that are detected and captured by the camera (i.e., detector 18), resulting in image 100 having a coordinate system for enabling correct orientation and alignment of subsequent images. The position of incubation station 16 in image 100 is shown by dashed line 104 for illustrative purposes and would not actually be visible in image 100.

[0079] During incubation, some of the samples in incubation station 16 will exhibit a fluorescent assay response, as shown by point 106 in FIG. 4 , which will be captured in image 102. Thus, electromagnetic radiation emitted from the samples and light from point sources 38a and 38b are detected simultaneously. The presence of light sources 38a and 38b in images 100 and 102 allows the images 100 and 102 to be properly oriented. Electromagnetic radiation emitted from the samples and light from point sources 38a and 38b may be detected, for example, using a multi-sensor dichroic prism or a pixelated multispectral filter array camera, or via a detector linked to a CCD or CMOS camera or beam splitter.

[0080] In one embodiment, system 10 is configured to simultaneously detect electromagnetic radiation emitted from multiple samples. In one embodiment, system 10 is configured to at least quasi-simultaneously detect electromagnetic radiation emitted from multiple samples using synchronous detection of light emitted from an optical-based datum position system. As used herein, the term "quasi-simultaneously" means that two processes occur in sequence, but at such a rate that the two processes are considered to occur substantially simultaneously.

[0081] In one embodiment, synchronous detection of light emitted from an optically-based datum system, such as point light sources 38a and 38b, can be used to at least quasi-simultaneously detect electromagnetic radiation emitted from multiple samples. When detector 20 and incubation zone 14 are movable relative to one another, system 10 may be configured such that at least quasi-simultaneous detection of electromagnetic radiation emitted from multiple samples includes detecting light from the optically-based datum system (e.g., point light sources 38a and 38b) either at a predetermined time interval immediately before or after detection of the electromagnetic radiation emitted from the multiple samples, followed by a time resolution that allows calculation of the positions of the multiple samples from the optically-based datum system by interpolating the trajectory of relative motion between the detector and incubation zone.

[0082] An advantage of using the optical-based datum system 40 to provide a reference for orienting images of samples within each incubation station 16 is that it eliminates the need for mechanical position measurement. For example, encoders and stepper motors can be used to monitor the relative position of one object to another, but achieving the required measurement accuracy for orienting subsequent images requires tight tolerances and expensive electronics. Such a mechanical position measurement setup would also limit the speed at which the detector 18 can be moved throughout the incubation zone 14, thereby reducing sample throughput and / or the accuracy of results. In contrast, the optical-based datum system 40 can use high-speed detector movement to achieve image alignment with pixel-level resolution. While mechanical position measurement must also be performed during pre-imaging / detection alignment, the optical-based datum system 40 enables post-imaging / detection alignment, meaning that image / detection capture is not a rate-limiting step during sample analysis in the screening system 10.

[0083] Although the optical-based datum system 40 has been described using point light sources 38a and 38b (as shown in FIG. 5), the optical-based datum system 40 can be implemented in other forms. For example, as shown in FIG. 6, the optical-based datum system 40 can use a single light source 38c with an asymmetrical profile. In another embodiment, as best shown in FIG. 7, the optical-based datum system 40 includes a photodetector 39 and a laser light source mounted on the gantry 22 and aimed toward the incubation zone 14. As the gantry 22 moves throughout the incubation zone 14 during incubation to detect and monitor the incubations in the incubation stations 16, laser light from the laser light source on the gantry 22 sweeps across the photodetector 39. When the photodetector 39 detects the laser light, this event is used as a trigger by the screening system 10 to detect / image the sample in the incubation station 16. In this manner, the use of the laser light and the photodetector 39 ensures that the detection / imaging is performed at the same position relative to the photodetector 39, thereby ensuring that any resulting images are correctly oriented.

[0084] In another embodiment, the optical-based datum system 40 may include an ultrasonic detector or laser that reflects off the end of the incubation zone 14 or another fixed location on the structure 12 to provide a distance reference along the length of the incubation zone 14. The predetermined position measured by the ultrasonic detector or reflected laser light may be used as a trigger by the screening system 10 to detect / image the sample in the incubation station 16.

