Abstract:
In one exemplary embodiment, a method (100) for calibrating an instrument is provided. The instrument includes an optical system capable of imaging florescence emission from a plurality of reaction sites. The method includes performing a region-of-interest (ROI) calibration (102) to determine reaction site positions in an image. The method further includes performing a pure dye calibration (108) to determine the contribution of a fluorescent dye used in each reaction site by comparing a raw spectrum of the fluorescent dye to a pure spectrum calibration data of the fluorescent dye. The method further includes performing an instrument normalization calibration (110) to determine a filter normalization factor. The method includes performing an RNase P validation (112) to validate the instrument is capable of distinguishing between two different quantities of sample.
Abstract:
According to one exemplary embodiment, a method for providing a amplification quality metric to a user is provided. The method includes receiving amplification data from an amplification of a sample to generate an amplification curve. The amplification curve includes an exponential region and a transition region. The method further includes determining a first value of the transition region and determining a second value of the transition region. The first value is the beginning of the transition region and the second value is the end of the transition region. Next, the amplification quality metric is calculated based on at least the first value and the second value. Then, the amplification quality metric is displayed to the user.
Abstract:
A biological analysis system (100) is provided. The system comprises a sample block assembly. The sample block assembly comprises a sample block (114) configured to accommodate a sample holder, the sample holder configured to receive a plurality of samples. The system also comprises a control system configured to cycle the plurality of samples through a series of temperatures. The system further comprises an automated tray (160) comprising a slide assembly, the tray (160) configured to reversibly slide the sample block assembly from a closed to an open position to allow user access to the plurality of sample holders.
Abstract:
A biological analysis system is provided. The system comprises a sample block assembly. The sample block assembly comprises a sample block configured to accommodate a sample holder, the sample holder configured to receive a plurality of samples. The system also comprises a control system configured to cycle the plurality of samples through a series of temperatures. The system further comprises an automated tray comprising a slide assembly, the tray configured to reversibly slide the sample block assembly from a closed to an open position to allow user access to the plurality of sample holders.
Abstract:
A computer-implemented method for designing a digital PCR (dPCR) experiment is provided. The method includes receiving, from a user, a selection of optimization type. The optimization type may be maximizing the dynamic range, minimizing the number of substrates including reaction sites needed for the experiment, determining a dilution factor, or determining the lower limit of detection, for example. The method further includes receiving, from the user, a precision measure for an experiment, and a minimum concentration of a target in a reaction site for the experiment. The method also includes determining a set of dPCR experiment design factors for the experiment based on the optimization type. The set of dPCR experiment design factors is then displayed to the user.
Abstract:
In one exemplary embodiment, a method for validating an instrument is provided. The method includes receiving amplification data from a validation plate to generate a plurality of amplification curves. The validation plate includes a sample of a first quantity and a second quantity, and each amplification curve includes an exponential region. The method further includes determining a set of fluorescence thresholds based on the exponential regions of the plurality of amplification curves and determining, for each fluorescence threshold of the set, a first set of cycle threshold (Ct) values of amplification curves generated from the samples of the first quantity and a second set of Ct values of amplification curves generated from the samples of the second quantity. The method includes calculating if the first and second quantities are sufficiently distinguishable based on Ct values at each of the plurality of fluorescence thresholds.
Abstract:
A biological analysis system is provided. The system comprises a sample block assembly. The sample block assembly comprises a sample block configured to accommodate a sample holder, the sample holder configured to receive a plurality of samples. The system also comprises a control system configured to cycle the plurality of samples through a series of temperatures. The system further comprises an automated tray comprising a slide assembly, the tray configured to reversibly slide the sample block assembly from a closed to an open position to allow user access to the plurality of sample holders.
Abstract:
A computer-implemented method for designing a digital PCR (dPCR) experiment is provided. The method includes receiving, from a user, a selection of optimization type. The optimization type may be maximizing the dynamic range, minimizing the number of substrates including reaction sites needed for the experiment, determining a dilution factor, or determining the lower limit of detection, for example. The method further includes receiving, from the user, a precision measure for an experiment, and a minimum concentration of a target in a reaction site for the experiment. The method also includes determining a set of dPCR experiment design factors for the experiment based on the optimization type. The set of dPCR experiment design factors is then displayed to the user.