Bioreactor system

Abstract

Provided herein are bioreactors, including a container used for growing, expanding, activating, and / or transfecting cells and, in general, to manipulate or modify cells in an aseptic way.

Description

Attorney Docket No.328202000440 BIOREACTOR SYSTEM CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the priority benefit of United States Provisional Patent Application Serial No.63 / 700,683, filed September 28, 2024, and of United States Provisional Patent Application Serial No.63 / 786,905, filed April 10, 2025, the contents of each of which are incorporated herein by reference in their entirety. FIELD

[0002] The present disclosure relates generally to methods, devices, and systems for culturing cells, and more specifically to methods, devices, and systems for growing, expanding, activating, and / or transfecting cells that allow real-time, aseptic monitoring, manipulation, and / or sampling of cells during the culturing process. BACKGROUND

[0003] Current methods of cell growth and expansion use rigid flasks or plates, bioreactor containers with membranes or bioreactor bags. These containers are usually housed in an incubator or device which may control temperature, humidity, CO2 levels, pressure and other environmental parameters, control the flow of fluids into and out of the containers and, in some cases, provide one or more degrees of motion for the cell containers (e.g., swirling).

[0004] The limitations and bottlenecks of the approaches currently adopted in the state of the art are similar, albeit to various degrees. They take significant space, affecting not only the need for clean- room space, but also making the logistics of moving consumables challenging. They are not designed to be automated, but are rather designed to be used by skilled scientists or operators.

[0005] They also typically require manual sampling, i.e., where cells are extracted from the container and transferred to other instruments for QC and data analytics, such as actual cell count and viability, thereby exposing the cell culture to risks such as contamination and human errors. Aliquoting small amounts of fluid requires pipetting, usually after opening the containers manually, 1MF-361080369Attorney Docket No.328202000440 which creates scalability bottlenecks - these steps need to be performed in ISO 5 cleanrooms or laminar flow biosafety cabinets - and create huge risks for contamination.

[0006] As the cells expand and the volume increases, often multiple containers are used, requiring the fluid to be transferred from one container to another. These operations are usually performed manually and, again, introduce high risks of contamination or cross-contamination between products.

[0007] Common bioreactors are bulky, complex to install with multiple tubing connections required, and require complex training and operational controls, making their use prone to quality control errors.

[0008] In addition, the recent promises of allogeneic therapies, as well as induced Pluripotent Stem Cell (iPSC) applications, require the handling of fluid volumes usually handled via pipettes in open fashion, as well as much larger volumes (>1 liter) during the same process. This poses challenges for the scalability of the process since the product cannot be produced in a closed system. BRIEF SUMMARY

[0009] Disclosed herein are multi-compartment and / or spiroidal bioreactor containers with a generally v-shaped cross-section, and which can be rotated along an axis internal to a path along which the shape of the cross-section is swept to create the internal volume of the container. The shape of the container, as well as the ability to rotate it, gives the system the additional degrees of freedom needed for handling several operations commonly performed on cells, such as enrichment, activation, transduction, wash, expansion, and fill & finish operations. The ability to spin the bioreactor allows automatic cell resuspension in a closed aseptic system, and provides centrifugal force to be used for the desired manipulation of cells, beads or particles. The generally v-shaped cross-section developed along a spiral path, allows the air-fluid surface within the container to increase as the volume increases, and it provides the ability to position the fluid, and the particles (e.g., cells) within it, along the outer surface of the container as it spins. The shape, which may have different elevations and average rotation radius, allows optimizing the cell growth based on the 2MF-361080369Attorney Docket No.328202000440 specific needs in terms of density, fluid volume to surface ratio, cluster or clumping prevention, media recirculation and exchange, etc. The location of particles (e.g., cells) within the container as a function of time is based on fluid and particle properties, such as particle mass and fluid viscosity for example. This in turn enables the system to position, e.g., cells at locations within the container (e.g., optical windows) that enable one image cells or particles without opening the system or extracting a sample. The presence of micro-cavities along the top of the inner container surface allows the selection and sampling, in a closed aseptic system, of small amounts of fluids that would otherwise require open system pipetting. These micro-cavities are filled with fluid during rotation of the container, and can be flushed and extracted as the rotation is stopped.