[0085] In one embodiment, the incubation stations 16 are fixed within the incubation zone. However, in another embodiment, as best shown in Figures 8 and 9, the incubation stations 16 are each in the form of an incubator unit 200 that is separately removable from the incubation zone 14. When the incubation stations 16 are each in the form of an incubator unit 200, the incubation zone 14 comprises one or more wells that can accommodate one or more incubator units 200. Thus, the terms incubation station and incubation well can be used interchangeably.

[0086] The incubator unit 200 includes a temperature controller or heating element in the form of a receptacle plate 210. The receptacle plate 210 is disposed or positioned on top of the incubation unit 200 during use and includes a plurality of receptacles 212, each capable of containing a sample. In the embodiment shown in FIG. 8, the receptacle plate 210 includes 96 receptacles 212, capable of accommodating inserts from a 96-well plate. A thermostatically controlled heating element is in thermal communication with the receptacle plate 210 to heat or cool the receptacle plate 210. Typically, the incubator unit 200 will heat the samples contained in the receptacles 212. However, in some cases, the incubator unit 200 will need to cool the samples contained in the receptacles 212. For example, if the incubator unit 200 is used in a hot climate and incubation conditions require an incubation temperature lower than ambient temperature, such as incubation conditions near 20° C., the incubator unit 200 is configured to cool the samples contained in the receptacles 212. In one embodiment, incubator unit 200 includes a piezoelectric or thermoelectric (Peltier) unit for heating or cooling vessel plate 210. Thus, the term "heating element" as used throughout this disclosure is not limited to heating but can also provide cooling. In this manner, the term "heating element" can be used interchangeably with the term "temperature regulator."

[0087] The incubation unit 200 also includes a source of electromagnetic radiation in the form of a light source 214, which is disposed or positioned beneath the incubation unit 200 during use. Each container 212 is optically connected to the light source 214. In the embodiment shown in Figures 1 and 9, each container 212 is optically connected to the light source 214 via a fiber optic cable 216. However, the use of a fiber optic cable is merely illustrative, and other optical coupling means may be used, such as direct illumination.

[0088] If each incubation unit 200 has its own heating element and light source, the incubation conditions in each incubation unit 200 can be unique and independent of one another. Referring to the screening system 10 as just one example, each of the 12 incubation stations 16 (i.e., wells) can house an incubation unit 200, and each incubation unit 200 can have its own incubation condition. Optionally, some of the incubation units 200 can be grouped together according to the incubation conditions. For example, a first set of incubation units 200 can have a first incubation condition, and a second set of incubation units 200 can have a second incubation condition. The incubation can be isothermal. Each incubator unit 200 can operate independently of one another.

[0089] In one embodiment, the culture units 200 are interchangeable, so that each culture unit 200 can be installed or removed independently of the others. The culture units 200 may be preprogrammed to perform a specific type of culture. For example, a first culture unit 200 may be programmed with first culture conditions to identify a first pathogen(s) or genetic difference(s), and a second culture unit 200 may be programmed with second culture conditions to identify a second pathogen(s) or genetic difference(s). For example, if the screening system 10 were equipped with a first culture unit and a second culture unit, the screening system could simultaneously identify two or more sets of pathogens or genetic differences based on various culture conditions. Culture conditions include heating characteristics, such as isothermal heating versus non-isothermal heating, and irradiation characteristics, such as driving a single light source or alternating multiple light sources.

[0090] An advantage of pre-programming the incubator units 200 is that it allows a user to easily change the type(s) of pathogen or genetic variation identified by the screening system and the type(s) of culture required. For example, if the screening system 10 is equipped with a first type of culture unit 200 having first culture conditions, a user can easily replace one or more of the first type of culture unit 200 with a second type of culture unit 200 having second culture conditions.

[0091] In one embodiment, the incubator unit 200 includes an identifier that can be read by the incubation station 16 or the screening system 10, e.g., by a central processing unit, upon installation of the incubator unit in the incubation station 16. For example, each incubation unit 200 may be provided with a unique code or the like that allows the incubation station 16 or the screening system 10 to identify the type of incubation unit 200 and the associated predefined incubation conditions. The identifier may be communicated to the incubation station 16 or the screening system 10 by a communication means such as RFID, CAN bus, Ethernet connection, optical scanning, barcode, or QR code. The incubation unit 200 may be powered by communicating the identifier using a wired connection. However, power may also be provided using a specific interface, such as a socket or plug, independent of the means for communicating the identifier.

