Abstract: A fluidic handling unit includes a baseplate, a fluidic inlet block, a fluidic outlet block, a pump in fluidic communication with the fluidic inlet block and the fluidic outlet block, a carrier control board in electrical communication with the pump, and a flow cell carrier comprising a microfluidic flow cell receiving area, wherein the flow cell carrier is configured to receive and retain the fluidic handling unit. A bottom surface of the fluidic handling unit is configured to complementary mate with a top surface of the flow cell carrier, or wherein a bottom surface of the flow cell carrier is configured to complementarily mate with a top surface of the fluidic handling unit.

Abstract: The present disclosure relates to approaches for assessing a sample or the presence of microorganisms. The sample, in certain implementations may be assessed for one or both of absence of microorganisms (sterility) and/or for concentration of said organisms (bio-burden). sample partition device may be employed that partitions the sample input volume into multiple discrete measurement zones with little or no loss of sample (e.g., zero-loss) and with little operator involvement, thereby reducing operator- and environment-based false positives.

Abstract: The present disclosure relates to a consumable sample partition device and it assembly and use. The sample partition device can be used to test a sample for absence of microorganisms (sterility) and/or for concentration of said organisms (bio-burden). The sample partition device partitions the sample input volume into multiple discrete measurement zones with little or no loss of sample (e.g., zero-loss) and with little operator involvement, thereby reducing operator- and environment-based false positives.

Abstract: A fluidic handling unit includes a baseplate, a fluidic inlet block, a fluidic outlet block, a pump in fluidic communication with the fluidic inlet block and the fluidic outlet block, a carrier control board in electrical communication with the pump, and a flow cell carrier comprising a microfluidic flow cell receiving area, wherein the flow cell carrier is configured to receive and retain the fluidic handling unit. A bottom surface of the fluidic handling unit is configured to complementary mate with a top surface of the flow cell carrier, or wherein a bottom surface of the flow cell carrier is configured to complementarily mate with a top surface of the fluidic handling unit.

Abstract: Systems and methods for processing biological specimens are provided. The biological specimen processing system generally includes a flow cell carrier for holding a microfluidic flow cell and a fluidic handling unit attachable to the flow cell carrier. The fluidic handling unit interfaces with the microfluidic flow cell and can include fluidic pumps, fluidic connections, integrated electronics, and processing software to facilitate processing of a biological specimen contained in the microfluidic flow cell.

Abstract: A microfluidic device for image multiplexing includes a base structure and a fluid well insert. The base structure comprises an optical window. The fluid well insert configured to be coupled to the base structure and to retain a microscope slide for mounting a biological sample within the microfluidic device. The fluid well insert is further configured to provide a fluid to the biological sample. A fluid well insert lid is coupled to the fluid well insert or the fluid well insert comprises a fluid well insert lid.

Abstract: The present invention relates to a microfluidic device 100 for image multiplexing. The microfluidic device 100 comprises a base structure 110 comprising an optical window 140 and a fluid well insert 120 coupled to the base structure 110. The fluid well insert 120 is configured to retain a microscope slide 130 for mounting of a biological sample 150 within the microfluidic device 100. The fluid well insert 120 is also configured to provide a fluid to said biological sample 150. A fluid well insert lid 160 coupled to the fluid well insert 120 is also provided.

Abstract: The present disclosure relates to a consumable sample partition device and it assembly and use. The sample partition device can be used to test a sample for absence of microorganisms (sterility) and/or for concentration of said organisms (bio-burden). The sample partition device partitions the sample input volume into multiple discrete measurement zones with little or no loss of sample (e.g., zero-loss) and with little operator involvement, thereby reducing operator- and environment-based false positives.

Abstract: The present disclosure relates to approaches for assessing a sample or the presence of microorganisms. The sample, in certain implementations may be assessed for one or both of absence of microorganisms (sterility) and/or for concentration of said organisms (bio-burden). sample partition device may be employed that partitions the sample input volume into multiple discrete measurement zones with little or no loss of sample (e.g., zero-loss) and with little operator involvement, thereby reducing operator- and environment-based false positives.

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 present approach relates to the measure of the planar tilt of a slide on a microscope using an integrated auto-focuser. The tilt of the slide can be used to detect improperly loaded slides (i.e. if the slide is resting on either the cover-slip or a printed barcode), compensate for misalignment between the microscope optical axis and the slide, and reduce subsequent focusing times.

Abstract: Systems and methods for processing biological specimens are provided. The biological specimen processing system generally includes a flow cell carrier for holding a microfluidic flow cell and a fluidic handling unit attachable to the flow cell carrier. The fluidic handling unit interfaces with the microfluidic flow cell and can include fluidic pumps, fluidic connections, integrated electronics, and processing software to facilitate processing of a biological specimen contained in the microfluidic 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 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: 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: The present approach relates to the measure of the planar tilt of a slide on a microscope using an integrated auto-focuser. The tilt of the slide can be used to detect improperly loaded slides (i.e. if the slide is resting on either the cover-slip or a printed barcode), compensate for misalignment between the microscope optical axis and the slide, and reduce subsequent focusing times.