[0010] The disclosed bioreactor containers address the limitations and bottlenecks of existing bioreactors as described above, including enabling multiple operations to be performed during cell culturing, as well as continuous cell monitoring and handling of small (<1 ml) and large (>100 ml) volumes of fluids in the same closed system. The disclosed bioreactor containers have a compact form factor for use in parallel operations, and can be easily handled by automation systems.

[0011] Disclosed herein are bioreactors comprising: a container comprising a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses an axis of rotation of the bioreactor, wherein not all cross-sectional profiles of the series are the same and / or not all cross-sectional profiles’ lowest points have the same elevation and / or wherein the path is not equidistant from the axis of rotation at all points along the path; and at least one fluid port configured to provide fluid communication with the internal volume of the container.

[0012] In some embodiments, at least one fluid port is configured to provide fluid communication between an external fluid source and the internal volume of the container as the bioreactor rotates about its axis. In some embodiments, at least one fluid port is configured to provide fluid communication between the interior volume of the container and a stationary exterior fluid reservoir as the bioreactor rotates about its axis. 3MF-361080369Attorney Docket No.328202000440

[0013] In some embodiments, the cross-sectional profiles of the series comprise a cross-section of a top plate, a first side-wall, and a second side-wall.

[0014] In some embodiments, the bioreactor further comprises at least one micro cavity feature integrated with the first side-wall and configured to sample an aliquot of fluid contained within the container. In some embodiments, the at least one micro cavity feature is integrated with a top edge of the first side-wall.

[0015] In some embodiments, the intersection of the first side-wall with a first imaginary plane parallel to a plane of the top plate defines a first diameter of the container; wherein the intersection of the second side-wall with a second imaginary plane parallel to the plane of the top plate defines a second diameter of the container; and wherein the second diameter is smaller than the first diameter. In some embodiments, the first side-wall and the second side-wall are slanted so as to intersect at an imaginary line which defines an angle between the first side-wall and the second side-wall at each cross-sectional profile of the series. In some embodiments, at least one of the first side-wall or the second side-wall is curved rather than planar. In some embodiments, the bioreactor further comprises a bottom surface that intersects with the first side-wall and the second side-wall.

[0016] In some embodiments, at least a portion of the top plate, the bottom surface, the first side- wall, and / or the second side-wall is composed of a gas permeable membrane.

[0017] In some embodiments, the first side-wall is an exterior side-wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable high speed imaging of particles suspended in a fluid contained within the container as the container rotates about its axis.

[0018] In some embodiments, the first side-wall is an exterior side-wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable high speed imaging of particles attached to an interior surface of the first side-wall as the container rotates about its axis.

[0019] In some embodiments, the first side-wall is an exterior side-wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable optical sensing of at 4MF-361080369Attorney Docket No.328202000440 least one of pH, dissolved oxygen (DO), O2, N2, CO2, metabolomic profile, glutamate, glutamine, lactate, glucose, volume, flow rate, pressure, and temperature in a fluid contained within the container as the container rotates about its axis.

[0020] In some embodiments, at least a portion of the bottom surface is optically transparent and configured to enable high speed imaging of particles suspended in a fluid contained within the container as the container rotates about its axis.

[0021] In some embodiments, at least a portion of the bottom surface is optically transparent and configured to enable high speed imaging of particles attached to the bottom surface as the container rotates about its axis.

[0022] In some embodiments, at least a portion of the bottom surface is optically transparent and configured to enable optical sensing of at least one of pH, dissolved oxygen (DO), O2, N2, CO2, metabolomic profile, glutamate, glutamine, lactate, glucose, volume, flow rate, pressure, and temperature in a fluid contained within the container as the container rotates about its axis.

[0023] In some embodiments, the at least one fluid port provides fluid communication between a stationary external fluid source and the interior volume of the container through a rotating fluid connector. In some embodiments, the at least one fluid port provides fluid communication between the interior volume of the container and a stationary exterior fluid reservoir through a rotating fluid connector. In some embodiments, the at least one fluid port comprises a filtration membrane and is configured for periodic or continuous removal of a fluid contained within the container.

