Non-contact mixing using modulated air jets.

Abstract

To provide a device for contactlessly mixing a fluid present on an upper surface of a slide.SOLUTION: A device provided herein comprises a first nozzle array and a second nozzle array, the first nozzle array being adapted to impart a bulk fluid flow to a fluid present on an upper surface of the slide, and the second nozzle array being adapted to impart at least a first regional fluid flow to at least a portion of the fluid present on the upper surface of the slide.SELECTED DRAWING: Figure 9B

Description

[Technical field]

[0001] (CROSS REFERENCE TO RELATED APPLICATIONS) This application claims the benefit of the filing date of U.S. Provisional Patent Application No. 62 / 589,234, filed November 21, 2017, the disclosure of which is incorporated herein by reference in its entirety. [Background technology]

[0002] Many tissues do not retain enough color after processing to make their components visible under a bright field microscope. Therefore, it is common practice to add color and contrast to tissue components by staining the tissue with various reagents. In the past, the step of staining tissue samples for histological or cytological analysis was performed manually (an inherently inconsistent process). Inconsistent staining makes it difficult for pathologists or other medical personnel to read slides and make comparisons between different samples. Therefore, several devices and methods have been described that help automate the staining process and reduce the inconsistency of staining.

[0003] Devices for automated staining, particularly for large volume staining with traditional reagents such as hematoxylin and eosin (H&E), are primarily of the "dip and dunk" type, in which a rack of slides is automatically lowered into and removed from a series of reagent baths. For example, U.S. Patent No. 4,911,098 to Tabata describes an automated staining apparatus in which microscope slides holding tissue specimens are immersed sequentially into multiple containers of chemical solution. The slides are mounted vertically in a slide holder basket, and clamps that engage and disengage the basket are used to move the slides from solution to solution. The clamps can include a mechanism for tilting the basket, which aids in removing excess solution before the basket is submerged in the next solution. Further automated staining devices of the "dip and dunk" type are described in U.S. Pat. No. 5,573,727 to Keef, U.S. Pat. No. 6,080,363 to Takahasi et al., U.S. Pat. No. 6,436,348 to Ljungmann et al., and U.S. Patent Application Publication No. 2001 / 0019703, which lists Thiem et al. as inventors.

[0004] Another type of automated stainer delivers fresh reagents directly to individual slides. For example, U.S. Patent No. 6,387,326 to Edwards et al. describes an apparatus for staining slides in which slides are ejected, one at a time, from a slide storage device and individually processed at various staining stations as they move along a conveyor belt transport. Additional devices for automatically staining individual slides are described in U.S. Patent No. 6,180,061 to Bogen et al., PCT Application WO 03 / 045560, which lists Tseung et al. as inventors, and U.S. Patent Application Publication No. 2004 / 0052685, which lists Richards et al. as inventors.

[0005] Efficient mixing of fluids is a critical step in many industrial, chemical, and pharmaceutical processes, as well as in biotechnological applications. Mixing on a small scale is often a difficult task. In some embodiments, molecular diffusion becomes the dominant mixing mechanism, slowing down the overall process. Integration of active mixers is often difficult, increasing the cost of any such device and introducing cross-contamination between samples. Summary of the Invention

[0006] Disclosed herein are systems and methods for non-contact dispersal, replenishment, and / or mixing (collectively referred to herein as "mixing") of one or more fluids on a substrate (e.g., a microscope slide). Applicant has discovered that the use of multiple gas streams directed to a fluid (e.g., a puddle of fluid) present on a surface (e.g., a flat support surface) of a substrate provides fluid movement and direction to a predetermined area of ​​the fluid, thus enabling mixing, distribution, and / or replenishment of the fluid or multiple components within the fluid. Applicant has also unexpectedly discovered that the introduction of such directed gas flows (such as separate or discrete streams) achieves bulk mixing of the fluid, as opposed to merely stirring or localized mixing. In fact, Applicant has discovered that the non-contact mixer of the present disclosure allows for improved mixing compared to simply stirring the fluid on the substrate with the induction of vortex flows (e.g., mixing by the non-contact mixer of the present disclosure allows for faster and more thorough mixing). Additionally, the non-contact mixers of the present disclosure allow for fluid movement at multiple locations across the slide so that air bubbles, if formed, can be displaced and / or removed In contrast, simple vortex mixing may displace air bubbles to the center of the fluid.

[0007] Applicants have also discovered that mixing fluids according to the methods described herein (i) reduces the risk of staining artifacts; (ii) allows for uniform reagent concentration across cells and / or tissues during staining, for example to reduce the formation of lightly stained areas (e.g., light spots) or darkly stained areas (e.g., dark spots); (iii) allows for increased mixing frequency; (iv) increases mixing efficacy; and / or (v) reduces or eliminates the presence of air bubbles within the fluid. It is also believed that the use of the devices and methods disclosed herein can allow for the use of lower concentrations of detection probes (e.g., antibodies) or other reagents in any histological or cytological staining procedure. Furthermore, the use of the devices and methods allows for lower manufacturing and maintenance costs, reduced process times, and / or reduced contamination. These and other advantages are further described herein.

[0008] One aspect of the present disclosure is a device that allows for non-contact mixing of a fluid on a substrate, the device being configured to direct multiple gas streams to a fluid and / or to a surface of a substrate such that at least two discrete fluid movements are imparted to a given portion of the fluid at different times, the two discrete fluid movements allowing for cross-mixing. In some embodiments, the device is configured such that the gas streams adequately mix the fluid present on the substrate surface while reducing loss of fluid from the substrate or splashing of fluid from the substrate onto an adjacent substrate.

[0009] Another aspect of the present disclosure is an automated slide processing device comprising at least one non-contact mixer for mixing fluids present on the upper surface of the slide, the non-contact mixer including a first nozzle set and a second nozzle set, the first nozzle set configured to impart a first motion to a first portion of the fluids present on the upper surface of the slide, and the second nozzle set configured to impart a second motion to at least a second portion of the fluids present on the upper surface of the slide. In some embodiments, the second motion induces cross-mixing of the fluids. In some embodiments, the first and second motions are opposite motions. In some embodiments, the second nozzle set imparts a second motion and a third motion, the second and third motions being the same or different, but at least one of the second or third motions being opposite to the first motion. In some embodiments, the gas flow allows the fluids or any portion of the fluids to move in a substantially circular path.

[0010] In some embodiments, the first set of nozzles operates independently and at different times from the second set of nozzles, i.e., the first set of nozzles operates exclusively from the second set of nozzles. Thus, the first set of nozzles can provide a first motion during at least the operation of the first set of nozzles, and the second set of nozzles can provide at least a second motion during at least the operation of the second set of nozzles. One skilled in the art will appreciate that the first set of nozzles can comprise multiple nozzles, each of the multiple nozzles of the first set of nozzles operating simultaneously to provide the first fluid motion. As an example, the first set of nozzles can comprise first and second nozzles directing a gas flow toward one area of ​​the fluid, and third and fourth nozzles simultaneously directing a gas flow toward another area of ​​the fluid, where the first and second nozzles can direct the gas in a first direction, and the third and fourth nozzles can direct the gas in a second opposite direction. Of course, the second nozzle operates in a similar manner but may be similarly configured to provide at least a second motion. In some embodiments, the automated slide processing device further includes a second non-contact mixer, e.g., one or more discrete nozzle sets, each discrete nozzle set capable of independent operation.

[0011] In some embodiments, the first portion is the majority of the fluid present on the slide. In some embodiments, the first motion is applied to the entirety of the fluid. In some embodiments, the first motion is one of clockwise or counterclockwise agitation. In still other embodiments, the first motion is applied to at least 60% of the fluid. In still further embodiments, the first motion is applied to at least 70% of the fluid. In still further embodiments, the first motion is applied to at least 80% of the fluid.

[0012] In some embodiments, the second motion is imparted to at least two discrete portions of the fluid present on the upper surface of the slide. In some embodiments, the second motion is imparted to at least three discrete portions of the fluid present on the upper surface of the slide. In some embodiments, the second motion is imparted to a central portion of the slide (e.g., the central third of the total fluid). In some embodiments, the second nozzle set is further adapted to impart a third motion to two ends of the fluid (e.g., the first third and the last third of the total fluid), each of the two ends of the fluid being adjacent to the central portion, and the third motion being opposite to the second motion. In some embodiments, the first motion is a counterclockwise agitation, the second motion is a clockwise agitation, and the third motion is a counterclockwise agitation.

[0013] In some embodiments, the second nozzle set is configured such that the second motion is applied to at least two different portions of the fluid, e.g., non-adjacent portions of the fluid. In some embodiments, the second nozzle set is further adapted to apply a third motion to a central portion of the fluid. In some embodiments, the first motion is a counterclockwise motion, the second motion is a clockwise motion, and the third motion is a counterclockwise motion, and the second motion is applied to two ends of the fluid located on either side of the central portion.

[0014] In some embodiments, the at least one non-contact mixer is positioned above the upper surface of the slide. In some embodiments, the at least one non-contact mixer is positioned between 0.3 inches (7.62 mm) and about 1.5 inches (38.1 mm) above the slide. In some embodiments, the at least one non-contact mixer is positioned substantially parallel to the upper surface of the slide. In some embodiments, the at least one non-contact mixer body is offset at an angle relative to the upper surface of the slide (e.g., offset at an angle between about 1 degree and about 20 degrees).

[0015] In some embodiments, the first and second nozzle sets are configured to direct the gas stream to a predetermined location on the upper surface of the slide. In some embodiments, the first and second nozzle sets are configured to direct the gas stream to a predetermined location on the upper surface of the slide at a predetermined angle of incidence with respect to the slide surface. In some embodiments, the angle of incidence of the gas stream with respect to the upper surface of the slide (e.g., an angle from a line normal to the surface) is between about 15 degrees and about 90 degrees. In some embodiments, the gas stream can be directed to a location between the fluid on the slide and the edge of the upper surface of the slide.

[0016] In some embodiments, the first nozzle set includes 2 to 6 nozzles. In some embodiments, the first nozzle set includes 4 to 6 nozzles. In some embodiments, the nozzles of the first nozzle set are grouped into two parallel rows along a longitudinal axis of the non-contact mixer. In some embodiments, each nozzle of the first nozzle set independently has a particular tilt angle and offset angle, as those terms are defined herein. In some embodiments, the second nozzle set includes 2 to 4 nozzles. In some embodiments, the nozzles of the second nozzle set are grouped into two substantially parallel rows along a longitudinal axis of the non-contact mixer. In some embodiments, each nozzle of the second nozzle set independently has a particular tilt angle and offset angle.

[0017] In some embodiments, the automated slide processing device is a staining device. In some embodiments, the automated slide processing device further comprises a control system, which is adapted to independently operate (e.g., pulse at a predetermined interval and / or at a predetermined frequency) the first and second nozzle sets to provide the first and second motions, and any additional motions if the non-contact mixer is so configured. In some embodiments, the automated slide processing device further comprises a third nozzle set to provide additional directional motions to the fluid present on the upper surface of the slide.

[0018] Another aspect of the disclosure is a method of operating a non-contact mixer, the non-contact mixer including a first nozzle set and a second nozzle set, the first nozzle set adapted to impart a first motion to a fluid present on an upper surface of a slide, and the second nozzle set adapted to impart a second motion to at least a portion of the fluid present on the upper surface of the slide, the method including operating the first nozzle set for a first period of time and thereafter operating the second nozzle set for a second period of time, provided that the first and second nozzle arrays are not operated simultaneously. In some embodiments, the first and second nozzle sets are operated together at least once. In some embodiments, the first and second nozzle sets are operated at least twice. In some embodiments, the first and second nozzle sets are communicatively coupled to a control system having one or more sensors, the sensors adapted to determine an extent of mixing during or after operation of the first and / or second nozzle sets.

