An apparatus includes a flow cell body with an array of reaction sites positioned along a floor of a channel. An optical filter layer is positioned under the floor of the channel and includes at least a portion spanning uninterruptedly along a length corresponding to the length of the array of reaction sites. Imaging regions are positioned under the optical filter layer. Each imaging region is positioned directly under a corresponding reaction site. The optical filter layer is configured to permit one or more selected wavelengths of light to pass from each reaction site to the imaging region forming a sensing pair with the reaction site. The optical filter layer is configured to reduce transmission of excitation light directed toward the reaction sites; and to reduce transmission of light emitted from each reaction site to imaging regions not forming a sensing pair with the reaction site.

A method and system for measuring the alignment between a substrate and a platform upon which it is disposed by using image processing algorithms are described herein. These algorithms automate the detection of edges of a microscope slide and the platform in a digital image. A reference line pattern in an image of the platform can be used to detect platform edges based on a computed location of the reference line pattern in the image.

A method and system for measuring the alignment between a substrate and a platform upon which it is disposed by using image processing algorithms are described herein. These algorithms automate the detection of edges of a microscope slide and the platform in a digital image. A reference line pattern in an image of the platform can be used to detect platform edges based on a computed location of the reference line pattern in the image.

A transmission type color calibration chart includes a transparent substrate and a color bar group formed on the transparent substrate, wherein the color bar group is constituted by color bars of a plurality of colors containing at least a first color and a second color arranged in a pattern in no particular order, coordinate points of the first color are within a region encompassed by the four points (0.351, 0.649), (0.547, 0.453), (0.380, 0.506) and (0.433, 0.464) on an xy chromaticity diagram, coordinate points of the second color are within a region encompassed by the four points (0.125, 0.489), (0.112, 0.229), (0.270, 0.407) and (0.224, 0.242) on an xy chromaticity diagram, and the transmission spectrum of the first color's color bar and the transmission spectrum of the second color's color bar have peak tops that are respectively separated.

A transmission type color calibration chart includes a transparent substrate and a color bar group formed on the transparent substrate, wherein the color bar group is constituted by color bars of a plurality of colors containing at least a first color and a second color arranged in a pattern in no particular order, coordinate points of the first color are within a region encompassed by the four points (0.351, 0.649), (0.547, 0.453), (0.380, 0.506) and (0.433, 0.464) on an xy chromaticity diagram, coordinate points of the second color are within a region encompassed by the four points (0.125, 0.489), (0.112, 0.229), (0.270, 0.407) and (0.224, 0.242) on an xy chromaticity diagram, and the transmission spectrum of the first color's color bar and the transmission spectrum of the second color's color bar have peak tops that are respectively separated.

An adapter is useful with a sample holder of a microscope. The adapter has at least one support region for reproducibly orienting the adapter in a mounted state in a sample holder support. The adapter also has a first coupling point for detachable connection to a coupling structure of a sample holder on one side, and a second coupling point for detachable connection to a coupling structure of a sample manipulator on a side of the adapter opposite to the first coupling point. The adapter is useful with the sample holder, a sample chamber, a microscope and a method for arranging a sample in a detection beam path of a microscope.

An adapter is useful with a sample holder of a microscope. The adapter has at least one support region for reproducibly orienting the adapter in a mounted state in a sample holder support. The adapter also has a first coupling point for detachable connection to a coupling structure of a sample holder on one side, and a second coupling point for detachable connection to a coupling structure of a sample manipulator on a side of the adapter opposite to the first coupling point. The adapter is useful with the sample holder, a sample chamber, a microscope and a method for arranging a sample in a detection beam path of a microscope.

A slide rack gripper apparatus is provided that simultaneously conveys a plurality of glass slides in the protection of a slide rack within a digital slide scanning apparatus. The slide rack gripper apparatus conveys the plurality of glass slides from a slide rack carousel to a scanning stage for processing. The slide rack gripper includes a first motor attached to a base configured to drive a finger mount attached to the base along a first linear axis. The slide rack gripper apparatus also includes a second motor attached to the finger mount and configured to drive opposing gripper fingers attached to the finger mount along a second linear axis. The second motor is also configured to drive individual gripper fingers along a third linear axis to move the gripper fingers toward each other and away from each other to grasp or release a slide rack.

A sample holder for holding a sample carrier carrying a sample includes a sample carrier fixing element. The sample carrier fixing element includes a first section configured, when in a first position, to fix the sample carrier to the sample holder, and, when in a second position, to release the sample carrier or to provide access to an area where the sample carrier is to be located. The sample carrier fixing element also includes a second section different from the first section, the second section being operable such that upon operation of the second section the first section switches from the first position into the second position or from the second position into the first position.

A sample holder transfer device is for use in cryo-microscopy and for transferring a sample holder to an analysing or processing unit. The sample holder is configured for holding a sample carrier carrying a sample. The sample holder transfer device is configured to receive the sample holder, the sample holder including a sample carrier fixing element. At least one section of the sample carrier fixing element is configured, when in a first position, to fix the sample carrier to the sample holder, and, when in a second position, to release the sample carrier or provide access to an area where the sample carrier is to be placed. The sample holder transfer device includes a switching mechanism operable to switch the at least one section of the sample carrier fixing element of the sample holder from the first to the second position or from the second to the first position.