[0024] In some embodiments, the path that encompasses the axis of rotation of the bioreactor is confined to a plane that is perpendicular to the axis of rotation. In some embodiments, the path that encompasses the axis of rotation of the bioreactor is not confined to a plane that is perpendicular to the axis of rotation. In some embodiments, the path is a closed path. In some embodiments, a portion of the path is an open path. In some embodiments, the path has a different radial distance from the axis of rotation of the bioreactor at different points along the path. In some embodiments, the path 5MF-361080369Attorney Docket No.328202000440 has a different radial distance from a central axis of symmetry at different points along the path, and wherein the central axis of symmetry is different from the axis of rotation of the bioreactor.

[0025] In some embodiments, some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series. In some embodiments, some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series.

[0026] In some embodiments, a height of the internal volume of the container at each point along the path is defined by a distance between an inner surface of the top plate and an inner surface of a bottom plate.

[0027] In some embodiments, an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. In some embodiments, an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

[0028] In some embodiments, the bioreactor further comprises at least one fluid channel configured to recirculation of a fluid contained within the internal volume of the container.

[0029] Also disclosed herein are systems comprising: at least one container comprising: a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses an axis of rotation of the container, wherein not all cross-sectional profiles of the series are the same and / or wherein the path is not equidistant from the axis of rotation at all points along the path; and at least one fluid inlet port configured to provide fluid communication with the internal volume of the container; and at least one drive mechanism comprising: a frame for mounting the container, wherein the frame is configured to allow the container to spin around its rotational axis; and at least one drive motor; wherein the drive mechanism is configured to control an angular velocity of the container as a function of time.

[0030] In some embodiments, the cross-sectional profiles of the series comprise a cross-section of a top plate, a first side-wall, and a second side-wall. 6MF-361080369Attorney Docket No.328202000440

[0031] In some embodiments, the at least one container comprises at least one micro cavity feature integrated with the first side-wall and configured to sample an aliquot of fluid contained within the container. In some embodiments, the at least one micro cavity feature is integrated with a top edge of the first side-wall. In some embodiments, the at least one micro cavity feature is configured to sample an aliquot of fluid contained within the container when an actuation force is applied to the at least one micro cavity feature. In some embodiments, the at least one micro cavity feature is configured to deliver the fluid aliquot to a stationary external fluid sample container.

[0032] In some embodiments, the frame comprises a self-centering engagement mechanism for attachment to a robotic actuator.

[0033] In some embodiments, the at least one drive motor of the drive mechanism comprises a servo motor. In some embodiments, the at least one drive mechanism further comprises a self-centering engagement mechanism for attachment to a robotic actuator. In some embodiments, the at least one drive mechanism further comprises a self-centering engagement mechanism for attachment to a rack configured to hold a plurality of drive mechanisms. In some embodiments, the at least one drive mechanism further comprises at least one optical encoder for monitoring the angular velocity of the container as a function of time. In some embodiments, the at least one drive mechanism is configured to vary the angular velocity of the container as a function of time in a programmable fashion.

[0034] In some embodiments, a variation in the angular velocity of the container as a function of time is used to control a composition of a fluid mixture that enters the at least one micro cavity feature.

[0035] In some embodiments, the at least one drive mechanism, or a housing thereof, further comprises at least one optical imaging camera configured to perform high speed imaging of particles suspended in the fluid contained within the container. In some embodiments, the at least one drive mechanism, or a housing thereof, further comprises at least one optical imaging camera configured to perform high speed imaging of particles attached to an interior surface of the first side-wall of the 7MF-361080369Attorney Docket No.328202000440 container. In some embodiments, the at least one drive mechanism, or a housing thereof, further comprises at least one optical sensor configured to perform optical sensing of at least one of pH, dissolved oxygen (DO), O2, N2, CO2, metabolomic profile, glutamate, glutamine, lactate, glucose, volume, flow rate, pressure, and temperature in a fluid contained within the container.

[0036] In some embodiments, the system further comprises a gas controller configured to provide control of the flow rate for at least one gas flowing into the container. In some embodiments, the system further comprises a housing configured to provide temperature control for the container.

[0037] In some embodiments, a geometry of the at least one micro cavity feature is configured to modify a shape of a cell that enters therein. In some embodiments, a geometry of the at least one micro cavity feature is configured to lyse a cell that enters therein.

[0038] In some embodiments, the system further comprises an electromagnetic device configured to modify a cell that enters the at least one micro cavity feature. In some embodiments, the system further comprises an electronic device configured to electroporate a cell that enters the at least one micro cavity feature.

[0039] In some embodiments, the path that encompasses the axis of rotation of the container is confined to a plane that is perpendicular to the axis of rotation. In some embodiments, the path that encompasses the axis of rotation of the container is not confined to a plane that is perpendicular to the axis of rotation. In some embodiments, the path is a closed path. In some embodiments, a portion of the path is an open path. In some embodiments, the path has a different radial distance from the axis of rotation of the container at different points along the path. In some embodiments, the path has a different radial distance from a central axis of symmetry at different points along the path, and wherein the central axis of symmetry is different from the axis of rotation of the container.

[0040] In some embodiments, some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series. In some embodiments, some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series. 8MF-361080369Attorney Docket No.328202000440

[0041] In some embodiments, a height of the internal volume of the at least one container at each point along the path is defined by a distance between the top fluid surface and an inner surface of a bottom plate.

[0042] In some embodiments, an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. In some embodiments, an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

[0043] In some embodiments, the at least one container further comprises at least one fluid channel configured for recirculation of a fluid contained within the internal volume of the container.

[0044] In some embodiments, at least one fluid port is configured to provide fluid communication between a stationary external fluid source and the internal volume of the container as the container rotates about its axis. In some embodiments, at least one fluid port is configured to provide fluid communication between the interior volume of the container and a stationary exterior fluid reservoir as the container rotates about its axis.

[0045] Disclosed herein are methods for culturing cells, the methods comprising: introducing cells into a fluid contained within a bioreactor comprising: a container comprising a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses an axis of rotation of the bioreactor, wherein not all cross-sectional profiles of the series are the same and / or wherein the path is not equidistant from the axis of rotation at all points along the path, and optionally, at least one micro cavity feature integrated with a first side-wall and configured to perform at least one of: (i) sampling an aliquot of fluid contained within the container when the container is rotated; and / or (ii) delivering the fluid aliquot to a stationary external fluid sample container; aerating and / or agitating the fluid contained within the container by rotating the container about its axis at a specified angular velocity; monitoring cell growth within the fluid by at least one of: performing high speed imaging of cells suspended in the fluid, performing high speed imaging of cells attached to an interior surface of the first side-wall of the container, or performing high speed 9MF-361080369Attorney Docket No.328202000440 imaging of cells contained in the at least on micro cavity feature; sampling an aliquot of the fluid using the at least one micro cavity feature by increasing an angular velocity for rotation of the container so that it exceeds a specified minimum angular velocity threshold, and delivering the aliquot of the fluid to a stationary external sample container for testing.

[0046] In some embodiments, sampling an aliquot of fluid contained within the container comprises applying a force to a valve mechanism integrated with the at least one micro cavity feature.

[0047] In some embodiments, the method further comprises use of different angular velocity settings to perform different cell culture functions. In some embodiments, the different cell culture functions comprise mixing, resuspension, temperature control, cell wash, cluster prevention, delivery of an aliquot of fluid to the at least one micro cavity for cell analysis and / or modification, or any combination thereof.

[0048] In some embodiments, the method further comprises monitoring at least one of pH, dissolved oxygen (DO), carbon dioxide (CO2) and temperature within the fluid as a function of time.

[0049] In some embodiments, prior to the sampling step, an angular velocity for rotation of the container is adjusted to select a subset of cells for sampling by the at least one micro cavity feature. In some embodiments, prior to the sampling step, an external force is applied to select a subset of cells for sampling by the at least one micro cavity feature.

[0050] In some embodiments, the path that encompasses the axis of rotation of the container is confined to a plane that is perpendicular to the axis of rotation. In some embodiments, the path that encompasses the axis of rotation of the bioreactor is not confined to a plane that is perpendicular to the axis of rotation. In some embodiments, the path is a closed path. In some embodiments, a portion of the path is an open path. In some embodiments, the path has a different radial distance from the axis of rotation of the container at different points along the path. In some embodiments, the path has a different radial distance from a central axis of rotation at different points along the path, and wherein the central axis of rotation is different from the axis of rotation of the container. 10MF-361080369Attorney Docket No.328202000440

[0051] In some embodiments, some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series. In some embodiments, some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series.

[0052] In some embodiments, a height of the internal volume of the container at each point along the path is defined by a distance between an inner surface of the top plate and an inner surface of a bottom plate.

[0053] In some embodiments, an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. In some embodiments, an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

[0054] The method of any one of claims 71 to 86, the container further comprises at least one fluid channel configured to recirculation of a fluid contained within the internal volume of the container.

[0055] Disclosed herein are bioreactors comprising: a container comprising a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses a central axis of the bioreactor, wherein not all cross-sectional profiles of the series are the same and / or wherein the path is not equidistant from the central axis at all points along the path; and at least one fluid port configured to provide fluid communication with the internal volume of the container.

[0056] In some embodiments, the bioreactor is configured to rotate about a rotation axis. In some embodiments, the rotation axis coincides with the central axis.

[0057] It should be appreciated that all combinations of the foregoing concepts and additional concepts discussed in greater detail below (provided such concepts are not mutually inconsistent) are contemplated as being part of the inventive subject matter disclosed herein. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are contemplated as being part of the inventive subject matter disclosed herein. 11MF-361080369Attorney Docket No.328202000440 INCORPORATION BY REFERENCE

[0058] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference in its entirety. In the event of a conflict between a term herein and a term in an incorporated reference, the term herein controls. BRIEF DESCRIPTION OF THE DRAWINGS

[0059] Various aspects of the disclosed methods, devices, and systems are set forth with particularity in the appended claims. A better understanding of the features and advantages of the disclosed methods, devices, and systems will be obtained by reference to the following detailed description of illustrative embodiments and the accompanying drawings, of which:

[0060] FIG. 1 provides a non-limiting illustration of a bioreactor assembly 10 housed in the frame 20, in accordance with one embodiment of the present disclosure.

[0061] FIG. 2 provides a non-limiting illustration of a cross section of the bioreactor container, in accordance with one embodiment of the present disclosure.

[0062] FIG. 3 provides a non-limiting illustration of a nest 400 and image capturing system 300, in accordance with one embodiment of the present disclosure.

[0063] FIG.4 provides a non-limiting illustration of a section of the bioreactor assembly 10, including the frame 20, in accordance with one embodiment of the present disclosure.

[0064] FIG. 5 provides another non-limiting view of nest 400, in accordance with one embodiment of the present disclosure.

[0065] FIG. 6A provides a non-limiting illustration of bioreactor container 100 with specialized sections of surface 160 for the selection of small quantities of fluids, in accordance with one embodiment of the present disclosure. 12MF-361080369Attorney Docket No.328202000440

[0066] FIG. 6B provides a non-limiting illustration of a valve system 180 with the valve in the closed position, in accordance with one embodiment of the present disclosure.

[0067] FIG. 6C provides a non-limiting illustration of a valve system 180 with the valve in the open position, in accordance with one embodiment of the present disclosure.

[0068] FIG. 6D provides a non-limiting illustration of the forces acting on the moving body 181, in accordance with one embodiment of the present disclosure.

[0069] FIG. 7 provides a non-limiting illustration of the main components of nest 400, in accordance with one embodiment of the present disclosure.

[0070] FIG. 8A provides a non-limiting illustration of a multi-compartment bioreactor container with the top surface 130 segmented into multiple compartments, separated by rigid walls 132, in accordance with one embodiment of the present disclosure.

[0071] FIG. 8B provides a non-limiting illustration of the multi-compartment bioreactor container with the top surface and top components removed to show the multiple compartments, in accordance with one embodiment of the present disclosure.

[0072] FIG. 8C provides a non-limiting illustration of how fluid is delivered to each compartment, in accordance with one embodiment of the present disclosure.

[0073] FIG. 8D provides a non-limiting illustration of how fluid is delivered to each compartment, in accordance with one embodiment of the present disclosure.