[0092] Using the identifier to inform the incubation station 16 or the screening system 10 of what type of incubation unit 200 is placed in the incubation station 16 helps to capture user input and any associated user errors when installing an incubation unit 200. This may be useful when a user needs to perform maintenance or when the incubation zone 14 needs to be updated, for example, by replacing an incubation unit 200 from one type to another. An embodiment in which the incubation stations 16 are each in the form of an incubator unit 200 that is separately removable from the incubation zone 14 helps the screening system 10 to be more flexible in the types of pathogens or genetic variations that it can identify, and their associated identification methods.

[0093] In one embodiment, incubation unit 200 includes an optically based datum system. As shown in Figure 8, incubation unit 200 can include point light sources 38a and 38b. Incorporating an optically based datum system into incubation unit 200 means that the datum point always remains in a fixed position relative to container 212, which helps to improve accuracy when aligning images of samples contained in container 212.

[0094] As best shown in Figures 10, 11, and 12, one embodiment of the screening system 10 includes an airflow system 300. Note that for ease of reference, not every feature of the screening system 10 is identified with a reference numeral in Figures 10, 11, and 12. The airflow system 300 includes an inlet 314 located outside the structure 12, such that the inlet 314 can draw air from the environment outside the screening system 10. The inlet 314 is provided with a filter, such as a HEPA filter. The filter is accessible by a user from outside the inlet 314. The inlet 314 also includes a motor unit 316 having a fan 318 that can draw air through the filter. The filter removes particulate matter from the air drawn through the inlet 314, thereby forming purified air. The purified air is then blown through a pipe 320, from which it is discharged through the outlet 310.

[0095] A housing 312 is provided throughout the pipetting system 34, forming a pipetting chamber 322. The pipetting chamber 322 can be considered a liquid handling chamber. An outlet 310 is disposed within the pipetting chamber 322, thereby allowing purified air to exit the outlet 310 and enter the pipetting chamber 322. In one embodiment, the airflow system 300 is configured to maintain a high pressure inside the pipetting chamber 322 compared to the environment outside the pipetting chamber 322. The window 30 allows air under a relative pressure to exit the pipetting chamber 322. This high pressure means that purified air exits the pipetting chamber 322 through the window 30, as illustrated by the travel path of the dashed line 324. The purified air may exit the window 30 continuously. The continuous exit of purified air from the pipetting chamber 322 helps reduce the possibility of foreign or particulate or aerosolized matter passing through the window 30 into the pipetting chamber 322 and contaminating the sample to be analyzed by the screening system 10. Purified air may also exit the pipetting chamber 322 on the pickup zone 31 side of the pipetting system 34 and be sent to the incubation zone 14.

[0096] In one embodiment, as best shown in FIG. 13 , the airflow system 300 includes a duct 326 defined between a sidewall 328 and the wall of the housing 312. The duct 326 has an opening 310 a disposed toward the top or upper portion of the pipetting chamber 322. The duct 326 directs purified air through the opening 310 a to the top of the pipetting chamber 322, so that the purified air flows downward across and / or through the components of the pipetting system 34 and outward through the window 30 or toward the incubation zone 14. This flow of purified air is indicated by arrows 330 in FIG. 13 . The duct 326 may help reduce circulation of the purified air within the pipetting chamber 322.

[0097] Referring back to FIG. 1 , in one embodiment, the screening system 10 includes a detector in the form of an ultrasonic detector 48 for detecting one or more physical conditions of the screening system 10. The ultrasonic detector 48 is attached to the robotic system 28 and can detect one or more physical conditions of the screening system 10 at one or more predetermined positions in an area below the robotic system 28. In one embodiment, the ultrasonic detector 48 can detect a height-based condition of a component of the screening system 10 at one or more predetermined positions, such as in the Z direction. For example, a particular action can result in the presence or absence of a component. Take the placement of a new set of samples in the incubation station 16 as an example, where there is a difference in height in the Z direction between the presence and absence of samples in the incubation station 16.

