Abstract: Methods and systems for providing multi-plane viewing of a digital image of a subject matter which do not require viewing multiple images taken at multiple image planes. Pseudo-focus images are generated from a flattened, merged image of a three-dimensional subject matter. The merged image is generated by merging a plurality of images taken at different focal planes of the subject matter which form a through-focus image stack. The merged image comprises the best focus pixels originating from different respective image planes. A depth map is also generated from the multiple images which associates each best focus pixel with a pixel depth value. A plane of interest (POI) is selected from the image planes. A pseudo-focus image is then generated using the merged image and pixel depth map by generating a blurred focus value for each best focus pixel based on the focus offset of each pixel from the POI.

Abstract: A method of configuring an optical system to reduce variations in measured properties of an analyte includes selecting a number of beams into which radiation from a source of radiation is to be split, wherein, upon irradiating the analyte from a plurality of directions by the number of beams, a variation of a resulting measurement of the analyte is at or below a threshold. The method further includes aligning the source of radiation and a plurality of optical elements optically coupled to the source of radiation such that the selected number of beams irradiate the analyte upon emission of radiation by the source of radiation.

Abstract: An apparatus for identifying analytes of a first type in a fluid sample having a plurality of types includes a closed flow cell. The flow cell includes a sample inlet, a sample outlet. A flow path, between the inlet and outlet, passing through an interrogation region and at least a portion extending from immediately upstream to immediately downstream of the interrogation region is bounded by a flow cell well to form a continuous closed flow path. The apparatus also includes a spherical element having a center point coincident with the interrogation region. A hydrodynamic focusing element upstream of the interrogation region creates a core-in-sheath flow along a flow axis of the flow path as it passes through the interrogation region. Further, the apparatus includes a concave, ellipsoidal collector element having a first focal point disposed in the interrogation region of the flow path.

Abstract: A method of configuring an optical system to reduce variations in measured properties of an analyte includes selecting a number of beams into which radiation from a source of radiation is to be split, wherein, upon irradiating the analyte from a plurality of directions by the number of beams, a variation of a resulting measurement of the analyte is at or below a threshold. The method further includes aligning the source of radiation and a plurality of optical elements optically coupled to the source of radiation such that the selected number of beams irradiate the analyte upon emission of radiation by the source of radiation.

Abstract: An apparatus for identifying analytes of a first type in a fluid sample having a plurality of types includes a closed flow cell. The flow cell includes a sample inlet, a sample outlet. A flow path, between the inlet and outlet, passing through an interrogation region and at least a portion extending from immediately upstream to immediately downstream of the interrogation region is bounded by a flow cell well to form a continuous closed flow path. The apparatus also includes a spherical element having a center point coincident with the interrogation region. A hydrodynamic focusing element upstream of the interrogation region creates a core-in-sheath flow along a flow axis of the flow path as it passes through the interrogation region. Further, the apparatus includes a concave, ellipsoidal collector element having a first focal point disposed in the interrogation region of the flow path.

Abstract: An apparatus for detecting an analyte in a sample includes an illumination source for generating electromagnetic energy to illuminate the sample at an interrogation region, a concave collector element having an optical axis, and a focal point, the interrogation region being coincident with the focal point of the concave collector element, a closed flow cell having a flow path defined between a sample inlet and a sample outlet, the flow path passing through the interrogation region and a sorting region disposed downstream of the interrogation region. The portion of the flow path passing through the interrogation region is coaxially aligned with the optical axis of the concave collector element. The apparatus further includes the sample comprising or suspected of comprising the analyte and flowing in the flow path, wherein the analyte generates a detectable signal in response to illumination. The apparatus also includes a detector for detecting the detectable signal.

Abstract: An apparatus for detecting an analyte in a sample includes an illumination source for generating electromagnetic energy to illuminate the sample at an interrogation region, a concave collector element having an optical axis, and a focal point, the interrogation region being coincident with the focal point of the concave collector element, a closed flow cell having a flow path defined between a sample inlet and a sample outlet, the flow path passing through the interrogation region and a sorting region disposed downstream of the interrogation region. The portion of the flow path passing through the interrogation region is coaxially aligned with the optical axis of the concave collector element. The apparatus further includes the sample comprising or suspected of comprising the analyte and flowing in the flow path, wherein the analyte generates a detectable signal in response to illumination. The apparatus also includes a detector for detecting the detectable signal.