[0074] FIG. 9A provides a non-limiting illustration of an embodiment of the bioreactor container 100 where the slanted surfaces are equipped with features specifically designed for organoid growth, in accordance with one embodiment of the present disclosure. 13MF-361080369Attorney Docket No.328202000440

[0075] FIG. 9B provides a non-limiting illustration of an embodiment of the bioreactor container 100 where similar inserts 650 are inserted at the bottom of the container rather than the sides, in accordance with one embodiment of the present disclosure.

[0076] FIG. 10 provides a non-limiting illustration of an imaging system, in accordance with one embodiment of the present disclosure.

[0077] FIGS.11A – 11C provide non-limiting illustrations of a spiroidal bioreactor container 100 where the generally v-shaped cross sections are not at the same elevation, in accordance with one embodiment of the present disclosure. FIG.11A: top view. FIG.11B: isometric view. FIG.11C: side view.

[0078] FIG. 12 provides a non-limiting illustration of a top view of the spiroidal bioreactor container 100 where the cross-sections are not all at the same distance from the rotation axis, in accordance with one embodiment of the present disclosure.

[0079] FIG. 13 provides a non-limiting illustration of an embodiment of the spiroidal bioreactor container 100 where two spiroidal paths, having either different vertical elevations, different radii, or both, are joined in a symmetrical container.

[0080] FIG. 14 provides a non-limiting illustration of an embodiment of the spiroidal bioreactor container 100 where the spiroidal path does not have a return and the fluid is recirculated.

[0081] FIG.15 provides a non-limiting illustration of a cross-sectional view of an embodiment of the spiroidal bioreactor container 100 where the walls can be curved or comprise different sections in the vertical direction.

[0082] FIG.16 provides a non-limiting illustration of an embodiment of the spiroidal bioreactor container 100 where the channels 166 are used for fluid recirculation.

[0083] FIG.17 provides a schematic illustration of a computer system, in accordance with some embodiments of the present disclosure. 14MF-361080369Attorney Docket No.328202000440

[0084] FIGS.18A – 18C provide non-limiting example of data for a comparison of Jurkat cell expansion in a prototype of the disclosed bioreactor to that in a flask or a commercial G-Rex6M multi-well culture plate at a fixed medium volume of 20 ml. FIG. 18A: fold expansion. FIG. 18B: cell density. FIG.18C: cell viability.

[0085] FIGS.19A – 19C provide non-limiting examples of data for a comparison of Jurkat cell expansion in two different prototypes of the disclosed bioreactor to that in a flask or a commercial G-Rex6M multi-well culture plate at an incremental medium volume adjusted from 2.5 to 80 ml. FIG.19A: fold expansion. FIG.19B: cell density. FIG.19C: cell viability. DETAILED DESCRIPTION

[0086] Multi-compartment and / or spiroidal bioreactor containers (also referred to herein simply as “bioreactor containers”) with a generally v-shaped cross-section, and which can be rotated along an axis internal to a path along which the shape of the cross-section is swept to create the internal volume of the container, are described. The disclosed bioreactor containers enable a number of operations commonly performed on cells, e.g., enrichment, activation, transduction, expansion, and fill & finish operations, to be performed in a closed aseptic system. The disclosed bioreactor containers are configured to enable monitoring, e.g., imaging, of cells or other particles without opening the system or extracting a sample. The bioreactor containers are also configured to allow the selection and sampling, in a closed aseptic system, of small amounts of fluid that would otherwise require open system pipetting.

[0087] The disclosed multi-compartment and / or spiroidal bioreactor containers address the limitations and bottlenecks of existing bioreactors, including enabling multiple operations to be performed during cell culturing, as well as continuous cell monitoring and handling of small (<1 ml) and large (>100s ml) volumes of fluids in the same closed system. The disclosed bioreactor containers have a compact form factor for use in parallel operations, and can be easily handled by automation systems. 15MF-361080369Attorney Docket No.328202000440

[0088] Although the following description is focused on the bioreactor container as used for growing cells and tissue culture applications, the same design can be generalized for use in processing different types of particles, from beads to small molecules to viruses, either in biological, chemical, pharmaceutical or other applications.

