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.

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.

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.

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 biological reaction apparatus for receiving at least one substrate having a sample located in a sample region, and a separate cover, such that a reaction chamber is formed between the cover and substrate over the sample region, wherein the apparatus includes a locating means to locate the substrate; a cover locating means for locating and moving the cover with respect to the substrate; a fluid dispensing means for dispensing fluid into the reaction chamber; and a draining mechanism; wherein the draining mechanism includes wicking means.

A system for performing coverslipping includes multiple zones, where a coverslipper device is designated to move from one or more zones. An input zone comprises a slide tray, which comprises a stack of stained slides and a slide that is designated to be picked up by a slide pick-up platform. The picked-up slide reaches a dispensation zone and a mountant medium is dispensed via a nozzle and the slide pickup platform moves to a coverslipping zone. The coverslipper device picks the cover slips from a slip pick-up zone and moves to a coverslipping zone. The slide pick-up platform positions itself in the coverslipping zone while the picked coverslip is mounted over the slide. The processed cover slipped slide is transported by a slide conveyor and inserted into a slide tray, which is moved up and down and is positioned to accommodate the next processed slide.

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 method and an automated apparatus for processing at least one biological sample arranged on a slide. At least one capillary staining module has a slide rack holder configured to detachably hold a slide rack configured to hold slides, and a capillary lid rack holder configured to detachably hold a capillary lid rack configured to hold capillary lids, wherein the slide rack can be removed independently of removing the capillary lid rack. A first fluid container has a first fluid. The apparatus being configured to automatically rotate the one or more slides, and to move the lids towards the slides to automatically form a capillary gap between each slide and each capillary lid, said capillary gap functioning as a capillary chamber; and to supply an amount of the first fluid to the slide.

A biological reaction apparatus for receiving at least one substrate having a sample located in a sample region, and a separate cover, such that a reaction chamber is formed between the cover and substrate over the sample region, wherein the apparatus includes a locating means to locate the substrate; a cover locating means for locating and moving the cover with respect to the substrate; a fluid dispensing means for dispensing fluid into the reaction chamber; and a draining mechanism; wherein the draining mechanism includes wicking means.

A system includes a base, a first accessory component, and a second accessory component. The base includes a receiving body and a control portion. The receiving body includes a receiver and a heating element proximate the receiver. The control portion includes one or more user interface features configured to control the heating element. The first accessory component is configured to process one or more tissue samples after sectioning using a microtome and is further configured for receipt with the receiver. The second accessory component is configured for receipt within the receiver. The first accessory component is configured for a different processing function of one or more tissue samples after sectioning using the microtome relative to the second accessory component. The first accessory component and the second accessory component are configured to be interchangeably received within the receiver.