[0019] Another aspect of the disclosure is an automated slide processing device, the automated slide processing device comprising: (i) at least one fluid dispenser configured to dispense a fluid onto an upper surface of a specimen-supporting slide; and (ii) a non-contact mixer for mixing fluids present on the upper surface of the slide, the non-contact mixer comprising a first nozzle array and a second nozzle array, the first nozzle array adapted to impart a bulk fluid flow to the fluids present on the upper surface of the slide, and the second nozzle array adapted to impart at least a first localized fluid flow to at least a portion of the fluids present on the upper surface of the slide. In some embodiments, the first localized fluid flow induces cross-mixing within the fluids. In some embodiments, the automated slide processing device is a staining device, the fluids present on the upper surface of the slide include a reagent, non-limiting examples of the reagent include a staining reagent, a counterstaining reagent, or a washing reagent. Other reagents and / or fluids that may be present on the surface of the slide are known to those of skill in the art.

[0020] In some embodiments, the bulk fluid flow is one of a clockwise or counterclockwise motion, such as stirring or other rotational motion. In some embodiments, the first localized fluid flow is the other of a clockwise or counterclockwise motion. In some embodiments, the first localized fluid flow is applied to the center of the fluid present on the upper surface of the slide. In some embodiments, the first localized fluid flow is applied to the center of the fluid present on the upper surface of the slide, the center representing about one third of the fluid present on the upper surface of the slide. Those skilled in the art will understand that the first localized fluid flow can be applied to any part of the fluid on the slide, provided that the first localized fluid flow allows cross-mixing with any additional localized fluid flow applied.

[0021] In some embodiments, the second nozzle array is further adapted to provide a second localized fluid stream and a third localized fluid stream, the second and third localized fluid streams occurring at two different ends of the fluid on the slide, each of the two ends being adjacent to a center portion, and the second and third localized fluid streams being opposite the first localized fluid stream. In some embodiments, the second localized fluid stream and the third localized fluid stream are provided substantially simultaneously from the second nozzle array.

[0022] In some embodiments, the automated slide processing device is a staining device and the fluid present on the upper surface of the slide includes, but is not limited to, a staining reagent, a counterstain reagent, or a washing reagent.

[0023] Another aspect of the present disclosure is a method of operating a non-contact mixer, the non-contact mixer comprising a first nozzle array and a second nozzle array, the first nozzle array adapted to impart a bulk fluid flow to a fluid (or a predetermined portion of the fluid) present on an upper surface of a slide, and the second nozzle array adapted to impart at least a first localized fluid flow to at least a portion of the fluid present on the upper surface of the slide, the method including operating the first nozzle array for a first period of time (e.g., to induce a bulk fluid flow during at least a portion of the time the first nozzle array is operated), and thereafter operating the second nozzle array for a second period of time (e.g., to induce at least one localized flow during at least a portion of the time the second nozzle array is operated), provided that the first and second nozzle arrays are not operated simultaneously. In some embodiments, one of the first or second periods of time is a predetermined period of time. In some embodiments, the duration of one of the first or second time periods is determined in real time using a feedback mechanism configured to interpret the level or degree of mixing achieved during operation of the first and / or second nozzle arrays. In some embodiments, the feedback mechanism includes one or more sensors communicatively coupled to the control system. In some embodiments, the first and second nozzle arrays are operated sequentially at least twice. In some embodiments, the operation of the first nozzle array always follows the operation of the second nozzle array, even if the operation of the second nozzle array is for a portion of the period during which the first nozzle array was operated. In other embodiments, the operation of the non-contact mixer can include (i) operating the first nozzle array; (ii) then operating the second nozzle array; and (iii) then operating the first nozzle array. In some embodiments, the second nozzle array is configured to induce at least second and third local fluid motions, the second and third local fluid motions being induced during operation of the second nozzle array, and both the second and third local fluid motions occurring substantially simultaneously.

[0024] Another aspect of the disclosure is an automated slide processing apparatus comprising: (a) at least one fluid dispenser configured to dispense fluid onto an upper surface of a specimen-supported slide; and (ii) a non-contact mixer for distributing fluid present on the upper surface of the slide, the non-contact mixer including a first nozzle array in fluid communication with a first plenum, the first nozzle array including a first set of primary nozzles directing a gas flow in a first direction and a second set of primary nozzles directing a gas flow in a second direction, and a second nozzle array in fluid communication with a second plenum. In some embodiments, the second nozzle array includes a first set of secondary nozzles directing a gas flow in a third direction and a second set of secondary nozzles directing a gas flow in a fourth direction. In some embodiments, the second nozzle array further includes an additional set of secondary nozzles, each additional set of nozzles adapted to direct a gas flow in another direction.

[0025] In some embodiments, the first and second directions are opposite to one another. In some embodiments, the gas streams emanating from the first and second sets of primary nozzles are directed substantially along a periphery of the fluid present on the upper surface of the slide and at any angle of incidence relative to the upper surface of the slide (or fluid positioned on the slide). In some embodiments, the gas streams emanating from the first and second sets of primary nozzles are directed at a portion of the slide adjacent the fluid and at any angle of incidence relative to the upper surface of the slide (or fluid positioned on the slide).

[0026] In some embodiments, the gas streams emanating from the first set of primary nozzles (relative to the fluid, to areas of the slide not containing fluid, or both) are directed substantially along a first longitudinal axis of the slide, and the gas streams emanating from the second set of primary nozzles are directed substantially along a second longitudinal axis of the slide. In some embodiments, the gas streams emanating from the first and second sets of primary nozzles form an angle of incidence with the surface of the slide that ranges from about 20 degrees to about 80 degrees. In some embodiments, the gas streams emanating from the first and second sets of primary nozzles are independently offset by up to + / - 15 degrees relative to the longitudinal axis of the slide.

[0027] In some embodiments, the first nozzle array imparts bulk fluid motion to fluid present on the upper surface of the slide. In some embodiments, each nozzle in the first set of secondary nozzles directs a gas stream to a different location on the upper surface of the slide, and each nozzle in the second set of secondary nozzles directs a gas stream to yet another different location on the upper surface of the slide. In some embodiments, the second nozzle array establishes at least two localized fluid streams. In some embodiments, the second nozzle array establishes at least three localized fluid streams.

[0028] Another aspect of the disclosure is a method of processing a specimen support slide, the method including (i) depositing a first fluid onto the specimen support slide, and (ii) uniformly distributing the deposited first fluid onto the specimen support slide, the deposited first fluid being distributed by introducing a first set of gas streams into the deposited first fluid, thereby providing a first fluid motion to a first portion of the deposited first fluid for a first predetermined time period, and introducing a second set of gas streams into the deposited first fluid, thereby providing at least a second fluid motion to at least a second portion of the deposited first fluid for a second predetermined time period. In some embodiments, the first and second motions provide cross-mixing. In some embodiments, the first fluid motion is provided by a first nozzle array, and the at least second fluid motion is provided by a second nozzle array. In some embodiments, the first portion is a majority of the first fluid on the slide, and the first set of gas streams induces a bulk fluid motion. In some embodiments, the second portion is a center of the first fluid on the slide (e.g., a center of a paddle of fluid). In some embodiments, the at least second motion is a localized fluid motion imparted to a center of the fluid on the slide. In some embodiments, the second motion induces cross-mixing. In some embodiments, the first fluid is a reagent. In some embodiments, the first fluid is a mixture having multiple components.

[0029] Another aspect of the disclosure is a method of processing a specimen support slide, the method including (i) depositing a first reagent onto the specimen support slide, and (ii) uniformly distributing the deposited first reagent onto the specimen support slide, the deposited first reagent being distributed by introducing a first set of pulsed gas jets into the deposited first reagent, thereby causing a first fluid motion on a first portion of the deposited first reagent for a first predetermined time period, and introducing a second set of pulsed gas jets into the deposited first reagent, thereby causing at least a second fluid motion on at least a second portion of the deposited first reagent for a second predetermined time period. In some embodiments, the first portion of the deposited first reagent comprises a majority of the deposited first reagent. In some embodiments, the first fluid stream is a bulk fluid stream. In some embodiments, the at least a second portion of the deposited first reagent is a central portion of the deposited first reagent. In some embodiments, the first and second motions are in the same direction. In some embodiments, the first and second motions are in opposite directions. In some embodiments, the first predetermined period of time is in the range of about 2 seconds to about 10 seconds. In some embodiments, the second predetermined period of time is in the range of about 2 seconds to about 10 seconds. In some embodiments, the first set of gas jets and the second set of gas jets each operate sequentially at least twice. In some embodiments, the first set of gas jets and the second set of gas jets each operate sequentially at least four times. In some embodiments, the pulsing of the first or second set of gas jets occurs at a frequency in the range of about 4 Hz to about 20 Hz. In some embodiments, additional reagent is dispensed onto the upper surface of the slide and mixing with the gas jets is performed again to mix the second reagent.

[0030] Another aspect of the disclosure is a non-contact mixer having a first nozzle array and a second nozzle array, the first nozzle array adapted to impart one or more gas flows to the fluid and / or substrate such that substantially an entirety of the fluid over the substrate moves along a first substantially circular path (a first "swirl" motion), and the second nozzle array adapted to impart one or more gas flows to the fluid and / or substrate such that three different portions of the fluid over the substrate move along second, third, and fourth substantially circular paths (first, second, and third "swirl" motions). In some embodiments, the second nozzle array is adapted to provide cross-mixing of the fluids. [Brief description of the drawings]

[0031] [Figure 1A] FIG. 2 illustrates a bottom view of a non-contact mixer having first and second nozzle arrays according to some embodiments. [Figure 1B] FIG. 2 is a bottom view of an alternative non-contact mixer having first and second nozzle arrays according to some embodiments. [Figure 2A] FIG. 2 illustrates a bottom view of a non-contact mixer having first and second nozzle arrays according to some embodiments. [Figure 2B] FIG. 2 is a bottom view of an alternative non-contact mixer having first and second nozzle arrays according to some embodiments. [Figure 3A] 1 is a perspective view of a non-contact mixer according to some embodiments. [Figure 3B] 1 is a perspective view of an alternative non-contact mixer according to some embodiments. [Figure 4A] 1 illustrates a side view of a non-contact mixer having a nozzle array configured to direct a flow of gas onto a surface of a substrate according to some embodiments. [Figure 4B] 1 is a side view of an alternative non-contact mixer having a nozzle array configured to direct a flow of gas onto a surface of a substrate according to some embodiments. [Figure 5A]1 is a perspective view of a non-contact mixer and gas flow emanating from a nozzle within the non-contact mixer according to some embodiments. [Figure 5B] 1 is a perspective view of a non-contact mixer and gas flow emanating from a nozzle within the non-contact mixer according to some embodiments. [Figure 6A] FIG. 1 illustrates local fluid motion induced by a nozzle array according to some embodiments. [Figure 6B] FIG. 1 illustrates local fluid motion induced by a nozzle array according to some embodiments. [Figure 6C] FIG. 1 illustrates bulk fluid motion induced by a nozzle array according to some embodiments. [Figure 6D] FIG. 1 illustrates bulk fluid motion induced by a nozzle array according to some embodiments. [Figure 7] 1A-1C illustrate a nozzle arrangement of a non-contact mixer according to some embodiments, where two sets of nozzles are shown, each set of nozzles in fluid communication with a separate plenum. [Figure 8] 1A-1C show alternative nozzle geometries for use in a non-contact mixer according to some embodiments. [Figure 9A] FIG. 1 illustrates a non-contact mixer having multiple nozzles, each nozzle directing a flow of gas to a predetermined location on a substrate (or a fluid positioned on a substrate), according to some embodiments. [Figure 9B] FIG. 1 illustrates a non-contact mixer having multiple nozzles, each nozzle directing a flow of gas to a predetermined location on a substrate (or a fluid positioned on a substrate), according to some embodiments. [Figure 10A] FIG. 1 illustrates a non-contact mixer having multiple inlets and nozzles. [Figure 10B] FIG. 1 illustrates the mixing of dye within a fluid, where the dye is substantially uniformly distributed within the fluid after operation of the non-contact mixer. [Figure 10C]FIG. 1 illustrates the mixing of dye within a fluid, where the dye is substantially uniformly distributed within the fluid after operation of the non-contact mixer. [Figure 11A] FIG. 1 illustrates a non-contact mixer having multiple inlets and nozzles. [Figure 11B] FIG. 1 illustrates the mixing of dye within a fluid, where the dye is substantially uniformly distributed within the fluid after operation of the non-contact mixer. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0032] regulations

[0033] It should also be understood that, unless expressly stated to the contrary, in any method claimed herein that includes two or more steps or acts, the order of the method steps or acts is not necessarily limited to the order in which the method steps or acts are recited.

