Abstract: The present teachings relate to a method of generating calibration information during a real-time polymerase chain reaction (RT-PCR) or other amplification reaction. A sample well plate or other support can contain one or more dyes or other reference materials that are subjected to the same RT-PCR thermal cycles or other conditions used to conduct amplification or other reactions on a biological sample. A set of maxima values and a set of minimum values, and/or other calibration information useful for adjusting emission data for sample dyes can be recorded, for example, for 10 cycles, 20 cycles, or each cycle of a complete RT-PCR run. Such testing of dye response under realistic operating conditions can enable more accurate characterization of plate, dye, filter, or instrument response and therefore more accurate calibration corrections and other and/or adjustments.

Abstract: Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained.

Abstract: The present teachings relate to a method of generating calibration information during a real-time polymerase chain reaction (RT-PCR) or other amplification reaction. A sample well plate or other support can contain one or more dyes or other reference materials that are subjected to the same RT-PCR thermal cycles or other conditions used to conduct amplification or other reactions on a biological sample. A set of maxima values and a set of minimum values, and/or other calibration information useful for adjusting emission data for sample dyes can be recorded, for example, for 10 cycles, 20 cycles, or each cycle of a complete RT-PCR run. Such testing of dye response under realistic operating conditions can enable more accurate characterization of plate, dye, filter, or instrument response and therefore more accurate calibration corrections and other and/or adjustments.

Abstract: Exemplary embodiments provide microfluidic devices and methods for their use. The microfluidic device can include an array of M×N reaction sites formed by intersecting a first and second plurality of fluid channels of a flow layer. The flow layer can have a matrix design and/or a blind channel design to analyze a large number of samples under a limited number of conditions. The microfluidic device can also include a control layer including a valve system for regulating solution flow through fluid channels. In addition, by aligning the control layer with the fluid channels, the detection of the microfluidic devices, e.g., optical signal collection, can be improved by piping lights to/from the reaction sites. In an exemplary embodiment, guard channels can be included in the microfluidic device for thermal cycling and/or reducing evaporation from the reaction sites.

Abstract: Exemplary embodiments provide microfludic devices and methods for their use. The microfluidic device can include an array of M×N reaction sites formed by intersecting a first and second plurality of fluid channels of a flow layer. The flow layer can have a matrix design and/or a blind channel design to analyze a large number of samples under a limited number of conditions. The microfluidic device can also include a control layer including a valve system for regulating solution flow through fluid channels. In addition, by aligning the control layer with the fluid channels, the detection of the microfluidic devices, e.g., optical signal collection, can be improved by piping lights to/from the reaction sites. In an exemplary embodiment, guard channels can be included in the microfluidic device for thermal cycling and/or reducing evaporation from the reaction sites.

Abstract: Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained.

Abstract: Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained.

Abstract: Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained.

Abstract: Implementations of the present invention describe an apparatus for generating calibration factors for a spectral detector instrument. The calibration factors are derived from a calibration plate containing one or more spectral species in each well of the calibration plate. Each well is then exposed to an excitation source that causes the one or more spectral species in each of the wells to fluoresce. The signal response is measured and associated with each spectral species at each different well position in the calibration plate. Next, the measured signal response from each spectral species at each well position in the calibration plate is compared with a predetermined signal response for each spectral species. The results of this comparison can be used to determine a calibration factor for each well and spectral species to compensate for the difference between the measured signal response and the predetermined signal response.

Abstract: Implementations of the present invention describe an apparatus for generating calibration factors for a spectral detector instrument. The calibration factors are derived from a calibration plate containing one or more spectral species in each well of the calibration plate. Each well is then exposed to an excitation source that causes the one or more spectral species in each of the wells to fluoresce. The signal response is measured and associated with each spectral species at each different well position in the calibration plate. Next, the measured signal response from each spectral species at each well position in the calibration plate is compared with a predetermined signal response for each spectral species. The results of this comparison can be used to determine a calibration factor for each well and spectral species to compensate for the difference between the measured signal response and the predetermined signal response.

Abstract: Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained.

Abstract: Systems and methods for normalizing detected emission data collected in real-time polymerase chain reaction (RT-PCR) and other reactions, are provided. In some embodiments, a sample plate can be loaded with a fluorescent dye and subjected to a real-time PCR reaction. During the initial cycles, detected emissions that correspond to the background signal contributed by the plate, buffer, and other non-reactant pieces of the reaction system and chemistry can be identified. The raw emission data can be normalized by dividing the emission data by the identified baseline signal. According to various embodiments, the normalized amplification profile can normalize to an initial value of 1, because the actual signal emerges from the baseline at the point exponential growth begins. A normalized amplification profile based on a ratio to the baseline can create a more uniformly scaled amplification curve across different samples, filters, wells, dyes, or machines.

Abstract: A method for calibrating temperature can include cycling temperatures of a set of wells, wherein each well of the set comprises a sample with a spectrally distinguishable species. The method can further include measuring a signal from the spectrally distinguishable species for each well at a temperature during a first temperature cycle, and calibrating the temperatures for measuring the signal from each well during subsequent temperature cycles.

Abstract: Methods and systems for processing signals to minimize the effects of dye crosstalk. Deconvolution of multiplexed dye signals can include corrections for residual error determined from experimental measurements. Residual error corrections can account for reaction or assay specific factors and modify the subsequent filtering of signals. Correction values can be determined for specific dye-probe conjugates to minimize dye crosstalk and may be combined with residual error correction to further minimize errors in spectral deconvolution. Apparatus, systems, and computer-readable media can process signals and modify filters based on values obtained using the methods.

Abstract: Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained.

Abstract: A device is provided that comprises one or more fluid retainment regions each having at least one wall, and one or more loops in heat-transfer communication with the at least one wall. Each of the loops can comprise an electrical conductor that surrounds the same or a different fluid retainment region. A device is provided that comprises one or more fluid retainment regions each having particulates disposed therein. A system is provided that includes a platen adapted to hold a device including fluid retainment regions and one or more electrical conductors in heat-transfer communication with the fluid retainment regions. Methods of heating a sample are also provided.

Abstract: A device is provided that comprises one or more fluid retainment regions each having at least one wall, and one or more loops in heat-transfer communication with the at least one wall. Each of the loops can comprise an electrical conductor that surrounds the same or a different fluid retainment region. A device is provided that comprises one or more fluid retainment regions each having particulates disposed therein. A system is provided that includes a platen adapted to hold a device including fluid retainment regions and one or more electrical conductors in heat-transfer communication with the fluid retainment regions. Methods of heating a sample are also provided.

Abstract: Method and system providing calibration of light detected from biological samples with a correction factor including components for each of a plurality of spectrally distinguishable species and/or for each well and/or for each filter.

Abstract: Methods for generating a calibration factor and for calibrating are provided whereby interstitial spacing between support locations of a platform is used to embed a detectable material, emissions from which are used to generate the calibration factor. In some embodiments, the external space, outer perimeter, and other areas of a platform are used to embed detection materials for the normalization, calibration, correction, compensation, or other method of adjustment for detected emission data. The emission data can be taken from an assay, amplification, reaction, analysis, or other process, for example, from a PCR run or other reaction. By calibrating or adjusting the sample support with the detected emission data, a more efficient detection of the assay, amplification, reaction, analysis, or other process, can be achieved.

Abstract: Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained.