Abstract: An instrument for processing and/or measuring a biological process comprises a sample processing system and an excitation source exhibiting a spectral function of output power or intensity verses wavelength of output power or intensity. The spectral function has a minima wavelength corresponding to a local minima value of the output power or intensity; a first maxima wavelength corresponding to a first local maxima of output power or intensity, the output power or intensity at the first local maxima being greater than the output power or intensity at any wavelength less than the minima wavelength; a second maxima wavelength corresponding to a second local maxima of output power or intensity, the output power or intensity at the second local maxima being greater than the output at any wavelength greater than the minima wavelength; the minima wavelength is between the first maxima wavelength and the second maxima wavelength.

Abstract: An instrument for processing and/or measuring a biological process comprises a sample processing system and an excitation source exhibiting a spectral function of output power or intensity verses wavelength of output power or intensity. The spectral function has a minima wavelength corresponding to a local minima value of the output power or intensity; a first maxima wavelength corresponding to a first local maxima of output power or intensity, the output power or intensity at the first local maxima being greater than the output power or intensity at any wavelength less than the minima wavelength; a second maxima wavelength corresponding to a second local maxima of output power or intensity, the output power or intensity at the second local maxima being greater than the output at any wavelength greater than the minima wavelength; the minima wavelength is between the first maxima wavelength and the second maxima wavelength.

Abstract: An instrument for processing and/or measuring a biological process contains a sample processing system, an excitation source, an excitation optical system, an optical sensor, and an emission optical system. The sample processing system is configured to retain a first sample holder and a second sample holder, wherein the number of sample cells is different for each sample holder or a characteristic dimension for the first sample cells is different from that of the second sample holder. The instrument also includes an excitation source temperature controller comprising a temperature sensor that is coupled to the excitation source. The temperature controller is configured to produce a first target temperature when the first sample holder is retained by the instrument and to produce a second target temperature when the second sample holder is retained by the instrument.

Abstract: A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.

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: 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: A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.

Abstract: An instrument for processing and/or measuring a biological process contains a sample processing system, an excitation source, an excitation optical system, an optical sensor, and an emission optical system. The sample processing system is configured to retain a first sample holder and a second sample holder, wherein the number of sample cells is different for each sample holder or a characteristic dimension for the first sample cells is different from that of the second sample holder. The instrument also includes an excitation source temperature controller comprising a temperature sensor that is coupled to the excitation source. The temperature controller is configured to produce a first target temperature when the first sample holder is retained by the instrument and to produce a second target temperature when the second sample holder is retained by the instrument.

Abstract: A method for calibrating a biological instrument is provided. The method comprises the steps of acquiring an image of at least one biological sample array, determining a first region of interest within the image, wherein the first region of interest comprises a first plurality of locations on the at least one biological array; and identifying within the first region of interest, a plurality of image elements associated with each of the first plurality of locations on the at least one biological array.

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: A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.

Abstract: A method for calibrating a biological instrument is provided. The method comprises the steps of acquiring an image of at least one biological sample array, determining a first region of interest within the image, wherein the first region of interest comprises a first plurality of locations on the at least one biological array; and identifying within the first region of interest, a plurality of image elements associated with each of the first plurality of locations on the at least one biological array.