[0098] If the ultrasonic detector detects that the height of a component is outside of predetermined conditions, a trigger may be activated to alert the user to an error in the screening system 10. For example, if the screening system 10 calculates that a sample should be present in a particular incubation station 16, which should be associated with the physical state of the incubation station 16 at a known height, but the ultrasonic detector 48 detects that the detected height is outside the range of the physical state of the sample in the incubation station 16, a trigger may be activated. Thus, the ultrasonic detector 48 may be used to detect the presence or absence of an object at one or more locations within the screening system 10. The physical state may include whether the gripper 52 of the robotic system 28 properly picked up a microplate. The physical state may also include the presence or absence of a microplate in the pickup zone 31 and / or the incubation station 16. In one embodiment, the robotic system 28 is configured to remove an individual sample or a group of samples from the incubator station 16, leaving behind an empty sample holder or group of sample holders. The robotic system 28 may be one outlined in PCT / AU2021 / 051209 or PCT / AU2022 / 051036.

[0099] The ultrasonic detector 48 can also be used to detect the fill level of the bin 50. In use, waste samples, such as waste microplates, are disposed of in the bin as described above. As more samples are placed in the bin 50, the fill level of the bin 50 increases. This increase in fill level is associated with a change in height in the Z direction. Thus, the ultrasonic detector 48 can be used to detect when the waste level within the bin has reached a maximum level. The fill level of the bin 50 need not be constant. For example, a user signal may be triggered when the bin reaches a first fill threshold, such as 80% full. Then, a second or higher fill threshold, such as 90% full, may be triggered. A final maximum fill level, such as 100% full, may be triggered to stop the screening system 10 from loading new samples until the user empties the bin 50. Thus, the ultrasonic detector 48 may be used to prevent fouling and / or damage to the screening system 10 and may improve accuracy or at least help detect sources of error during incubation and analysis.

[0100] The above-described embodiments relate to a screening system 10 having multiple incubation stations 16. However, the principles of the present disclosure also relate to screening systems having one or two incubation stations. For example, in such embodiments, the detector may be fixed, and movement of the detector (e.g., 18) relative to the incubation station(s) may be achieved by manually moving the incubation station(s) relative to the detector. Other principles of the present disclosure, such as embodiments relating to the use of an optical-based datum system, a removable incubation unit, an airflow system, etc., also apply to screening systems having one or two incubation stations.

[0101] Although the detailed description refers to 96-well plates, the present disclosure is not limited to 96-well plates and can include any type of microplate, such as 6-well plates, 24-well plates, 48-well plates, 96-well plates, 384-well plates, 1536-well plates, etc.

[0102] In the appended claims and the foregoing description, unless the context requires otherwise by clear language or necessary implication, the term "comprise" or variations such as "comprises" or "comprising" are used in their inclusive sense, i.e., they are used to specify the presence of stated features but do not exclude the presence or addition of further features in various embodiments of the present disclosure.

[0103] Modifications and variations that would be apparent to a person skilled in the art are deemed to be within the scope of this disclosure.

Claims

1. 1. A screening system configured to identify a biological agent, biological variance, pathogen, and / or genetic variance, comprising: an incubation zone having incubation stations for incubating a plurality of samples; an incubator unit that can be accommodated in the incubation station and is replaceable; a temperature regulator having a plurality of containers each capable of containing a sample, the temperature regulator being configured to heat or cool the plurality of containers; and an incubator unit comprising an electromagnetic radiation source for irradiating one or more of said vessels; a detector for detecting electromagnetic radiation emitted from said plurality of samples; A screening system comprising:

2. 10. The screening system of claim 1, comprising a plurality of incubation stations, each capable of accommodating an incubator unit.

3. 3. The screening system of claim 2, wherein each incubator unit is operable independently of the others.

4. 4. A screening system according to any one of claims 1 to 3, wherein the temperature regulator is located at or forms an upper part of the incubator unit when in use, and the electromagnetic radiation source is located at or forms a lower part of the incubator unit when in use.

