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Methods and optical systems for scanning of a target sample, including methods and systems using a low mass scan head and methods and systems for conducting a scanned optically transduced assay where the scanning includes at least one first relative angular motion and at least one second angular mot

Methods and optical systems for scanning of a target sample, including methods and systems using a low mass scan head and methods and systems for conducting a scanned optically transduced assay where the scanning includes at least one first relative angular motion and at least one second angular motion or at least one linear motion. The present invention also relates to methods and systems for performing sample assays, and for producing and measuring optical responses and signatures.

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What is claimed is: 1. An optical system, comprising: a) a sample substrate having a surface, the surface defining a 2-dimensional sample plane; b) an excitation source configured to provide excitation light to the sample substrate; c) an optical detector configured to receive emission light from t

What is claimed is: 1. An optical system, comprising: a) a sample substrate having a surface, the surface defining a 2-dimensional sample plane; b) an excitation source configured to provide excitation light to the sample substrate; c) an optical detector configured to receive emission light from the sample substrate and generate detection data; d) a scan head configured at least (i) to direct the excitation light towards the sample substrate, (ii) to receive emission light from the sample substrate and direct the emission light towards the optical detector, and (iii) for scanning relative to the sample substrate; and e) actuators configured to scan the scan head relative to the sample substrate, wherein the actuators comprise at least one of (1) a linear actuator and a rotary actuator, and the scanning comprises a relative linear motion of the linear actuator and a relative angular motion of the rotary actuator about a rotational axis generally perpendicular to the sample plane and (2) two rotary actuators, and the scanning comprises relative angular motions of the two angular actuators about two respectively different rotational axes generally perpendicular to the sample plane. 2. An optical system according to claim 1, wherein the system is configured for rectilinear scanning of the scan head relative to the sample substrate surface. 3. An optical system according to claim 1, wherein the system is configured for point-by-point scanning of the scan head relative to the sample substrate surface. 4. An optical system according to claim 1, wherein the optical detector comprises first and second optical detectors configured to receive the emission light from the sample substrate and generate the detection data, wherein the first optical detector is configured to receive a first optically distinct range of the emission light and the second optical detector is configured to receive a second optically distinct range of the emission light. 5. An optical system according to claim 1, wherein the excitation source comprises the first and second LEDs, the first and second LEDs being configured to provide respectively optically distinct ranges of excitation light. 6. An optical system according to claim 1, wherein the actuators comprise the linear actuator and the rotary actuator, and the scanning comprises the relative linear motion and the relative angular motion, the linear actuator has a linear travel axis aligned generally parallel to the sample plane and is configured to provide linear movement of the scan head relative to the sample substrate along the linear travel axis; and the rotary actuator has a fixed base and a shaft configured for rotation about a rotational axis aligned generally perpendicular to the sample plane, wherein the fixed base is connected to the linear actuator, the system further comprising a first arm having a longitudinal axis, a first end, and a second end, wherein the first end is connected to the rotational actuator shaft and the second end is connected to the scan head; the first arm being configured for rotation of its longitudinal axis generally perpendicularly about the rotational axis. 7. An optical system according to claim 6, further comprising at least one bushing aligned parallel to the linear travel axis; and a platform connected to the linear actuator and configured to travel along the at least one bushing, wherein the fixed base of the rotary axis is connected to the platform. 8. An optical system according to claim 1, wherein the actuators comprise the two rotary actuators, and the scanning comprises the two relative angular motions, the first rotary actuator has a fixed base and a shaft configured for rotation about a first rotational axis aligned generally perpendicular to the sample plane; and the second rotary actuator has a fixed base and a shaft configured for rotation about a second rotational axis aligned generally perpendicular to the sample plane, wherein the second rotational axis is aligned generally parallel to the first rotational axis, the system further comprising a first arm having a longitudinal axis, a first end, and a second end, wherein the first end is connected to the first rotational actuator shaft and the second end connected to the second rotational actuator fixed base; the first arm being configured for rotation of its longitudinal axis generally perpendicularly about the first rotational axis; and a second arm having a longitudinal axis, a first end, and a second end, wherein the first end is connected to the second rotational actuator shaft and the second end is connected to the scan head; the second arm being configured for rotation of its longitudinal axis generally perpendicularly about the second rotation axis. 9. An optical system according to claim 1, further comprising at least one optical fiber having distal and proximal ends, wherein the at least one optical fiber is configured to conduct the emission light from its proximal to its distal end; and a fixed optical head comprising the distal end of the optical fiber and the optical detector, wherein the fixed optical head is configured to direct the emission light from the distal end of the optical fiber towards the optical detector, wherein the scan head is a low mass scan head comprising the proximal end of the at least one fiber optic and further configured to direct the emission light to the proximal end of the at least one optical fiber. 