[0034] As used herein, the singular terms "a," "an," and "the" include plural referents unless the context clearly indicates otherwise. Similarly, the word "or" is intended to include "and" unless the context clearly indicates otherwise. The term "include" is defined inclusively, such that "includes A or B" means including A, B, or A and B.

[0035] As used herein and in the claims, "or" should be understood to have the same meaning as "and / or" as defined above. For example, when separating items in a list, "or" or "and / or" shall be construed as being inclusive, i.e., including at least one, but more than one of a number or list of elements and optionally additional unlisted items. Only terms clearly indicated to the contrary, such as "only one of" or "exactly one of," or when used in the claims, "consisting of" will refer to the inclusion of exactly one element of a number or list of elements. In general, the term "or" as used herein, when preceded by terms of exclusivity, such as "either," "one of," or "exactly one of," shall be construed merely as indicating exclusive alternatives (i.e., "one or the other but not both"). "Consisting essentially of," when used in the claims, shall have its ordinary meaning as used in the field of patent law.

[0036] As used herein and in the claims, the phrase "at least one," with reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed in the list of elements, and not excluding any combination of elements in the list of elements. This provision similarly allows for elements other than those specifically identified in the list of elements to which the phrase "at least one" refers, whether related or unrelated to the specifically identified elements, can optionally be present. Thus, as a non-limiting example, "at least one of A and B" (or, equivalently, "at least one of A or B," or, equivalently, "at least one of A and / or B") refers to, in one embodiment, at least one A, optionally including more than one, in the complete absence of B (and, optionally, including elements other than B); in another embodiment, at least one B, optionally including more than one, in the complete absence of A (and, optionally, including elements other than A); in yet another embodiment, at least one A, optionally including more than one, and at least one B, optionally including more than one, (and, optionally, including other elements); etc.

[0037] As used herein, the terms "comprising," "including," "having," and the like are used interchangeably and have the same meaning. Similarly, "comprises," "includes," "has," and the like are used interchangeably and have the same meaning. In particular, each of the terms is defined without conflict with the general U.S. Patent Law provision of "comprising," and therefore is interpreted as being open terms meaning "at least the following," and is similarly interpreted as not excluding additional features, limitations, aspects, etc. Thus, for example, "a device having components a, b, and c" means that the device includes at least components a, b, and c. Similarly, the phrase: "a method involving steps a, b, and c" means that the method includes at least steps a, b, and c. Additionally, although steps and processes may be outlined in a particular order herein, one of ordinary skill in the art will recognize that the ordering of the steps and processes may vary.

[0038] As used herein, the term "biological sample" or "tissue sample" refers to any sample containing biological molecules (proteins, peptides, nucleic acids, lipids, carbohydrates, or combinations thereof) obtained from any organism, including viruses. Other examples of organisms include mammals (such as humans; domestic animals such as cats, dogs, horses, cows, and pigs; and laboratory animals such as mice, rats, and primates), insects, annelids, arachnids, marsupials, reptiles, amphibians, bacteria, and fungi. Biological samples include tissue samples (such as tissue sections and needle biopsies of tissues), cell samples (such as cytological smears, such as Pap smears or blood smears, or samples of cells obtained by microdissection), or cell fractions, cell debris, or organelles (such as those obtained by lysing cells and separating the components of the cells by centrifugation or other methods). Other examples of biological samples include blood, serum, urine, semen, feces, cerebrospinal fluid, interstitial fluid, mucus, tears, sweat, pus, biopsy tissue (e.g., obtained by open or needle biopsy), nipple aspirate, earwax, milk, vaginal fluid, saliva, swabs (such as buccal swabs), or any substance that contains a biological molecule derived from a first biological sample. In certain embodiments, the term "biological sample" as used herein refers to a sample (such as a homogenized or liquefied sample) prepared from a tumor or a portion of a tumor obtained from a subject.

[0039] As used herein, the phrase "bulk fluid flow" refers to the motion imparted to the bulk of a fluid over a substrate. The bulk fluid flow can follow a circular path. The bulk fluid flow can be in a particular direction, for example, clockwise or counterclockwise.

[0040] As used herein, the term "fluid" refers to any liquid, including water, solvents, solutions (e.g., buffers), and the like. The term "fluid" similarly refers to any mixture, colloid, suspension, and the like. The term "fluid" similarly encompasses reagents, stains, and other specimen treatments (e.g., adhesives, fixatives, and the like) that can be applied to a microscope slide and / or specimen. Fluids can be aqueous or non-aqueous. Further examples include solutions or suspensions of antibodies, solutions or suspensions of nucleic acid probes, and solutions or suspensions of dyes or stain molecules (e.g., H&E staining solutions, Pap staining solutions, and the like). Still further examples of fluids include solvents and / or solutions for deparaffinizing paraffin-embedded biological specimens, aqueous washes, and hydrocarbons (e.g., aromatic compounds such as alkanes, isoalkanes, xylenes, and the like). Still further examples of fluids include solvents (and mixtures thereof) used to dehydrate or rehydrate biological specimens.

[0041] As used herein, the terms "nozzle array," "nozzle set," and "set of nozzles" each refer to a series of nozzles adapted together to provide a fluid flow, such as a bulk fluid flow or a localized fluid flow. In some embodiments, a "nozzle array" can itself include multiple "sets of nozzles" or at least two series of nozzles.

[0042] As used herein, the term "plurality" refers to two or more, for example, three or more, four or more, five or more, etc.

[0043] As used herein, the term "reagent" refers to any liquid or liquid composition used in a specimen processing operation that involves applying a liquid or liquid composition to a slide. Examples of reagents and processing liquids include solutions, emulsions, suspensions, and solvents (pure or mixtures thereof). These and other examples can be aqueous or non-aqueous. Further examples include solutions or suspensions of specific binding entities, antibodies, solutions or suspensions of nucleic acid probes, and solutions or suspensions of dye or stain molecules (e.g., H&E staining solutions, Pap staining solutions, etc.). Still further examples include solvents and / or solutions for deparaffinizing paraffin-embedded biological specimens, aqueous washes, and hydrocarbons (e.g., aromatic compounds such as alkanes, isoalkanes, xylenes, etc.).

[0044] As used herein, the phrase "regional fluid flow" refers to a flow of fluid that is within a particular portion or area of ​​the fluid on the substrate, but less than the majority of the fluid on the substrate. The local fluid flow can be in a particular direction, for example, clockwise or counterclockwise. Those skilled in the art will understand that any fluid present on the substrate can be divided into several areas, regions, or portions, and that a local fluid flow can be provided to any of these areas, regions, or portions.

[0045] As used herein, the term "slide" refers to any substrate of any suitable dimensions (e.g., a substrate made entirely or partially of glass, quartz, plastic, silicon, etc.) on which a biological specimen is placed for analysis, and more specifically, a "microscope slide" such as a standard 3" x 1" microscope slide or a standard 75mm x 25mm microscope slide. Examples of biological specimens that may be placed on a slide include, without limitation, cytological smears, thin tissue sections (such as from a biopsy), and arrays of biological specimens, such as tissue arrays, cell arrays, DNA arrays, RNA arrays, protein arrays, or any combination thereof. Thus, in one embodiment, tissue sections, DNA samples, RNA samples, and / or proteins are placed at specific locations on the slide. In some embodiments, the term slide can refer to SELDI and MALDI chips as well as silicon wafers.

[0046] As used herein, the terms "stain", "staining", or the like generally refer to any treatment of a biological specimen to detect and / or differentiate the presence, location, and / or amount (such as concentration) of a particular molecule (such as a lipid, protein, or nucleic acid) or a particular structure (such as a normal or malignant cell, cytosol, nucleus, Golgi apparatus, or cytoskeleton) in the biological specimen. For example, staining can provide contrast between a particular molecule or a particular cellular structure and the surrounding portions of the biological specimen, and the intensity of the staining can provide a measure of the amount of a particular molecule in the specimen. Staining can be used to aid in the observation of molecules, cellular structures, and organisms not only by bright field microscopes, but also by other observation tools such as phase contrast microscopes, electron microscopes, and fluorescence microscopes. Some staining performed by System 2 can be used to visualize the outline of a cell. Other staining performed by System 2 can rely on staining certain cellular components (such as molecules or structures) without or with relatively little staining of other cellular components. Examples of types of staining methods that may be performed by System 2 include, without limitation, histochemical methods, immunohistochemical methods, and other methods based on reactions between molecules (including non-covalent interactions), such as hybridization reactions between nucleic acid molecules. Specific staining methods include, but are not limited to, primary staining methods (e.g., H&E staining, Pap staining, etc.), enzyme-linked immunohistochemical methods, and in situ RNA and DNA hybridization methods, such as fluorescence in situ hybridization (FISH).

[0047] As used herein, the term "substantially" refers to the qualitative condition of exhibiting the entire or nearly entire extent or degree of a feature or characteristic of interest. In some embodiments, "substantially" means within about 20%. In some embodiments, "substantially" means within about 15%. In some embodiments, "substantially" means within about 10%. In some embodiments, "substantially" means within about 5%.

[0048] Devices and Systems

[0049] One aspect of the present disclosure is a non-contact mixer device configured to introduce a gas, such as a pulse of gas, into a fluid on the surface of a substrate, e.g., a specimen-supporting microscope slide, to effect mixing of one or more components within the fluid (a puddle of fluid on the upper surface of the microscope slide). In some embodiments, the substrate or microscope slide contains a biological sample including cells and / or tissue, and the mixing with the pulse of gas occurs without damaging the cells and / or tissue within the sample and / or with minimal waste, i.e., the pulse of gas serves to minimize the amount of fluid that is directed away from the surface of the substrate.

[0050] In some embodiments, the gas flow or pulses of gas are generated by a non-contact mixer device, the non-contact mixer including multiple nozzles adapted to direct the gas flow or pulses of gas to different areas (e.g., at a predetermined angle, at a predetermined area, at a predetermined location) on the surface of the substrate. In doing so, the directed gas flow allows any fluid present on the slide to vibrate, move, and / or agitate. As further described herein, the multiple nozzles are fluidly connected to a plenum, which is in further communication with an inlet. The non-contact mixer can include one or more plenums, each in fluid communication with a different inlet, and each in further communication with a different set of nozzles.

[0051] 1A-1B and 2A-2B, the non-contact mixer 10 can include one or more plenums 11A and 11B, each having a plurality of nozzles 12A or 12B in fluid communication with the respective plenum. In some embodiments, the one or more plenums 11A and 11B are in independent fluid communication with inlets 13A and 13B, respectively. Thus, gas streams entering through inlets 13A and 13B can enter plenums 11A or 11B, respectively, where the gas streams are distributed to individual gas nozzles 12A or 12B, respectively, and discharged as gas streams or jets. Although Figures 1A and 1B show that the non-contact mixer can have two sets of nozzles, each set of nozzles in fluid communication with a plenum 11A or 11B, which in turn is in communication with an inlet 13A or 13B, the non-contact mixer can include only a single plenum or can have three or more plenums.

[0052] In fact, while the non-contact mixer shown in Figures 2A and 2B is shown as a monolithic device, one skilled in the art will understand that two or more non-contact mixers can be positioned over the substrate, each of which can include multiple nozzles in fluid communication with one or more plenums and / or inlets. Thus, one or more non-contact mixers can be appropriately configured to direct gas flows or pulses of gas to different areas on the surface of the substrate, as detailed herein. For example, the system herein can include two or more non-contact mixers, each of which includes a single inlet in communication with a single plenum, which in turn is in communication with multiple nozzles.