5. 5. A screening system according to any one of claims 1 to 4, wherein each container is optically connected to the electromagnetic radiation source via a fiber optic cable.

6. 6. The screening system of claim 1, wherein the incubator unit includes an identifier that can be read by the incubation station when the incubator unit is placed in the incubation station, and the identifier is used to identify a predetermined operating state of the incubator unit.

7. 7. The screening system of claim 1, wherein the incubator unit comprises an optically based datum system capable of generating light used as a reference point for orienting an image of the incubation station captured by the detector.

8. 1. A screening system configured to identify a biological agent, a biological variance, a biologically active agent, a pathogen, and / or a genetic variance, comprising: an incubation zone having an incubation station for incubating a plurality of samples, the incubation station having an optical-based datum system; a source of electromagnetic radiation for illuminating the plurality of samples; a detector for detecting electromagnetic radiation emitted from said plurality of samples; Equipped with A screening system wherein the optical-based datum system is used as a reference point for orienting an image of the incubation station captured by the detector.

9. 10. The screening system of claim 8, comprising a plurality of incubation stations.

10. the incubation station includes an incubator having a temperature controller for heating or cooling the sample contained in the incubator unit; The incubator system is interchangeable, 10. The screening system of claim 8 or 9, wherein the optical-based datum system is located on the temperature controller.

11. The screening system of claim 10 , wherein the incubator unit comprises the electromagnetic radiation source for irradiating the plurality of samples.

12. 12. The screening system of claim 7, wherein the electromagnetic radiation source is configured to illuminate the plurality of samples in a first wavelength range, and the detector is configured to detect electromagnetic radiation emitted from the plurality of samples in a second wavelength range, the second wavelength range being different from the first wavelength range, and the optical-based datum system is visible in the second wavelength range.

13. 13. The screening system of claim 7, wherein the detector is configured to detect light emitted from the light-based datum system.

14. 14. The screening system of claim 7, wherein the optical-based datum system includes two optical-based datums located at the incubator station.

15. 15. A screening system according to any one of claims 7 to 14, configured to enable simultaneous detection of the electromagnetic radiation emitted from the plurality of samples and the light from the optical-based datum system.

16. 15. A screening system according to any one of claims 7 to 14, configured to enable simultaneous detection of the electromagnetic radiation emitted from the plurality of samples.

17. 15. A screening system as claimed in any one of claims 7 to 14, configured to enable at least quasi-simultaneous detection of the electromagnetic radiation emitted from the plurality of samples using synchronous detection of light emitted from an optically based datum position system.

18. 18. The screening system of claim 7, wherein the light-based datum system comprises a light source disposed in the incubation station.

19. 19. The screening system of claim 1, wherein the detector and incubation station are movable relative to each other.

20. 20. The screening system of claim 19, further comprising a movement mechanism configured to move the detector throughout the incubation zone.

21. 21. The screening system of claim 20, wherein the detector is configured to move continuously throughout the incubation zone during use of the system.

22. A screening system as described in any one of claims 19 to 21 when dependent on claim 17, wherein the at least quasi-simultaneous detection of the electromagnetic radiation emitted from the multiple samples is configured to include detecting light from the optical-based datum system at either a predetermined time interval immediately before or after the detection of the electromagnetic radiation emitted from the multiple samples, followed by a time resolution that enables the positions of the multiple samples to be calculated relative to the optical-based datum system by interpolating the trajectory of relative movement between the detector and the culture zone.

23. 19. The screening system of any one of claims 1 to 18, wherein the detector is a fixed detector and has a field of view that captures at least one incubation station.

24. 24. A screening system according to any one of claims 1 to 23, comprising a plurality of detectors.

25. 25. The screening system of claim 24 when dependent on claim 23, comprising a plurality of incubation stations, each of the plurality of fixed detectors configured to record radiation emitted from a portion of the plurality of incubation stations such that the plurality of fixed detectors collectively record radiation emitted from the plurality of incubation stations.

26. 26. A screening system as described in claim 24 or 25, wherein each detector of the plurality of detectors is configured to record radiation emitted from the plurality of samples at a predetermined wavelength or at one or more predetermined wavelengths different from the other wavelengths of the detectors of the plurality of detectors.

