Abstract: A system for extracting material from a region of interest includes a fluid delivery base comprising an inlet channel and an outlet channel formed within the fluid delivery base, a gasket affixed to the fluid delivery base, wherein the gasket comprises at least one opening exposing an open end of the inlet channel and an open end of the outlet channel; a support comprising a sample-supporting surface facing the gasket and an opposing surface; and an alignment member coupled to the opposing surface in a fixed position and such that the support is positioned between the fluid delivery base and the alignment member, wherein one or both of the alignment member or the fluid delivery base are biased towards one another by a force (e.g., a magnet or spring force) and wherein the fluid delivery base is separable from the support and configured to move along a plane of the sample-supporting surface to align with the alignment member.

Abstract: Approaches are disclosed for calibrating a plurality of imaging devices, such as microscopes. In certain implementations, a calibration plate is employed that include a variety of calibration features. Imaging devices calibrated in accordance with the present approaches may be used to generate images having consistent attributes, such as brightness, regardless of which imaging device is employed.

Abstract: A system for extracting material from a region of interest includes a fluid delivery base comprising an inlet channel and an outlet channel formed within the fluid delivery base, a gasket affixed to the fluid delivery base, wherein the gasket comprises at least one opening exposing an open end of the inlet channel and an open end of the outlet channel; a support comprising a sample-supporting surface facing the gasket and an opposing surface; and an alignment member coupled to the opposing surface in a fixed position and such that the support is positioned between the fluid delivery base and the alignment member, wherein one or both of the alignment member or the fluid delivery base are biased towards one another by a force (e.g., a magnet or spring force) and wherein the fluid delivery base is separable from the support and configured to move along a plane of the sample-supporting surface to align with the alignment member.

Abstract: A system for extracting material from a region of interest includes a fluid delivery base comprising an inlet channel and an outlet channel formed within the fluid delivery base; a gasket affixed to the fluid delivery base, wherein the gasket comprises at least one opening exposing an open end of the inlet channel and an open end of the outlet channel; a support comprising a sample-supporting surface facing the gasket and an opposing surface; and an alignment member coupled to the opposing surface in a fixed position and such that the support is positioned between the fluid delivery base and the alignment member, wherein one or both of the alignment member or the fluid delivery base are biased towards one another by a force (e.g., a magnet or spring force) and wherein the fluid delivery base is separable from the support and configured to move along a plane of the sample-supporting surface to align with the alignment member.

Abstract: The invention provides a slide holder that utilizes edge detection algorithms to determine the location of various edges of a slide. From these edges, and integrating characteristic slide dimension, both linear offset of the edge of the slide in the holder and any rotation of the slide relative to the microscope stage axis are determined. The process of using the slide holder of the invention ensures precise and accurate placement of a slide during a first round of imaging and for reload in subsequent rounds.

Abstract: A system for extracting material from a region of interest includes a fluid delivery base comprising an inlet channel and an outlet channel formed within the fluid delivery base; a gasket affixed to the fluid delivery base, wherein the gasket comprises at least one opening exposing an open end of the inlet channel and an open end of the outlet channel; a support comprising a sample-supporting surface facing the gasket and an opposing surface; and an alignment member coupled to the opposing surface in a fixed position and such that the support is positioned between the fluid delivery base and the alignment member, wherein one or both of the alignment member or the fluid delivery base are biased towards one another by a force (e.g., a magnet or spring force) and wherein the fluid delivery base is separable from the support and configured to move along a plane of the sample-supporting surface to align with the alignment member.

Abstract: The invention provides a slide holder that utilizes edge detection algorithms to determine the location of various edges of a slide. From these edges, and integrating characteristic slide dimension, both linear offset of the edge of the slide in the holder and any rotation of the slide relative to the microscope stage axis are determined. The process of using the slide holder of the invention ensures precise and accurate placement of a slide during a first round of imaging and for reload in subsequent rounds.

Abstract: Approaches are disclosed for calibrating a plurality of imaging devices, such as microscopes. In certain implementations, a calibration plate is employed that include a variety of calibration features. Imaging devices calibrated in accordance with the present approaches may be used to generate images having consistent attributes, such as brightness, regardless of which imaging device is employed.

Abstract: A microfluidic flow cell subassembly, which may be assembled into a flow cell having fluidic connections outside of the main substrate, is described for encapsulating a sample to allow for subsequent controlled delivery of reagents to the sample, such as multiplexed in situ biomarker staining and analysis. The fluidic connectors are thin film fluidic connectors capable of connecting to a fluid delivery system. The subassembly may be sealed against a solid support to form a flow cell. Methods of use are also disclosed.

Abstract: The invention provides a coverslip for automated decoverslipping of a tissue bearing slide comprising a horizontal base portion having a length, width, and height, at least two side wall portions extending downward from opposite sides of the base portion each having a length and width and h; and wherein the total wall volume to base volume ratio is greater than or equal to approximately 0.025.

Abstract: A microfluidic flow cell subassembly, which may be assembled into a flow cell having fluidic connections outside of the main substrate, is described for encapsulating a sample to allow for subsequent controlled delivery of reagents to the sample, such as multiplexed in situ biomarker staining and analysis. As configured, the subassembly comprises a substrate layer forms a flexible optically transparent lid which is capable of bending in either direction to alter the internal dimensions of the subassembly. Methods of use are also disclosed.

Abstract: A microfluidic flow cell subassembly, which may be assembled into a flow cell having fluidic connections outside of the main substrate, is described for encapsulating a sample to allow for subsequent controlled delivery of reagents to the sample, such as multiplexed in situ biomarker staining and analysis. As configured, the subassembly comprises a substrate layer forms a flexible optically transparent lid which is capable of bending in either direction to alter the internal dimensions of the subassembly. Methods of use are also disclosed.

Abstract: A microfluidic flow cell subassembly, which may be assembled into a flow cell having fluidic connections outside of the main substrate, is described for encapsulating a sample to allow for subsequent controlled delivery of reagents to the sample, such as multiplexed in situ biomarker staining and analysis. The fluidic connectors are thin film fluidic connectors capable of connecting to a fluid delivery system. The subassembly may be sealed against a solid support to form a flow cell. Methods of use are also disclosed.