Abstract: Various embodiments of the present disclosure disclose methods and systems for actively monitoring an opto-fluidic instrument for vibrational disturbances and correcting images obtained during the detected disturbances. In various embodiments, an optical imaging system may acquire Z-stack images of samples supported by an XY-stage. Vibrations can cause individual stacks to be sheared, i.e., to not be co-located with respect to neighboring Z-stacks. In various embodiments, an offset between the measured positions and the expected positions of the sheared stacks may be computed, and a determination as to whether to correct or reacquire the Z-stack images may be made based at least in part on the computed offset.

Abstract: Various embodiments of the present disclosure disclose methods and systems for actively monitoring an opto-fluidic instrument for vibrational disturbances and correcting images obtained during the detected disturbances. In various embodiments, an optical imaging system may acquire Z-stack images of samples supported by an XY-stage. Vibrations can cause individual stacks to be sheared, i.e., to not be co-located with respect to neighboring Z-stacks. In various embodiments, an offset between the measured positions and the expected positions of the sheared stacks may be computed, and a determination as to whether to correct or reacquire the Z-stack images may be made based at least in part on the computed offset.

Abstract: The present disclosure relates in some aspects to methods and compositions for assessing system performance for in situ analyte detection. In some aspects, performance of an individual instrument can be assessed, or the performance of two or more instruments can be assessed and optionally compared. In some aspects, disclosed herein is a method comprising using rolling circle amplification products (RCPs) deposited on a cell-free and tissue-free quality control (QC) slide to assess performance of instrument workflow, where an instrument is used to decode signals associated with the RCPs on the QC slide. Quality metrics associated with the decoding (e.g., a percentage of RCPs successfully decoded to genes) can be used to qualify a system comprising the instrument and reagents for in situ analyte detection in cells or tissue samples, e.g., using in situ probe hybridization or in situ sequencing performed on the instrument.

Abstract: Various embodiments of the present disclosure disclose methods and systems for actively monitoring an opto-fluidic instrument for vibrational disturbances and correcting images obtained during the detected disturbances. In various embodiments, an optical imaging system may acquire Z-stack images of samples supported by an XY-stage. Vibrations can cause individual stacks to be sheared, i.e., to not be co-located with respect to neighboring Z-stacks. In various embodiments, an offset between the measured positions and the expected positions of the sheared stacks may be computed, and a determination as to whether to correct or reacquire the Z-stack images may be made based at least in part on the computed offset.