27. 26. A screening system as described in claim 24 or 25, wherein at least one of the plurality of detectors is configured to record radiation emitted from the plurality of samples at a predetermined wavelength that is distinct from the detector of at least one of the plurality of detectors, and wherein at least one detector of the plurality of detectors is configured to record radiation at a time point similar to other times but distinguished by time-resolved detection of asynchronous radiation in response to an excitation pulse.

28. 28. A screening system as described in any one of claims 1 to 27, further comprising a liquid handling system for transferring liquid reagents to the plurality of samples, the liquid handling system comprising pipettes for transferring liquids and capable of receiving and dispensing pipette tips from a pipette tip rack during use.

29. 30. The screening system of claim 28, further comprising a detector for visually detecting the presence or absence of one or more pipette tips in the pipette tip rack.

30. an airflow system having an inlet for drawing air from an environment external to the screening system, a filter, and an outlet located within a chamber housing the liquid handling system; drawing air through the inlet and filter to form purified air, and then blowing the purified air into the chamber housing the liquid handling system; 30. A screening system according to claim 28 or 29, further comprising an air flow system configured to maintain the chamber housing the liquid handling system at an elevated pressure compared to the environment outside the chamber housing the liquid handling system.

31. and a robotic system for loading and unloading samples, wherein the system for screening for pathogens or genetic differences is configured to identify if and when the screening and / or processing for an individual sample or group of samples in the incubation zone is complete, and wherein the robotic system: removing the individual sample or group of samples from the incubator station, leaving an empty sample holder or group of sample holders, and removing a sample or group of samples from a location surrounded by or adjacent to a sample or group of samples for which screening and / or processing has not been completed; and then Obtain an unused sample or group of samples, then filling the vacant space in the incubator with said unused sample; 31. A screening system according to any one of claims 1 to 30, whereby the system is configured to be suitable for continuous throughput of samples.

32. 32. The screening system of any one of claims 1 to 31, further comprising an ultrasound detector for detecting one or more physical conditions of the system.

33. 33. The screening system of claim 32, wherein the one or more physical conditions of the system include the presence or absence of a sample at a predetermined location in the incubation zone.

34. 34. The screening system of any one of claims 1 to 33, further comprising a bin configured to contain waste generated by the screening system.

35. 35. A screening system according to claim 34 when dependent on claim 32, wherein the ultrasonic detector is configured to measure the fill level of the bin.

36. 1. A screening system configured to identify a biological agent, biological variance, pathogen, and / or genetic variance, comprising: an incubation zone having incubation stations for incubating a plurality of samples; a source of electromagnetic radiation for illuminating the plurality of samples; a detector for detecting electromagnetic radiation emitted from the plurality of samples; a chamber housing a liquid handling system for transferring liquid reagents to said plurality of samples; an airflow system having an inlet positioned to draw air from an environment external to the screening system, a filter, and an outlet positioned within the chamber; drawing air through the inlet and filter to form purified air, and then blowing the purified air into the chamber; an airflow system configured to maintain the chamber at an elevated pressure relative to an environment outside the chamber; A screening system comprising:

37. 37. The screening system of claim 36, wherein the incubation station comprises an optical-based datum system, the optical-based datum system being used as a reference point for orienting an image of the incubation station captured by the detector.

38. The incubation station further includes an incubator unit that can be housed in the incubation station, and the incubator unit is replaceable; a temperature controller having a plurality of containers each capable of containing a sample, the temperature controller being configured to heat or cool the plurality of containers; a source of electromagnetic radiation for irradiating one or more of the containers.

39. 1. A screening system configured to identify a biological agent, biological variance, pathogen, and / or genetic variance, comprising: an incubation zone having incubation stations for incubating a plurality of samples; a source of electromagnetic radiation for illuminating the plurality of samples; a detector for detecting electromagnetic radiation emitted from said plurality of samples; Equipped with A screening system wherein the incubation station and the detector are in a movable or fixed relationship relative to each other.

40. 40. A screening system according to any one of claims 36 to 39 as defined in any one of claims 1 to 35.

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