10. An optical system according to claim 9, wherein the low mass scan head further comprises an LED as the excitation source. 11. An optical system according to claim 9, wherein the fixed optical head comprises the excitation source and is configured to direct the excitation light into the distal end of the at least one optical fiber, the optical fiber is configured to direct the excitation light from its distal to its proximal end, and the low mass scan head is configured to direct the excitation light from the fiber optic proximal end towards the sample substrate. 12. An optical system according to claim 9, wherein the fixed optical head comprises a dispersive spectrometer comprising a dispersive element and an array detector or multiple optical detectors configured to measure spectral properties of the collected emission light. 13. An optical system according to claim 9, comprising an LED as the excitation source; a thermal control system comprising a temperature dependent unit comprising at least one of the LED and the optical detector; and at least one of (1) an active temperature compensation system comprising a temperature sensor configured to (i) monitor at least one temperature dependent property of the temperature dependent unit, and (ii) generate a thermal control signal related to the at least one temperature dependent property, and an active temperature compensation system configured to receive the thermal control signal and regulate at least one of (i) an operating temperature of the temperature dependent unit and (ii) the detection data from the optical detector to form temperature compensated detection data, wherein the regulation is based at least partially on the thermal control signal, and (2) a passive temperature compensation system comprising at least one of (i) an insulating oven at least partially encompassing the temperature dependent unit, and (ii) a thermally conductive substrate in thermal contact with the temperature dependent unit and configured to conduct thermal energy between the temperature dependent unit and the thermally conductive substrate. 14. An optical system according to claim 9, comprising an LED as the excitation source; a thermal control system comprising a temperature dependent unit comprising at least one of the LED and the optical detector; and an active temperature compensation system comprising a temperature sensor configured to (i) monitor at least one temperature dependent property of the temperature dependent unit, and (ii) generate a thermal control signal related to the at least one temperature dependent property, and an active temperature compensation system configured to receive the thermal control signal and regulate at least one of (i) an operating temperature of the temperature dependent unit and (ii) the detection data from the optical detector to form temperature compensated detection data, wherein the regulation is based at least partially on the thermal control signal. 15. An optical system according to claim 9, comprising an LED as the excitation source; a thermal control system comprising a temperature dependent unit comprising at least one of the LED and the optical detector; and a passive temperature compensation system comprising at least one of (i) an insulating oven at least partially encompassing the temperature dependent unit, and (ii) a thermally conductive substrate in thermal contact with the temperature dependent unit and configured to conduct thermal energy between the temperature dependent unit and the thermally conductive substrate. 16. An optical system according to claim 13, wherein the at least one temperature dependent property comprises at least one of a temperature, a temperature dependent optical property, a temperature dependent electronic property of the temperature dependent unit or the temperature sensor, or any combination thereof. 17. An optical system according to claim 13, wherein the temperature dependent unit comprises the temperature sensor. 18. An optical system according to claim 13, wherein the temperature sensor is in thermal contact with the temperature dependent unit. 19. An optical system according to claim 13, wherein the temperature sensor is configured to monitor at least one temperature dependent optical property of the temperature dependent unit. 20. A method for conducting a scanned optically transduced assay, comprising a) using an optical system according to claim 1, b) directing excitation light from the scan head to the sample substrate, c) receiving with the optical detector emission light from the sample substrate, and generating detection data based on the received emission light, d) scanning the scan head relative to the sample substrate, the scanning comprising at least one of (1) a relative linear motion and a relative angular motion about a rotational axis generally perpendicular to the sample plane and (2) two relative angular motions about two respectively different rotational axes generally perpendicular to the sample plane; e) tracking a position of the scan head relative to the substrate, and f) correlating the detection data with the position of the scan head.