[0053] As shown in FIGS. 3A and 3B, in some embodiments, the nozzle, plenum, and inlet are housed within a body 14, e.g., a monolithic body or a body comprised of multiple components, which is configurable for incorporation into a larger structure, e.g., a staining device. The body 14 can include one or more mounting or attachment points 15 so that the non-contact mixer can be removably incorporated into a staining device or other equipment. In some embodiments, and as shown in FIGS. 4A and 4B, the mounting or attachment points can be open at both the top and bottom, allowing multiple points for connection to another device or equipment. The body 14 can be comprised of a metal, alloy, polymer, or copolymer. In some embodiments, the body 14, plenum, inlet, and nozzle can be fabricated by machining, molding, or otherwise fastening multiple components together from a solid block to form the non-contact mixer 10. In some embodiments, the non-contact mixer and all of its components can be fabricated using 3D printing.

[0054] In some embodiments, and with reference to at least FIGS. 1A and 1B, a plurality of nozzles 12A or 12B are arranged along the lower surface 16 of the non-contact mixer 10. In some embodiments, the plurality of nozzles are arranged in two or more rows. In some embodiments, the nozzles can be arranged parallel to one another, for example, in rows parallel to the longitudinal axis 20 of the non-contact mixer. In other embodiments, the nozzles can be arranged in a staggered configuration. In other embodiments, the nozzles can be randomly configured with respect to one another. In embodiments where there are multiple sets of nozzles, each set of nozzles can be independently configured. For example, FIG. 7 shows a first set of nozzles (each individual nozzle is labeled 12B) that are parallel to the longitudinal axis 20; and a second set of nozzles (each individual nozzle is labeled 12A) that are substantially parallel to the longitudinal axis 20.

[0055] Those skilled in the art will appreciate that there are many variables that can determine the flow rate of gas through any individual gas nozzle, including the size and shape of the nozzle, the number of nozzles in fluid communication with any individual plenum, as well as the gas pressure supplied to the plenum through the inlet.

[0056] In some embodiments, each inlet is configured to receive pressurized gas from an external gas source (e.g., a pump, air compressor, blower, fan, or other means sufficient to pressurize the gas from the gas source if it is not already sufficiently pressurized). In some embodiments, the flow rate of gas through each inlet independently ranges from about 1 L / min to about 5 L / min. In other embodiments, the flow rate of gas through each inlet independently ranges from about 2 L / min to about 25 L / min. Without being bound to any particular theory, it is believed that the flow rate through each nozzle in communication with an inlet is approximately the same.

[0057] The nozzles can have any size or shape. For example, the nozzles can be conical (or substantially conical), helically striated ports, small arrays of angled orifices with small internal conical openings, or arrays with uniform rounded internal profiles and external bosses. Non-limiting examples of such additional nozzle shapes are shown in FIG. 8. In some embodiments, and regardless of the size or shape of the nozzles, the nozzles can be grouped together, and in some embodiments, simultaneous operation of a group of nozzles can allow the individual gas streams emanating from each individual nozzle to merge.

[0058] In some embodiments, the nozzles have openings with diameters ranging from about 0.025 inches (0.635 mm) to about 0.035 inches (0.889 mm). In other embodiments, the nozzles have openings with diameters ranging from about 0.010 inches (0.254 mm) to about 0.030 inches (0.792 mm). In yet other embodiments, the nozzles have openings with diameters of about 0.050 inches (1.27 mm). One skilled in the art will appreciate that the nozzles can each have openings of the same or different diameters.

[0059] In some embodiments, the nozzles are evenly spaced apart from one another. For example, considering a nozzle having a circular opening, the nozzles 12 can be spaced apart from one another by about 0.150 inches (3.81 mm) to about 0.300 inches (7.96 mm), measured from the center of one circular opening to the center of another. In another example, and again assuming circular openings, the nozzles can be spaced apart from one another by about 0.300 inches (7.96 mm) to about 0.500 inches (12.7 mm). In yet another example, and again assuming circular openings, the nozzles can be spaced apart from one another by about 1.00 inches (25.4 mm). Of course, one of ordinary skill in the art will appreciate that the nozzles can have any geometric shape, such as circular, oval, triangular, square, etc.

[0060] The nozzles can be provided at various angles so that the gas flow from each nozzle can be directed as desired (e.g., at a particular angle in any of the coordinate directions toward the surface of the substrate) (see, for example, FIGS. 4A and 4B). If any nozzle is considered as a single point, one skilled in the art will understand that the nozzles can be formed at any angle and in any direction (x, y, or z) within the body of the non-contact mixer such that a gas stream or jet emanates from the nozzle (12A or 12B) and is aimed at the substrate surface (70) at a predetermined location with a predetermined angle of incidence. One skilled in the art will further understand that by combining nozzles having different angles in any of the x, y, or z dimensions into an array, the various angles along the various coordinates will allow for the movement of the fluid on the substrate in the direction dictated by the set of nozzles.

[0061] 5A and 5B show two nozzle angles, designated as "slant angle" and "offset angle". One skilled in the art will appreciate that by independently adjusting the slant and offset angles of each nozzle, the gas jets can be directed from the nozzles to different areas or locations (and at specific entry angles) on the substrate positioned below the non-contact mixer. In general, the slant angle refers to the angle relative to the substrate planar surface (i.e., a 90 degree slant angle is straight down (perpendicular to the surface); a 0 degree slant is parallel to the substrate surface). In some embodiments, the slant angle allows the gas stream emanating from the nozzle to impart motion to the fluid on the substrate. In some embodiments, the slant angle can be defined by considering the incidence angle formed between the gas stream emanating from the nozzle and the surface of the substrate positioned below the non-contact mixer. In some embodiments, it is believed that the jets fluidically interact with each other in a similar manner, making the actual point of incidence on the substrate governed by a combination of compressible fluid dynamics and nozzle direction, rather than being "unpredictable". For example, in Figure 5A, gas flow 30 has a 55 degree angle of incidence with the substrate, while, also shown in Figure 5B, gas flow 31 has a 60 degree angle of incidence with the substrate.

[0062] In some embodiments, the tilt angle ranges from about 5 degrees to about 90 degrees. In other embodiments, the tilt angle ranges from about 10 degrees to about 70 degrees. In other embodiments, the tilt angle ranges from about 15 degrees to about 65 degrees. In yet other embodiments, the tilt angle ranges from about 20 degrees to about 60 degrees. In a further embodiment, the tilt angle ranges from about 25 degrees to about 55 degrees. In yet a further embodiment, the tilt angle ranges from about 30 degrees to about 55 degrees.

[0063] In addition to the tilt angle, the nozzles can be defined by an offset angle, which refers to the angle at which the gas nozzle deviates from an axis parallel to the longitudinal axis 20 or from an axis parallel to the horizontal axis 21 (see FIGS. 5A and 5B). In some embodiments, the offset angle allows the gas flow emanating from the nozzle to direct the fluid onto the substrate. In some embodiments, the offset angle ranges from about 0 degrees to about 25 degrees. In other embodiments, the offset angle ranges from about 5 degrees to about 15 degrees. In yet other embodiments, the offset angle ranges from about 10 degrees to about 15 degrees.

[0064] According to another example, Figure 5B shows a gas flow 31 having a 60 degree inclination angle with respect to a plane parallel to the horizontal axis 21, which gas flow also has a 10 degree offset angle with respect to an axis parallel to the horizontal axis 21. Similarly, Figure 5A shows a gas flow 30 having a 55 degree inclination angle with respect to a plane perpendicular to the longitudinal axis 20, which gas flow is offset by 5 degrees with respect to an axis parallel to the longitudinal axis 20.

[0065] In the context of a microscope slide positioned under the non-contact mixer 10, in some embodiments, a set of nozzles (e.g., 4 to 12 nozzles) is arranged to enable bulk fluid flow relative to the fluid positioned on the surface of the slide. In some embodiments, jets of gas emanating from some of the nozzles in the set of nozzles are directed toward the longitudinal edge of the slide or toward the fluid near the longitudinal edge of the slide.

[0066] By way of example, and with reference to Figures 6C and 6D, a first nozzle array can be adapted to impart a bulk fluid motion 50 to a fluid present on the surface of a substrate. Here, the nozzles in the first nozzle array are arranged such that the gas flow is directed substantially toward, but not completely parallel to, the edge 60 of the microscope slide. While the resulting bulk fluid motion shown in Figures 6C and 6D is in a counterclockwise direction, one skilled in the art will appreciate that the nozzle array can be configured such that the bulk fluid motion is in a clockwise direction. Figures 6A and 6B similarly show three discrete localized fluid flows 51, 52, and 53, or 54, 55, and 56, each of which is imparted by a second nozzle array configured to direct a gas flow to a predetermined location on the surface of the slide at a predetermined angle of incidence. In Figure 6A, the localized fluid flows 51 and 53 are shown in a counterclockwise direction, while the localized fluid flow 52 is in a clockwise direction. 6B, local fluid flows 55 and 56 are shown in a clockwise direction, while local fluid flow 54 is in a counterclockwise direction. Those skilled in the art will similarly appreciate that the nozzles in the second nozzle array can be further adapted such that four or more local fluid flows are provided, with each adjacent local fluid flow being in a different direction.

[0067] Automated Slide Processing System

[0068] Another aspect of the disclosure is an automated slide processing device comprising at least one non-contact mixer configured to introduce pulses of gas into a fluid or paddle on a surface of a specimen-supporting microscope slide to effect mixing of one or more components within the fluid or paddle. In some embodiments, the automated slide processing system includes at least one non-contact mixer having two discrete nozzle arrays, each nozzle array adapted to impart a flow to at least a portion of the fluid on the surface of the slide. In some embodiments, the automated slide processing system includes a non-contact mixer having two discrete nozzle arrays, a first nozzle array adapted to impart a bulk fluid flow in a first direction and a second nozzle array adapted to impart at least one localized fluid flow to at least a portion of the fluid, the at least one localized fluid flow being in a direction opposite to the imparted bulk fluid flow. In some embodiments, the automated slide processing device includes at least two non-contact mixers.

[0069] In some embodiments, the specimen processing device is an automated device, such as the BENCHMARK XT instrument, SYMPHONY instrument, or BENCHMARK ULTRA instrument sold by Ventana Medical Systems, Inc. Ventana Medical Systems, Inc. is the assignee of several U.S. patents that disclose systems and methods for performing automated analyses, including U.S. Patent Nos. 5,650,327, 5,654,200, 6,296,809, 6,352,861, 6,827,901, and 6,943,029, and U.S. Published Patent Application Nos. 20030211630 and 20040052685, each of which is incorporated herein by reference in its entirety. Alternatively, specimens may be processed manually.

[0070] Examples of commercially available H&E stainers include the VENTANA SYMPHONY (individual slide stainer) and VENTANA HE 600 (individual slide stainer) series H&E stainers from Roche; the Dako CoverStainer (batch stainer) from Agilent Technologies; the Leica ST4020 Small Linear Stainer (batch stainer), Leica ST5020 Multi Stainer (batch stainer), and Leica ST5010 Automated Stainer XL Series (batch stainer) H&E stainers from Leica Biosystems Nussloch GmbH. The non-contact mixers described herein can be added to any of the above specimen processing systems.

[0071] The specimen processor may apply fixatives to the specimen. Fixatives may include crosslinkers (aldehydes, such as formaldehyde, paraformaldehyde, and glutaraldehyde, as well as non-aldehyde crosslinkers), oxidants (e.g., metal ions and complexes, such as osmium tetroxide and chromate), protein denaturants (e.g., acetic acid, methanol, and ethanol), fixatives of unknown mechanism (e.g., mercuric chloride, acetone, and picric acid), combination reagents (e.g., Carnoy fixative, methacin, Bouin's solution, B5 fixative, Rossmann's solution, and Gendre's solution), microwave, and miscellaneous fixatives (e.g., excluded volume fixative and vapor fixative). A non-contact mixer in fluid communication with the microscope slide may be used to distribute any of these fixatives evenly onto the slide or within another fluid, as detailed herein.

[0072] If the specimen is a sample embedded in paraffin, the sample may be deparaffinized by a specimen processor using an appropriate deparaffinization fluid(s). After the waste remover removes the deparaffinization fluid(s), any number of substances may be applied to the specimen in succession. The substances may be for pretreatment (e.g., protein cross-linking, nucleic acid exposure, etc.), denaturation, hybridization, washing (e.g., stringency washing), detection (e.g., linking visual or marker molecules to probes), amplification (e.g., amplification of proteins, genes, etc.), counterstaining, coverslipping, or the like. Again, any of these substances applied may be mixed or dispensed through the use of the non-contact mixer described herein.

[0073] The specimen processor can apply a wide range of substances to the specimen, which can then be uniformly distributed and / or mixed using a non-contact mixer in fluid communication with the slide holder. The substances include, without limitation, stains, probes, reagents, rinses, and / or conditioning agents. The substances can be fluids (e.g., gases, liquids, or gas / liquid mixtures) or the like. The fluids can be solvents (e.g., polar solvents, non-polar solvents, etc.), solutions (e.g., aqueous or other types of solutions), or the like. The reagents can be, without limitation, stains, wetting agents, antibodies (e.g., monoclonal antibodies, polyclonal antibodies, etc.), antigen retrieval solutions (e.g., aqueous or non-aqueous based light source activation solutions, antigen retrieval buffers, etc.), or the like. The probes can be isolated nucleic acids or isolated synthetic oligonucleotides attached to a detectable label. The labels can include radioisotopes, enzyme substrates, cofactors, ligands, chemiluminescent or fluorescent agents, haptens, and enzymes.

[0074] An automated IHC / ISH slide stainer typically includes at least reservoirs of the various reagents used in the staining protocol, a reagent dispensing unit in fluid communication with the reservoirs for dispensing the reagents onto the slides, a waste removal system for removing used reagents and other waste from the slides, and a control system for coordinating the operation of the reagent dispensing unit and the waste removal system. In addition to performing the staining steps, many automated slide stainers may also perform steps incidental to staining (or be compatible with separate systems that perform such incidental steps), including slide baking (to fix the sample to the slide), dewaxing (also called deparaffinization), antigen retrieval, counterstaining, dehydration and clearing, and coverslipping. Prichard, Overview of Automated Immunohistochemistry, Arch Pathol Lab Med., Vol. 138, pp. 1578-1582 (2014), which is incorporated herein by reference in its entirety, describes several specific examples of automated IHC / ISH slide stainers and their various features, including intelliPATH (Biocare Medical), WAVE (Celerus Diagnostics), DAKO OMNIS and DAKO AUTOSTAINER LINK 48 (Agilent technologies), BENCHMARK (Ventana Medical Systems, Inc.), Leica BOND, and Lab Vision Autostainer (Thermo Scientific) automated slide stainers. Additionally, Ventana Medical Systems, Inc. is the assignee of several U.S. patents disclosing systems and methods for performing automated analyses, including U.S. Patent Nos. 5,650,327, 5,654,200, 6,296,809, 6,352,861, 6,827,901, and 6,943,029, and U.S. Published Patent Application Nos. 20030211630 and 20040052685, each of which is incorporated by reference in its entirety herein.

[0075] Commercially available dyeing units usually operate on one of the following principles: The principles are: (1) open individual slide staining, where the slide is positioned horizontally and reagents are dispensed as paddles on the surface of the slide containing the tissue sample (as implemented on DAKO AUTOSTAINER LINK 48 (Agilent technologies) and intelliPATH (Biocare Medical) stainers); (2) liquid overlay technique, where reagents are covered with or dispensed through an inert fluid layer that is deposited over the sample (as implemented on BENTANA BenchMark and DISCOVERY stainers); and (3) capillary gap staining, where the slide surface is placed close to another surface (which can be another slide or a cover plate) to create a narrow gap through which capillary forces draw up the liquid reagents and keep them in contact with the sample (such as the staining principle used by DAKO TECHMATE, Leica BOND, and DAKO OMNIS stainers). Some iterations of capillary gap staining do not mix the fluids in the gap (such as on the DAKO TECHMATE and Leica BOND). In a variation of capillary gap staining called dynamic gap staining, capillary forces are used to apply the sample to the slide, and then the parallel surfaces translate relative to each other to agitate the reagents during incubation, thereby resulting in reagent mixing (such as the staining principle implemented on the DAKO OMNIS slide stainer (Agilent)). In translational gap staining, a translatable head is positioned over a slide. The lower surface of the head is spaced from the head by a first gap that is small enough to allow a meniscus of the liquid to form on the slide from the liquid during translation of the slide. A mixing extension having a lateral dimension smaller than the width of the slide extends from the lower surface of the translatable head to define a second gap between the mixing extension and the slide that is smaller than the first gap.During translation of the head, the lateral dimension of the mixing extension is sufficient to generate a lateral movement of liquid on the slide in a direction extending approximately from the second gap to the first gap. See WO2011-139978A1. The use of inkjet technology to deposit reagents on slides has recently been proposed. This list of staining techniques is not intended to be exhaustive, and any of the non-contact mixers described herein can be used in conjunction with such a system to provide distribution and mixing of any fluid present on a specimen-supporting microscope slide, including staining reagents.

[0076] Some embodiments are apparatus for automatically processing biological specimens, the apparatus comprising: at least one slide tray (as described herein) that holds a plurality of slides in a substantially horizontal position, with the biological specimens located on the slides; one or more workstations that receive the slide tray and perform one or more slide processing operations on the plurality of slides held in the slide tray; a transporter that moves the slide tray into and out of the one or more workstations; a fluidics module in fluid communication with the one or more workstations that supplies reagents to the one or more workstations; a pneumatic module in fluid communication with the one or more workstations and the fluidics module, the pneumatic module providing negative and / or pressurized gas to the one or more workstations and the fluidics module; a non-contact mixer positioned above the slides in the slide tray to effect mixing; and a control module in electrical communication with the transporter, the one or more workstations, the fluidics module, and the pneumatic module that coordinates the functioning of the components of the apparatus (including the non-contact mixer and its various components) during processing of the biological specimens.

[0077] In some embodiments, the apparatus for automatically processing biological specimens further includes a control system for independently controlling each non-contact mixer such that mixing is adjusted for each slide. In some embodiments, the apparatus for automatically processing biological specimens further includes one or more sensors or other feedback mechanisms to enable monitoring of the mixing and / or distribution of fluids dispensed onto the surface of the slide. In some embodiments, the control system includes a microprocessor and one or more microcontrollers, where the one or more microcontrollers receive instructions from the microprocessor and separately control one or more of the one or more workstations, the fluidics module, the non-contact mixer, and / or the transporter. In some embodiments, at least one of the workstations includes a movable nozzle assembly, where the nozzle assembly includes one or more nozzles through which reagents are delivered to the slide. The nozzles can be dispensing nozzles.

[0078] In some embodiments, the workstation may perform slide processing operations on one or more slides in a slide tray, e.g., at least two or four slides in a slide tray, or the workstation may perform slide processing operations (including mixing operations with a non-contact mixer) on all slides in a slide tray simultaneously. In some embodiments, the one or more workstations dispense reagents onto slides in a slide tray without a significant amount of reagent contacting a first slide contacting a second slide, thereby minimizing cross-contamination between slides. Such a workstation may include one or more directional nozzles that dispense reagents onto the slides, e.g., the one or more directional nozzles may include a pair of directional nozzles that dispense reagents in opposite directions across the surface of the slide. In more specific embodiments, the one or more directional nozzles may further include a directional nozzle that dispenses reagents toward the bottom surface of the slide. In other embodiments, one or more workstations may simultaneously dispense a reagent (e.g., the same reagent) onto at least two slides held in a slide tray within a given workstation, or one or more workstations may simultaneously dispense a reagent (e.g., the same reagent) onto all of the slides held in a slide tray within a given workstation. Following dispensing of fluids and / or reagents, the non-contact mixer can be independently activated to distribute and / or mix the fluid on the surfaces of the slides.

[0079] Some embodiments are automated methods for processing a plurality of slides bearing biological tissue samples, the method including performing a set of slide processing operations on a plurality of slides in one or more workstations while the plurality of slides are held in a spatially coplanar and substantially horizontal position in a slide tray, each of the plurality of slides being positioned proximate to at least one non-contact mixer; the set of slide processing operations includes staining the samples on the slides in the spatially coplanar and substantially horizontal position by flowing one or more staining agents from at least one reagent container through a fluidics module and out of at least one dispensing nozzle positioned above the slide tray. and solvent exchanging; transporting a slide tray holding the plurality of slides to an automated coverslipper workstation after performing a set of slide processing operations including at least staining and solvent exchanging; coverslipping the plurality of slides held in the slide tray with separate respective coverslips using the automated coverslipper workstation while the plurality of slides are held in a spatially coplanar and substantially horizontal position in the slide tray, whereby the coverslips on the slides are spaced apart from one another; and removing the slide tray holding the coverslipped slides from the automated coverslipper workstation.In some embodiments, the processing includes (i) baking the sample under a radiant heater; (ii) deparaffinizing the sample; (iii) staining the sample by pumping one or more staining agents through one or more fluidic components and out of one or more nozzles positioned generally above a slide tray, the one or more fluidic components fluidly connecting at least one reagent container holding the one or more staining agents to the one or more nozzles; (iv) solvent exchanging the sample; and (v) coverslipping the sample with a separate coverslip, wherein the above steps are performed automatically by an apparatus comprising two or more workstations between which a slide tray holding the slides moves during processing.

[0080] In some embodiments, after the specimen has been processed, the user may transport the specimen-bearing slide to the imaging device. In some embodiments, the imaging device is a brightfield imager slide scanner. One brightfield imager is the iScan Coreo™ brightfield scanner sold by Ventana Medical Systems, Inc. In an automated embodiment, the imaging device is a digital pathology device as disclosed in International Patent Application No. PCT / US2010 / 002772 (Patent Publication No. WO / 2011 / 049608) entitled "IMAGING SYSTEMS AND TECHNIQUES" or as disclosed in U.S. Patent Application Publication No. 2014 / 0178169, filed February 3, 2014, entitled "IMAGING SYSTEMS, CASSETTES, AND METHODS OF USING THE SAME." International Patent Application No. PCT / US2010 / 002772 and U.S. Patent Application Publication No. 2014 / 0178169 are incorporated by reference in their entireties. In other embodiments, the imaging device includes a digital camera coupled to a microscope.

[0081] Control System

[0082] In some embodiments, the non-contact mixer can be controlled by a controller. In some embodiments, the control system can be in communication with the actuators, valves, and / or solenoids to control air entering the inlet of the non-contact mixer or enable pulsing of gas flow from each of the nozzles in fluid communication with the inlet. In some embodiments, the control system further includes a computer (at least one processor and a non-tangible memory for containing instructions and recording information), which controls the opening and closing of the actuators, valves, and / or solenoids such that the nozzle array or set of nozzles forming part of the non-contact mixer are operated (e.g., pulsed at regular time intervals or at regular frequencies). The control system enables dynamic adjustment of the actuators, valves, and / or solenoids such that flow and pressure are independently controlled along each plenum.

[0083] In some embodiments, the control system may further comprise one or more sensors for monitoring the gas jet directed toward the microscope slide, hi other embodiments, the control system may comprise one or more feedback mechanisms for monitoring the mixing of one or more fluids present on the surface of the slide.

[0084] In some embodiments, the control system may further comprise one or more sensors for monitoring surface tension, volume of fluid, temperature of the fluid, and other mechanical properties of the fluid on the microscope slide. In other embodiments, the control system may comprise one or more feedback mechanisms to monitor the integrity of the fluid on the slide and dynamically adjust actuators, valves, and / or solenoids to prevent or reduce forcing one or more fluids off the slide such that flow and pressure are independently controlled along each plenum.

[0085] Optical or video detection and analysis can be used to optimize mixing. As an example, optical or video detection can be used to detect color changes as colored reagents mix into a clear fluid. Other optical measurements, such as spectral excitation, absorption, light scattering, fluorescence, luminescence, emission, polarized light microscopy, Raman scattering, and spectral analysis, can be used to monitor the mixing of fluids in contact with a sample on the surface of a microscope slide. Data can be collected and analyzed by a computer or control system controlling the mixing process. For example, if sufficient mixing is achieved based on the data received, the non-contact mixer can be turned off. As another example, if mixing is insufficient based on the data received, the controller can increase the time the non-contact mixer is turned off, or the controller can change one or more of the parameters associated with non-contact mixing, such as the gas jet pulse frequency, the gas pressure, or the set of nozzles that deliver the gas.

