Abstract: Approaches are disclosed for calibrating a plurality of imaging devices, such as microscopes. In certain implementations, a calibration plate is employed that includes a variety of calibration features. The calibration features comprise a geometric calibration, an illumination calibration, and an optical calibration. 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: 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 method for processing and imaging a first and second plurality of samples, comprising processing at least one sample from the first plurality of samples, imaging the at least one sample from the first plurality of samples, while being capable of simultaneously processing at least one sample from the second plurality of samples; and imaging the at least one processed sample from the second plurality of samples.

Abstract: A method of analyzing a biological sample suspected of having classic Hodgkin lymphoma, comprising (1) detecting, in a single sample, for the expression of at least two biomarkers selected from CD30, CD15, CD20, CD45, CD3, Pax-5, CD79A, BOB1 and OCT-2; and (b) analyzing the sample based on the presence, absence and/or expression level of the at least two biomarkers. Also provided is a method wherein all the nine biomarkers are analyzed on a single sample. Further provided are method for diagnosing classical Hodgkin lymphoma, as well as system and kit that comprise the means for executing the novel methods.

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 method for processing and imaging a first and second plurality of samples, comprising processing at least one sample from the first plurality of samples, imaging the at least one sample from the first plurality of samples, while being capable of simultaneously processing at least one sample from the second plurality of samples; and imaging the at least one processed sample from the second plurality of samples.

Abstract: A method for providing a composite image of a single biological sample from a patient suspected of having classical Hodgkin lymphoma, comprising the steps of generating a first image of the biological sample including the presence, absence and/or expression level of a first biomarker, generating a second image of the biological sample including the presence, absence and/or expression level of a second biomarker, and generating a composite image that provides the relative location or expression of both biomarkers. Also provided is a method of analyzing a biological sample, comprising providing a composite image of the biological sample according to the method for providing a composite image, and analyzing the expression of the biomarkers of interest from the composite image. Further provided are method for diagnosing classical Hodgkin lymphoma, as well as system and kit that comprise the means for executing the novel methods.

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. Methods for fabricating the subassembly and assembled flow cell are also provided. The method includes the steps of adhering a gasket layer to a substrate layer, wherein the gasket layer may contain enclosed features and adhering an adherent layer to the gasket layer. The subassembly may be sealed against a solid support to form a flow cell.

Abstract: Referencing of image acquired in multiple rounds of imaging is disclosed. In certain implementations, a baseline round of images are acquired and registered to one another to establish a global transformation matrix. In a subsequent round of image acquisition, a limited number of field of view images are initially acquired and registered to the corresponding baseline images to solve for translation, rotation, and scale. The full set of baseline images is then acquired for the subsequent round and each image is pre-rotated and pre-scaled based on the transform determined for the subset of images. The pre-rotated, pre-scaled images are then registered using a translation-only transform.

Abstract: A closed loop automated method for staining of a biological sample is provided. The method comprises providing a biological sample, staining at least a portion of the biological sample by flowing in a reagent, monitoring one or more optical characteristics of the biological sample, and calculating a figure of merit based on at least one of the optical characteristics. An automated device for iterative staining of a biological sample is also provided.

Abstract: An open top microfluidic device comprising a microfluidic slide carrier and one or more multiplexing stations is provided which allows sequential staining and imaging without the need for using or removing a coverslip on a mounted biological sample.

Abstract: A method for processing and imaging a first and second plurality of samples, comprising processing at least one sample from the first plurality of samples, imaging the at least one sample from the first plurality of samples, while being capable of simultaneously processing at least one sample from the second plurality of samples; and imaging the at least one processed sample from the second plurality of samples.

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. Methods for fabricating the subassembly and assembled flow cell are also provided. The method includes the steps of adhering a gasket layer to a substrate layer, wherein the gasket layer may contain enclosed features and adhering an adherent layer to the gasket layer. The subassembly may be sealed against a solid support to form a flow cell.

Abstract: Provided is a device, such as a switch structure, that includes a contact and a conductive element that is configured to be deformable between a first position in which the conductive element is separated from the contact and a second position in which the conductive element contacts the contact. The conductive element can be formed substantially of metallic material configured to inhibit time-dependent deformation. For example, the metallic material may be configured to exhibit a maximum steady-state plastic strain rate of less than 10?12 s?1 when subject to a stress of at least about 25 percent of a yield strength of the metallic material and a temperature less than or equal to about half of a melting temperature of the metallic material. The contact and the conductive element may be part of a microelectromechanical device or a nanoelectromechanical device. Associated methods are also provided.

Abstract: A closed loop automated method for staining of a biological sample is provided. The method comprises providing a biological sample, staining at least a portion of the biological sample by flowing in a reagent, monitoring one or more optical characteristics of the biological sample, and calculating a figure of merit based on at least one of the optical characteristics. An automated device for iterative staining of a biological sample is also provided.

Abstract: A micro electromechanical system switch having an electrical pathway is presented. The switch includes a first portion and a second portion. The second portion is offset to a zero overlap position with respect to the first portion when the switch is in open position (or in the closed position depending on the switch architecture). The switch further includes an actuator for moving the first portion and the second portion into contact.

Abstract: Provided is a device, such as a switch structure, that includes a contact and a conductive element that is configured to be deformable between a first position in which the conductive element is separated from the contact and a second position in which the conductive element contacts the contact. The conductive element can be formed substantially of metallic material configured to inhibit time-dependent deformation. For example, the metallic material may be configured to exhibit a maximum steady-state plastic strain rate of less than 10?12 s?1 when subject to a stress of at least about 25 percent of a yield strength of the metallic material and a temperature less than or equal to about half of a melting temperature of the metallic material. The contact and the conductive element may be part of a microelectromechanical device or a nanoelectromechanical device. Associated methods are also provided.

Abstract: A micro electromechanical system switch having an electrical pathway is presented. The switch includes a first portion and a second portion. The second portion is offset to a zero overlap position with respect to the first portion when the switch is in open position (or in the closed position depending on the switch architecture). The switch further includes an actuator for moving the first portion and the second portion into contact.