The systems and methods disclosed herein permit automated preparation of biological specimens for examination. The disclosed systems and methods provide fast, efficient, and highly uniform specimen processing using minimal quantities of fluids. The methods include at least a fixing phase for fixing a biological specimen to a substrate such as a microscope slide, a staining phase for staining the specimen, and a rinsing phase for rinsing the specimen. One or more of the fixing, staining, and rinsing phases include one or more agitation cycles for distributing reagents evenly and uniformly across the specimen. The systems can be implemented as a standalone device or as a component in a larger system for preparing and examining biological specimens.

In some instances, an apparatus can include a light sensitive imaging sensor having a surface to receive a fluid sample, a body to be moved relative to the light sensitive imaging sensor and having a surface to touch a portion of the fluid sample, and a carrier to move the body toward the surface of the light sensitive imaging sensor to cause the surface of the body to touch the portion of the fluid sample, so that as the surface of the body touches the portion of the fluid, the surface of the body (i) is parallel to the surface of the light sensitive imaging sensor, and (ii) settles on top of the fluid sample independently of motion of the carrier.

A specimen processing system is capable of processing specimens carried on slides. The specimen processing system can sequentially deliver slides and opposables to specimen processing stations. The specimen processing stations can use the opposables to apply a series of liquids to the specimens. The applied liquid can be moved along the slide using capillary action while the specimen processing stations control the processing temperatures. The applied liquid can be in a fluid-carrying gap. The opposable can contact the slide to vary a cross section of the fluid-carrying gap.

In some instances, an apparatus can include a light sensitive imaging sensor having a surface to receive a fluid sample, a body to be moved relative to the light sensitive imaging sensor and having a surface to touch a portion of the fluid sample, and a carrier to move the body toward the surface of the light sensitive imaging sensor to cause the surface of the body to touch the portion of the fluid sample, so that as the surface of the body touches the portion of the fluid, the surface of the body (i) is parallel to the surface of the light sensitive imaging sensor, and (ii) settles on top of the fluid sample independently of motion of the carrier.

A system is capable of detecting substrates and can differentiate between zero, one, or multiple transparent or semi-transparent substrates in a stack. The system can include an optical sensor, an optically anti-reflective element, and a detector. The optical sensor outputs light towards the optically anti-reflective element. The light detector is positioned to detect light from the light source that is reflected by substrates, if any, positioned within a detection zone between the optically anti-reflective element and the detector.

An apparatus for treating biological samples disposed on substrates, including: an input buffer for receiving one or more substrate holders each being adapted to support a plurality of the substrates; a treatment zone including a plurality of treatment stations each being adapted to receive one of the substrates; a reagent dispenser configured by a controller to dispense reagents to the substrates at the treatment stations; a substrate transport device configured by the controller to transport individual substrates between the substrate holders in the input buffer and the treatment stations.

A system is capable of detecting substrates and can differentiate between zero, one, or multiple transparent or semi-transparent substrates in a stack. The system can include an optical sensor, an optically anti-reflective element, and a detector. The optical sensor outputs light towards the optically anti-reflective element. The light detector is positioned to detect light from the light source that is reflected by substrates, if any, positioned within a detection zone between the optically anti-reflective element and the detector.

In some instances, an apparatus can include a light sensitive imaging sensor having a surface to receive a fluid sample, a body to be moved relative to the light sensitive imaging sensor and having a surface to touch a portion of the fluid sample, and a carrier to move the body toward the surface of the light sensitive imaging sensor to cause the surface of the body to touch the portion of the fluid sample, so that as the surface of the body touches the portion of the fluid, the surface of the body (i) is parallel to the surface of the light sensitive imaging sensor, and (ii) settles on top of the fluid sample independently of motion of the carrier.

In some instances, an apparatus can include a light sensitive imaging sensor having a surface to receive a fluid sample, a body to be moved relative to the light sensitive imaging sensor and having a surface to touch a portion of the fluid sample, and a carrier to move the body toward the surface of the light sensitive imaging sensor to cause the surface of the body to touch the portion of the fluid sample, so that as the surface of the body touches the portion of the fluid, the surface of the body (i) is parallel to the surface of the light sensitive imaging sensor, and (ii) settles on top of the fluid sample independently of motion of the carrier.

The systems and methods disclosed herein permit automated preparation of biological specimens for examination. The disclosed systems and methods provide fast, efficient, and highly uniform specimen processing using minimal quantities of fluids. The methods include at least a fixing phase for fixing a biological specimen to a substrate such as a microscope slide, a staining phase for staining the specimen, and a rinsing phase for rinsing the specimen. One or more of the fixing, staining, and rinsing phases include one or more agitation cycles for distributing reagents evenly and uniformly across the specimen. The systems can be implemented as a standalone device or as a component in a larger system for preparing and examining biological specimens.