[0086] method

[0087] The present disclosure also provides a method of mixing fluids present on a substrate, e.g., a slide, using the non-contact mixer described herein. By "mixed with the contactless mixer," it is meant that the non-contact mixer operates to effect mixing, distribution, or replenishment of fluids within a paddle on the surface of a specimen support slide. As noted herein, the non-contact mixer is configured such that a pulse of gas (e.g., a jet or stream of gas) emanating from a series of multiple nozzles or sets of nozzles of the non-contact mixer imparts a fluid flow (e.g., agitation) to the fluid(s) and causes fluid movement in at least one direction within at least one area of ​​the slide. As used herein, a "pulse" of gas can mean that the gas flow is "turned on" for a certain period of time, e.g., one second, and then "turned off." This can be considered a continuous stream. Similarly, a "pulse" can equally mean "turning on" a gas flow for a set period of time during which the gas is modulated at a particular frequency, e.g., a 1 Hz frequency is applied to the gas flow for a period of 5 seconds (i.e., a pulse can be a series of "turning on" and "turning off" for a set period of time).

[0088] Accordingly, another aspect of the present disclosure provides a method of distributing and / or mixing a fluid on a surface of a microscope slide by introducing pulses of gas to a paddle on the surface of the specimen support slide. In some embodiments, the introduction of a pulsed gas jet into the fluid causes motion and / or vibration of the fluid, thus providing bulk and / or localized fluid flow, ultimately enabling a substantially uniform distribution of the fluid across the biological sample. For example, and in some embodiments, the fluid can be dispensed in a predetermined area on the surface of the microscope slide, and by activation of the non-contact mixer and introduction of the pulsed gas jet, the fluid can be distributed beyond the initial area of ​​dispensing. In some embodiments, the distribution of fluid on the surface of the microscope slide by introduction of the pulsed gas jet can be used to facilitate replenishment of fluid (e.g., reagent) to a biological sample mounted on the surface of the slide. For example, the biological sample can absorb reagents that are deposited on its surface (or can absorb reagents unevenly), and eventually, an amount of reagent in contact with the biological sample may be substantially depleted (or depleted from certain areas or portions of the sample). Activation of the non-contact mixer (or even individual nozzle arrays within the non-contact mixer) can facilitate dispensing of another aliquot of the same reagent to the biological sample, thus replenishing the reagent in contact with the biological sample. Activation of the non-contact mixer (or individual nozzle arrays) can similarly facilitate redistribution of reagent from other areas of the slide to the biological sample faster than diffusion means, thus replenishing the fluid or reagent in contact with the biological sample.

[0089] In other embodiments, a first fluid may already be present on the surface of a microscope slide (e.g., a fluid paddle), and following the introduction of a second fluid, e.g., a reagent introduced via a dispenser, the second fluid may be substantially uniformly distributed within the first fluid following the introduction of a pulsed gas jet from a non-contact mixer. In some embodiments, by "substantially uniformly distributed" it is meant that the reagent concentration between two separate points on the slide differs in magnitude by no more than 10%. In other embodiments, by substantially uniformly distributed it is meant that the reagent concentration between two separate points on the slide differs in magnitude by no more than 5%. In yet another embodiment, by substantially uniformly distributed it is meant that the reagent concentration between two separate points on the slide differs in magnitude by no more than 2%. Of course, one of skill in the art will understand that any number of fluids may be deposited on the surface of a microscope slide, and each of those fluids may be mixed, i.e., substantially uniformly distributed within each other, by the introduction of a pulsed air jet.

[0090] In some embodiments, the methods disclosed herein are suitable for dispensing and / or mixing any volume of fluid on the surface of a slide. In some embodiments, the volume of fluid that can be dispensed and / or mixed according to the methods disclosed herein ranges from about 50 μL to about 2000 μL. In some embodiments, the volume of fluid that can be dispensed and / or mixed according to the methods disclosed herein ranges from about 50 μL to about 1000 μL. In other embodiments, the volume of fluid that can be dispensed and / or mixed according to the methods disclosed herein ranges from about 50 μL to about 750 μL. In yet other embodiments, the volume of fluid that can be dispensed and / or mixed according to the methods disclosed herein ranges from about 50 μL to about 500 μL. In yet other embodiments, the volume of fluid that can be dispensed and / or mixed according to the methods disclosed herein ranges from about 100 μL to about 500 μL. One skilled in the art would be able to select an appropriately configured non-contact mixing nozzle array (e.g., using specific nozzles having specific configurations, air jet pulse frequencies, times, pressures, and / or flow rates) including all operating parameters.

[0091] In general, the method includes (i) introducing a fluid to a surface of the slide; and (ii) introducing a pulse of a gas jet to the slide, the pulse of the gas jet introducing fluid motion and / or vibration to the slide. In some embodiments, the method includes further steps, including, but not limited to, (a) a detection step for feedback control of the non-contact mixer, (b) a fluid removal step; and (c) a further fluid dispensing step.

[0092] In some embodiments, a method of processing a specimen support slide includes (i) contacting a sample on the specimen support slide with a first reagent; and (ii) uniformly distributing the first reagent on the specimen support slide by introducing a pulsed air jet to the specimen support slide. As noted herein, the pulsed air jet can be delivered to the paddle through a suitably configured non-contact mixer, such as at least a non-contact mixer described herein that facilitates bulk mixing of fluids or reagents in the paddle and / or localized mixing of fluids or reagents. In some embodiments, the pulsed jet of air emanates from a first nozzle array and a second nozzle array of the non-contact mixer. In some embodiments, the pulsed jet of air from the first and second nozzle arrays are staggered in time, thus allowing alternating periods of bulk and localized fluid flow. In some embodiments, the uniform distribution allows for advancement of fluid to areas of the slide that are devoid of fluid.

[0093] In some embodiments, the reagent is introduced into a first fluid paddle (e.g., a paddle containing a buffer) on the surface of the slide or in close proximity to the first paddle on the slide. In some embodiments, the reagent is a detection probe. In some embodiments, the detection probe is a binding moiety specific for a particular target in a biological sample. In some embodiments, the detection probe utilized is a primary antibody, i.e., a primary antibody that allows for detection of a protein target (or an epitope of a protein target) in the sample. In some embodiments, the primary antibody is conjugated to a detectable label, such as a fluorophore, a hapten, or an enzyme. In other embodiments, the detection probe is a nucleic acid probe that allows for detection of a nucleic acid sequence target in the sample. In other embodiments, the specific binding moiety is a nucleic acid probe, and the nucleic acid probe is conjugated to a detectable label, such as a fluorophore, a hapten, or an enzyme.

[0094] In some embodiments, pulsing through any one of the nozzles occurs at a frequency ranging from about 0.5 Hz to about 15 Hz. In some embodiments, the acoustic source operates at a frequency ranging from about 0.5 Hz to about 10 Hz. In some embodiments, pulsing through any one of the nozzles occurs at a frequency ranging from about 1 Hz to about 10 Hz. In some embodiments, pulsing through any one of the nozzles occurs at a frequency ranging from about 1 Hz to about 20 Hz.

[0095] In some embodiments, a first set of nozzles can operate at a first frequency or a range of frequencies; while a second set of nozzles can operate at a second frequency or a range of frequencies. Similarly, any set of nozzles of a non-contact mixer can operate at a first frequency for a first period of time and then at a second frequency for a second period of time. In other embodiments, a particular set of nozzles of a non-contact mixer can initially operate at a first frequency, and the frequency can increase or decrease over time (e.g., ramp up or down over time at predetermined intervals). For example, the first frequency can be 10 Hz, the second frequency can be 20 Hz, and the frequency can be ramped from 10 Hz in 1 Hz increments every 0.5 seconds until the 20 Hz frequency is achieved. In other embodiments, the pneumatic source uses frequency modulation, whereby the frequency is excursed by a value that is + / - 20% of the predetermined frequency value.

[0096] In some embodiments, following introduction of the reagents, a gas jet pulse is delivered from at least one nozzle array of the non-contact mixer to the paddle to effect at least bulk fluid mixing within the paddle. In some embodiments, the pulsed gas jet is introduced for a total period ranging from about 0.5 seconds to about 30 seconds. In some embodiments, the pulsed gas jet is introduced for a total period ranging from about 0.5 seconds to about 20 seconds. In other embodiments, the pulsed gas jet is introduced for a total period ranging from about 1 second to about 15 seconds. In other embodiments, the pulsed gas jet is introduced for a total period ranging from about 5 seconds to about 15 seconds. In other embodiments, the pulsed gas jet is introduced for a total period of about 10 seconds.

[0097] In some embodiments, the pulsing of the sample with the gas jet can be at regular intervals. For example, the sample is pulsed with the gas jet for some predetermined time (e.g., 0.5 second intervals) followed by a predetermined time during which no gas jet is introduced (e.g., 1 second intervals). In other embodiments, the pulsing of the sample with the gas jet can be at non-regular intervals. In other embodiments, the decision as to whether to pulse the sample with the gas jet can be determined by using a detector that provides feedback on the degree of mixing or that can detect whether a portion of the slide or sample needs refilling.

[0098] In some embodiments, the sample can be pulsed by a pulsed gas jet for a set period during which the reagent is in contact with the sample (e.g., during the incubation period). For example, if an antibody is introduced to the sample and a protocol requires that the antibody remain in contact with the sample for a 360 second period (e.g., the incubation period), a gas jet can be introduced into the sample for a set interval of time during the incubation period. For example, pulses of gas can be introduced for 5 second time intervals at times 0, +30 seconds, +60 seconds, +90 seconds, +120 seconds, +150 seconds, +180 seconds, +210 seconds, +240 seconds, +270 seconds, +300 seconds, and +330 seconds following the introduction of the antibody. Of course, rather than pulsing the sample with a gas jet at a set interval or for a set time, a feedback control device (such as described herein) can be utilized to determine whether or not a pulse needs to be introduced, including the length of time during which the non-contact mixer can operate.

[0099] In embodiments where the non-contact mixer includes multiple nozzle arrays, the gas jets can be pulsed from each nozzle array in sequence. For example, the gas jets can be pulsed from the first nozzle array for a first period of time, followed by pulsing of the gas jets from the second nozzle array for a second period of time. The sequential operation of the first and second nozzle arrays can occur one or more times, for example, 1 to 20 times. As an example, the gas jets in the first nozzle array can be pulsed for a period of 5 seconds to provide a bulk fluid flow to a paddle present on the upper surface of the slide. Then, pulsing of the gas jets from the second nozzle array for 5 seconds can provide a localized fluid flow to a predetermined portion of the fluid present on the slide. In this example, the process of sequential operation can be repeated three or more times. One skilled in the art will appreciate that each nozzle array can be operated independently, and each array can be pulsed for any period of time to provide sufficient mixing.

[0100] In other embodiments, the slide or sample can be pulsed with gas (from one or more sets of nozzles or any of the nozzle arrays) from the non-contact mixer each time fluid is dispensed onto the slide or sample and for any purpose (i.e., fluid refill, fluid dispense, and / or fluid mixing). For example, if a protocol calls for adding a constant aliquot of fluid every two minutes, a pulse of gas can be delivered to the slide and / or sample for at least the predetermined time each time an aliquot is added. Of course, additional pulses can be delivered between dispense cycles as needed.

[0101] In some embodiments, the method further includes detecting (e.g., by using a feedback mechanism described herein) whether the fluids and / or reagents are properly dispensed or mixed. If the detecting step determines that the fluids and / or reagents are not properly mixed, the operating parameters of the non-contact mixer, such as pulse frequency, time, pressure, flow rate, and / or nozzle selection, can be adjusted.

[0102] Additionally, if a particular system or instrument requires the slide to be moved between different stations or processing areas of the system or instrument (e.g., sample staining area, sample incubation area), a non-contact mixer can be utilized to deliver a pulsed jet of gas before and / or after the slide movement, thereby ensuring that fluids are properly distributed and / or mixed before, during, and after any such movement. Following mixing of the first reagent into the first fluid paddle, the mixed first reagent / fluid paddle can be removed from the surface of the slide. A first detection reagent can then be introduced and then dispensed onto the surface of the slide or mixed with a second fluid paddle present on the slide. In some embodiments, the first detection reagent is specific for the label of the detection probe. For example, if the label is an enzyme, a substrate for the enzyme (detectable moiety, e.g., chromogenic moiety) can be introduced so that a colored precipitate is detected. In yet other embodiments, an anti-label antibody (secondary antibody) is introduced to elicit detection, the anti-label antibody being specific for the label of the conjugate. For example, if the label is a hapten, an anti-hapten antibody specific for the hapten label is introduced, and the anti-hapten antibody contains a detectable moiety. In some embodiments, the detectable moiety of the anti-hapten antibody is an enzyme, and a substrate for the enzyme is further introduced to detect the conjugate and the target. The detectable moiety can then be detected according to processes known to those skilled in the art. The introduction of the detection probe and / or detection reagent can be repeated "n" times to reflect any desired number of targets in the sample.

[0103] The method disclosed herein is also suitable for multiplex assays. For example, a first detection probe specific to a first target and a second detection probe specific to a second target can be introduced simultaneously or sequentially. Once both the first and second detection probes are introduced to the sample, a non-contact mixer can be utilized to introduce a pulse of gas into the sample so that the first and second detection probes are mixed and evenly distributed. Without being bound to any particular theory, it is believed that the even distribution of the first and second detection probes can promote a uniform detection probe concentration during staining and / or reduced staining artifacts. Those skilled in the art will understand that any number of detection probes can be introduced simultaneously or sequentially into the sample on the surface of a slide, and a number of "n" detection probes can be mixed by the non-contact mixer of the present disclosure. Following the introduction of the detection probe, one or more detection reagents can also be introduced simultaneously and / or sequentially and also mixed by the non-contact mixer.

[0104] In some embodiments, the method of replenishing a fluid or reagent includes (i) contacting a sample on a specimen support slide with a first reagent; allowing time for the reagent to react with or be absorbed by the sample; and (iii) distributing the first reagent evenly on the specimen support slide by introducing a pulse of gas from a non-contact mixing device to the specimen support slide, thereby replenishing the reagent in areas where the reagent has been at least partially depleted. In some embodiments, the method optionally includes a step of introducing an additional aliquot of the first reagent before distributing the first reagent evenly through the introduction of the pulse of gas. In some embodiments, the reagent is introduced into a first fluid paddle (e.g., a paddle with a buffer) on the surface of the slide. In some embodiments, the reagent is a detection probe. In some embodiments, the detection probe is a binding moiety specific for a particular target in a biological sample. In some embodiments, the detection probe utilized is a primary antibody, i.e., a primary antibody that allows for detection of a protein target (or an epitope of a protein target) in the sample. In some embodiments, the primary antibody is conjugated to a detectable label, such as a fluorophore, a hapten, or an enzyme. In other embodiments, the detection probe is a nucleic acid probe that allows detection of a nucleic acid sequence target in a sample. In other embodiments, the specific binding moiety is a nucleic acid probe, and the nucleic acid probe is conjugated to a detectable label, such as a fluorophore, a hapten, or an enzyme.

[0105] In some embodiments, the method of processing a specimen-supporting slide includes (i) dispensing a first fluid onto a first portion of the microscope slide; and (ii) distributing the first fluid on the microscope slide by introducing a pulse of gas to the specimen-supporting slide by a non-contact mixer device. In some embodiments, the first fluid is distributed from the first portion of the microscope slide to at least a second portion of the microscope slide. In some embodiments, the first portion of the slide is a portion that does not contain a sample, and the second portion of the slide includes a biological sample. In some embodiments, the fluid includes a detection probe. In some embodiments, the detection probe is a binding moiety specific for a particular target within the biological sample. In some embodiments, the method further includes introducing an additional aliquot of the fluid to the slide (at any region) and then distributing the fluid through the introduction of a pulsed jet of gas.

[0106] Working Example

[0107] Example 1 - Non-contact mixer

[0108] A nozzle array (see FIG. 10A) was developed to allow mixing in two deliberate stages. During the first stage, the entire slide will be mixed with a single swirl, and then during the second stage, the slide will be split into three swirls for "cross-mixing" of the single swirl results. Only two jets were used for each stage to simplify the design and reduce the chance of interference between the jets. This array gave an idea of ​​the entire slide and cross-mixing. FIG. 10B and FIG. 10C show the result where the dye is mixed with the fluid (e.g., reaction buffer) after the operation of the non-contact mixer.

[0109] Example 2 - Non-contact mixer

[0110] A nozzle array (see FIG. 11A) was developed to allow mixing in two deliberate stages. During the first stage, the entire slide will be mixed in a single swirl, and then during the second stage, the slide will be split into three swirls for "cross-mixing" of the single swirl results. This array demonstrated the idea of ​​whole slide and cross-mixing as well. FIG. 11B shows the result where the dye is mixed with the fluid (e.g., reaction buffer) after operation of the non-contact mixer.

[0111] Example 3 - Pulse drive method

[0112] The nozzle array of a non-contact mixer (e.g., the non-contact mixer of FIG. 10A or FIG. 11A) is pulsed using a function generator that uses fast (2 ms response time) valves and a modulation technique called "pulse with modulation" (PWM) for a set frequency, varying the amount of "on time" versus "off time" during each period. This ratio is called the duty cycle. So a 20% duty cycle at any frequency means it is "on" 20% of the time and "off" 80% of the time. The frequency simply determines how often it switches on versus off. For example, at 1 Hz, 80% duty cycle, the valve will be turned on for 800 ms, turned off for 200 ms, and repeat indefinitely. At a 50% duty cycle and 1 Hz, it will be on for 500 ms and off for 500 ms. In any case, the period is independent of the duty cycle at 1000ms, and the ratio of "on" to "off" time is what indicates the duty cycle. So, for example, at a 20% duty cycle and 10Hz, the valve will turn on for 20ms, turn off for 80ms, and repeat (100ms period).

[0113] At a 20% duty cycle, increasing the frequency to 8 or 16 Hz "evens out" the small pulses, which create smaller waves (less agitation), meaning that the short 20% duty cycle simply isn't pumping out as much air. As the PWM frequency increases, it approaches similarity to the basic (non-PWM) air stream with 20% less air delivery. At a 50% duty cycle and any frequency, the results are generally less impressive than at 20% or 80% duty cycles. 50% seems low enough to significantly reduce the overall airflow, but not low enough to allow standing wave agitation, nor high enough to provide good bulk fluid movement.

[0114] At an 80% duty cycle and any frequency, mixing is usually better than at 20% or 50%. An 80% duty cycle and 4Hz starting frequency sometimes provides a combination of agitation and bulk fluid movement, but at 16Hz mixing is usually best for almost all nozzles.

[0115] Based on these tests, it appears that bulk fluid motion allows for sufficient mixing throughout the slide - much more important than local agitation - and that the steady non-PWM nozzle is likely to provide most of the bulk fluid motion.

[0116] Further embodiments and / or components

[0117] One aspect of the present disclosure is an automated slide processing device, the automated slide processing device comprising: (a) at least one fluid dispenser configured to dispense fluid onto an upper surface of a specimen-supporting slide; and (b) at least one non-contact mixer for mixing fluids present on the upper surface of the slide, the non-contact mixer comprising a first nozzle set and a second nozzle set, the first nozzle set configured to impart a first motion to fluids present on the upper surface of the slide, and the second nozzle set configured to impart a second motion to at least a portion of the fluids present on the upper surface of the slide (e.g., including but not limited to, a portion of the fluid at which the first motion was induced). In some embodiments, the second motion induces cross-mixing of the fluids. In some embodiments, the first nozzle set operates independently and at a different time than the second nozzle set, i.e., the first nozzle set operates exclusively from the second nozzle set. In some embodiments, the automated slide processing device includes a second non-contact mixer. In some embodiments, the first motion is clockwise or counterclockwise, hi some embodiments, the second motion is the other of clockwise or counterclockwise.

[0118] Another aspect of the disclosure is an automated slide processing device, (i) comprising a non-contact mixer for mixing fluids present on an upper surface of a slide, the non-contact mixer comprising a first nozzle array and a second nozzle array, the first nozzle array adapted to impart a bulk fluid flow to the fluids present on the upper surface of the slide, and the second nozzle array adapted to impart at least a first localized fluid flow to at least a portion of the fluids present on the upper surface of the slide. In some embodiments, the first localized fluid flow induces cross-mixing within the fluids. In some embodiments, the automated slide processing device is a staining device, and the fluids present on the upper surface of the slide include a reagent, non-limiting examples of which include a staining reagent, a counterstain reagent, or a washing reagent.

[0119] As described herein, the automated slide processing device can be tied to an imaging device. In some embodiments, the imaging system or device can be a multispectral imaging (MSI) system or a fluorescence microscopy system. The imaging system used herein is MSI. MSI generally equips the analysis of pathology specimens with computerized microscope-based imaging systems by providing access to the spectral distribution of the image at the pixel level. Although a variety of multispectral imaging systems exist, an operational aspect common to all of these systems is the ability to form multispectral images. A multispectral image is an image that captures image data at specific wavelengths or at specific spectral bandwidths across the electromagnetic spectrum. These wavelengths can be selected by optical filters or by the use of other instruments capable of selecting predetermined spectral components, including electromagnetic radiation at wavelengths beyond the visible light range, such as infrared (IR).

[0120] The MSI system may include an optical imaging system, some of which include a spectrally selective system that is adjustable to define a predetermined number N of discrete optical bands. The optical system may be adapted to image a tissue sample illuminated in transmission by a broadband light source onto an optical detector. The optical imaging system, which in one embodiment may include a magnification system such as a microscope, has a single optical axis that is approximately spatially aligned with a single optical output of the optical system. The system forms a sequence of images of the tissue because the spectrally selective system is adjusted or adjusted (e.g., by a computer processor), such as to ensure that images are taken at different discrete spectral bands. The device may further include a display, on which at least one visually recognizable image of the tissue appears from the sequence of images taken. The spectrally selective system may include a light-dispersing element such as a diffraction grating, a collection of optical filters such as thin-film interference filters, or any other system adapted to select specific passbands from the spectrum of light transmitted from the light source through the sample to the detector in response to user input or commands of a preprogrammed processor.

[0121] In an alternative implementation, the spectrally selective system defines several optical outputs corresponding to N discrete spectral bands. This type of system takes the transmitted light output from the optical system and spatially redirects at least a portion of the light output along N spatially distinct light paths such that an image of the identified spectral band is imaged on the detector system along the light path corresponding to the identified spectral band.

[0122] Embodiments of the subject matter and operations described herein may be implemented in digital electronic circuitry, or in computer software, firmware, or hardware, including the structures disclosed herein and structural equivalents thereof, or in one or more combinations thereof. For example, a control system may comprise computer hardware and / or software, including any of the components described herein. Embodiments of the subject matter described herein may be implemented as one or more computer programs, i.e., one or more modules of computer program instructions encoded on a computer storage medium for execution by or for controlling the operation of a data processing device. Any of the modules described herein may include logic executed by a processor(s). As used herein, "logic" refers to any information in the form of instruction signals and / or data that can be applied to affect the operation of a processor. Software is an example of logic.

[0123] A computer storage medium may be or may be included in a computer readable storage device, a computer readable storage substrate, a random or serial access memory array or device, or one or more combinations thereof. Additionally, a computer storage medium is not a propagating signal, but a computer storage medium may be a source or destination of computer program instructions encoded in an artificially generated propagating signal. A computer storage medium may also be or may be included in one or more separate physical components or media (e.g., multiple CDs, disks, or other storage devices). The operations described herein may be implemented as operations performed by a data processing apparatus on data stored on one or more computer readable storage devices or received from other sources.

[0124] The term "programmed processor" encompasses all kinds of apparatus, devices, and machines for processing data, including, by way of example, programmable microprocessors, computers, systems on chips, or a plurality or combination of the above. An apparatus may include special purpose logic circuitry, such as a field programmable gate array (FPGA) or application specific integrated circuit (ASIC). In addition to hardware, an apparatus may also include code that creates an execution environment for a subject computer program, such as code that constitutes a processor firmware, a protocol stack, a database management system, an operating system, a cross-platform runtime environment, a virtual machine, or one or more combinations thereof. The apparatus and execution environment may implement a variety of different computing model infrastructures, such as web services, distributed computing, and grid computing infrastructures.

[0125] A computer program (also known as a program, software, software application, script, or code) can be written in any form of programming language, including compiled or interpreted languages, declarative or procedural languages, and the computer program can be deployed as a stand-alone program or as a module, component, subroutine, object, or other unit suitable for use in a computing environment. A computer program can, but need not, correspond to a file in a file system. A program can be stored in part of a file that holds other programs or data (e.g., one or more scripts stored in a markup language document), in a single file dedicated to the program in question, or in multiple coordinated files (e.g., files that store one or more modules, subprograms, or portions of code). A computer program can be deployed to run on one computer or on multiple computers, located at one site or distributed across multiple sites and interconnected by a communication network.

[0126] The processes and logic flows described herein may be performed by one or more programmable processors executing one or more computer programs to perform actions by operating on input data and generating output. The processes and logic flows may also be performed by, or implemented as, special purpose logic circuitry, for example an FPGA (field programmable gate array) or an ASIC (application specific integrated circuit).

[0127] Processors suitable for executing computer programs include, by way of example, both general-purpose and special-purpose microprocessors, as well as any one or more processors of any kind of digital computer. In general, a processor will receive instructions and data from a read-only memory or a random-access memory, or both. The essential elements of a computer are a processor for performing actions according to the instructions, and one or more memory devices for storing instructions and data. In general, a computer will include one or more mass storage devices, such as magnetic disks, magneto-optical disks, or optical disks, for storing data, or be operatively coupled to receive data from or transfer data to them, or both. However, a computer need not necessarily have such devices. Furthermore, a computer may be embedded in another device, such as a mobile phone, a personal digital assistant (PDA), a portable audio or video player, a game console, a global positioning system (GPS) receiver, or a portable storage device (e.g., a universal serial bus (USB) flash drive), to name a few. Devices suitable for storing computer program instructions and data include all forms of non-volatile memory, media, and memory devices, including, by way of example, semiconductor memory devices, such as EPROM, EEPROM, and flash memory devices; magnetic disks, such as internal hard disks or removable disks; magneto-optical disks; and CD-ROM and DVD-ROM disks. The processor and memory may be supplemented by, or incorporated in, dedicated logic circuitry.

[0128] All U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent applications, and non-patent publications mentioned herein and / or listed in the Application Data Sheet are incorporated herein by reference in their entirety. Aspects of the embodiments may be modified, if necessary, to employ concepts from the various patents, applications, and publications, thereby providing still further embodiments.

[0129] Although the present disclosure has been described with reference to several illustrative embodiments, it should be understood that numerous other modifications and embodiments may be devised by those skilled in the art which fall within the spirit and scope of the principles of the present disclosure. More particularly, reasonable variations and modifications are possible in the component parts and / or arrangements of the subject combinations and arrangements within the scope of the above disclosure, the drawings, and the appended claims, without departing from the spirit of the present disclosure. In addition to variations and modifications of the component parts and / or arrangements, alternative uses will likewise be apparent to those skilled in the art.

Claims

1. 1. An automated slide processing apparatus comprising: at least one fluid dispenser configured to dispense a fluid onto an upper surface of the specimen support slide; a non-contact mixer for mixing fluid present on the upper surface of the slide, the non-contact mixer comprising a first nozzle set and a second nozzle set, the first nozzle set including a plurality of first nozzles in fluid communication with a first plenum, adapted to impart a first fluid motion to the fluid present on the upper surface of the slide by directing gas supplied via the first plenum from the plurality of first nozzles towards the upper surface of the slide, the second nozzle set adapted to direct gas supplied via the first plenum from the plurality of first nozzles towards the upper surface of the slide, and a plurality of second nozzles in fluid communication with a second plenum independent of a first nozzle and adapted to emit gas supplied through the second plenum from the plurality of second nozzles toward the upper surface of the slide to impart at least a second fluid motion to at least a portion of the fluid present on the upper surface of the slide, the first fluid motion being one of clockwise or counterclockwise agitation and the second fluid motion being the other of the clockwise or counterclockwise agitation.

2. The automated slide processing apparatus of claim 1 , wherein the second fluid motion is imparted to a central portion of the fluid.

3. 3. The automated slide processing apparatus of claim 2, wherein the second set of nozzles is further adapted to impart a third fluid motion to two portions of the fluid located on either side of the central portion, the third fluid motion being an agitation in an opposite direction to the second fluid motion, one of the clockwise or counterclockwise agitation.

4. 4. The automated slide processing device of claim 3, wherein said first fluid motion is counterclockwise agitation, said second fluid motion is clockwise agitation, and said third fluid motion is counterclockwise agitation.

5. The automated slide processing apparatus of claim 1 , wherein the second fluid motion is imparted to at least two portions of the fluid.

6. 6. The automated slide processing device of claim 5, wherein the second nozzle set is further adapted to impart a third fluid motion to a central portion of the fluid, the third fluid motion being one of the clockwise or counterclockwise agitation in an opposite direction to the second fluid motion.

7. 7. The automated slide processing apparatus of claim 6, wherein the first fluid motion is a counterclockwise motion, the second fluid motion is a clockwise motion, and the third fluid motion is a counterclockwise motion, and the second fluid motion is imparted to two portions of the fluid located on either side of the central portion.

8. 4. The automated slide processing apparatus of claim 3, wherein the first plurality of nozzles are grouped into two parallel rows along a longitudinal axis of the non-contact mixer and the second plurality of nozzles are grouped into two substantially parallel rows along the longitudinal axis of the non-contact mixer.

9. The automated slide processing apparatus of claim 1 , wherein the first fluid motion is imparted to a majority of the fluid on the upper surface of the slide.

10. The automated slide processing apparatus of claim 1 , wherein the second fluid motion is imparted to at least two discrete portions of the fluid present on the upper surface of the slide.

11. 1. An automated slide processing apparatus comprising: at least one fluid dispenser configured to dispense a fluid onto an upper surface of the specimen support slide; and a non-contact mixer for mixing fluids present on the upper surface of the slide, the non-contact mixer comprising a first nozzle set and a second nozzle set, the first nozzle set including a plurality of first nozzles in fluid communication with a first plenum and adapted to impart a first fluid motion to the fluids present on the upper surface of the slide by directing gas supplied through the first plenum from the plurality of first nozzles towards the upper surface of the slide, and the second nozzle set in fluid communication with a second plenum independent of the first plenum.

13. The automated slide processing apparatus of claim 12, further comprising: a plurality of second nozzles in fluid communication with said slide surface; and adapted to impart at least a second fluid motion to at least a portion of said fluid present on said upper surface of said slide by directing gas supplied through said second plenum from said plurality of second nozzles toward said upper surface of said slide, said first fluid motion being a bulk fluid flow and said second fluid motion being a first localized fluid flow, said bulk fluid flow being in a clockwise or counterclockwise direction and said first localized fluid flow being in the other of said clockwise or counterclockwise direction.

12. 1. An automated slide processing apparatus comprising: at least one fluid dispenser configured to dispense a fluid onto an upper surface of the specimen support slide; and a non-contact mixer for mixing fluids present on the upper surface of the slide, the non-contact mixer comprising a first nozzle set and a second nozzle set, the first nozzle set including a plurality of first nozzles in fluid communication with a first plenum and adapted to impart a first fluid motion to the fluids present on the upper surface of the slide by emitting gas supplied via the first plenum from the plurality of first nozzles towards the upper surface of the slide, and the second nozzle set including a plurality of second nozzles in fluid communication with a second plenum independent of the first plenum and adapted to impart a first fluid motion to the fluids present on the upper surface of the slide by emitting gas supplied via the second plenum from the plurality of second nozzles towards the upper surface of the slide.

11. An automated slide processing apparatus adapted to impart at least a second fluid motion to at least a portion of the fluid, wherein the first fluid motion is a bulk fluid flow and the second fluid motion is a first localized fluid flow, the first localized fluid flow being imparted to a central portion of the fluid on the upper surface of the slide, the second nozzle set being further adapted to impart a second localized fluid flow and a third localized fluid flow, the second localized fluid flow and the third localized fluid flow occurring in two distinct portions of the fluid on the slide located on either side of the central portion, the first localized fluid flow being a fluid flow in one of a clockwise or counterclockwise direction, and the second localized fluid flow and the third localized fluid flow being fluid flows in an opposite direction to the first localized fluid flow, the clockwise or counterclockwise direction.

13. The automated slide processing device of claim 1, wherein the non-contact mixer is positioned above and substantially parallel to the upper surface of the slide.

14. 14. The automated slide processing apparatus of claim 1, further comprising a third nozzle set including a plurality of third nozzles in fluid communication with a third plenum independent of the first plenum and the second plenum, the third nozzle set ejecting gas supplied through the third plenum from the plurality of third nozzles toward the upper surface of the slide to impart additional fluid motion to the fluid present on the upper surface of the slide.

15. 1. A method for processing a specimen-bearing slide, comprising the steps of: Dispensing a fluid onto an upper surface of a specimen support slide; mixing a fluid present on the upper surface of the slide, comprising: directing gas from a first plurality of nozzles toward the upper surface of the slide to impart a first fluid motion to the fluid present on the upper surface of the slide; and and directing gas toward the upper surface of the slide from a plurality of second nozzles distinct from the plurality of first nozzles to impart at least a second fluid motion to at least a portion of the fluid present on the upper surface of the slide. mixing the fluid present on the upper surface of the slide, comprising: Including, The method of claim 1, wherein the first fluid motion is one of a clockwise or counterclockwise stirring and the second fluid motion is the other of the clockwise or counterclockwise stirring.

16. A method for processing a specimen-bearing slide, comprising the steps of: Dispensing a fluid onto an upper surface of a specimen support slide; mixing a fluid present on the upper surface of the slide, comprising: directing gas from a first plurality of nozzles toward the upper surface of the slide to impart a first fluid motion to the fluid present on the upper surface of the slide; and and directing gas toward the upper surface of the slide from a plurality of second nozzles distinct from the plurality of first nozzles to impart at least a second fluid motion to at least a portion of the fluid present on the upper surface of the slide. mixing the fluid present on the upper surface of the slide, comprising: Including, The method, wherein the first fluid motion is a bulk fluid flow and the second fluid motion is a first localized fluid flow, the bulk fluid flow being in a clockwise or counterclockwise direction and the first localized fluid flow being in the other of the clockwise or counterclockwise directions.

17. A method for processing a specimen-bearing slide, comprising the steps of: Dispensing a fluid onto an upper surface of a specimen support slide; mixing a fluid present on the upper surface of the slide, comprising: directing gas from a first plurality of nozzles toward the upper surface of the slide to impart a first fluid motion to the fluid present on the upper surface of the slide; and and directing gas toward the upper surface of the slide from a plurality of second nozzles distinct from the plurality of first nozzles to impart at least a second fluid motion to at least a portion of the fluid present on the upper surface of the slide. mixing the fluid present on the upper surface of the slide, comprising: Including, 11. A method according to claim 10, wherein the first fluid motion is a bulk fluid flow and the second fluid motion is a first localized fluid flow, the first localized fluid flow being provided at a central portion of the fluid on the upper surface of the slide, the plurality of second nozzles further providing a second localized fluid flow and a third localized fluid flow, the second localized fluid flow and the third localized fluid flow occurring at two different portions of the fluid on the slide located on either side of the central portion, the first localized fluid flow being a fluid flow in one of a clockwise or counterclockwise direction, and the second localized fluid flow and the third localized fluid flow being fluid flows in an opposite direction to the first localized fluid flow in the clockwise or counterclockwise direction.

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