[0089] Various modifications to the described embodiments will be readily apparent to those persons skilled in the art, and the generic principles described herein may be applied to other embodiments. Thus, the present invention is not intended to be limited to the embodiment(s) shown but is to be accorded the widest scope consistent with the principles and features described herein. Definitions

[0090] Unless otherwise defined, all of the technical terms used herein have the same meaning as commonly understood by one of ordinary skill in the art in the field to which this disclosure belongs.

[0091] As used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural references unless the context clearly indicates otherwise. Any reference to “or” herein is intended to encompass “and / or” unless otherwise stated, and encompasses any and all possible combinations of one or more of the associated listed items.

[0092] As used herein, the terms “includes, “including,” “comprises,” and / or “comprising” specify the presence of stated features, integers, steps, operations, elements, components, and / or units but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, units, and / or groups thereof.

[0093] Throughout this application, various parameter values may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity, and should not be construed as an inflexible limitation on the scope of the disclosure. Accordingly, the description of a range should be considered to have specifically disclosed all possible subranges as well as individual numerical values within that range, irrespective of whether a specific numerical value or specific sub-range is expressly stated. For example, description of a range such as from 1 to 16MF-361080369Attorney Docket No.328202000440 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6, etc., as well as individual numbers within that range, for example, 1, 1.4, 2, 3, 3.6, 4, 5, 5.8, and 6. This applies regardless of the breadth of the range.

[0094] Numbers may be expressed herein as being “about” a particular value. Similarly, ranges may be expressed herein as from “about” one particular value and / or to “about” another particular value. The terms “about” and “approximately” shall generally mean an acceptable degree of error or variation for a given value or range of values, such as, for example, a degree of error or variation that is within 20 percent (%), within 15%, within 10%, or within 5% of a given value or range of values.

[0095] The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. The description is presented to enable one of ordinary skill in the art to make and use the invention, and is provided in the context of a patent application and its requirements. Multi-compartment and / or spiroidal bioreactor containers and systems

[0096] FIG. 1 shows the overview of the a bioreactor assembly 10 housed in the frame 20.

[0097] FIG. 2 shows a cross section of the bioreactor container, on which we would focus first. The bioreactor container 100 is composed of plastic parts assembled together via common means, such as ultrasonic welding, molding or bonding, as well as membrane and filters suitable for the application. The bioreactor container has slanted walls 110 and 115 connected by a bottom floor 120. Either of these surfaces can be composed of rigid plastics, materials with biocompatible coatings and / or fiber mesh 112 to allow the cells to exchange gasses and heat with the external air and to adhere to the membrane in case of adherent cells. The advantage of having slanted surfaces is that as the fluid amount increases, also the fluid-air surface increases. The angle of the slanted walls 110 and 115 relative to vertical can be chosen according to the need of the process and materials used, and could be varied also as function of the height of fluid. The slanted walls 110 and 115 can 17MF-361080369Attorney Docket No.328202000440 thus be curved or have different sections vertically, for example to allow a more gentle increase of fluid-air surface area, with close to vertical surfaces, or a more drastic increase of air-exchange with shallow walls, as shown in FIG. 15. This enables the bioreactor to allocate larger amounts of fluids, for example needed in allogeneic processes, starting from small amounts of fluid within the same container.

[0098] FIG. 11A – FIG.11C shows an embodiment of the spiroidal bioreactor container 100 where the generally v-shaped cross sections are not at the same elevation (FIG. 11A: top view. FIG. 11B: isometric view. FIG.11C: side view.). This can be relative to gravity and / or relative to a plane normal to the rotation axis. A fluid return section 101 reconciles the two ends of the helical spiral making the container continuous. This allows the container to gradually fill up, making it usable with very low volumes. In general the elevation can be designed as needed for specific applications and usage to match a desired volume to surface ratio as the volume changes during the process. The return also allows to accelerate the fluid and the media or other particles, allowing the selection, resuspension, oxygen and temperature exchanges needed for the specific process.

[0099] Similarly FIG. 12 shows a top view of an embodiment of the container 100 where the cross sections are not all at the same distance from the rotation axis, creating a differential in the centrifugal force according to the radius. The furthest out point can be used as a location for the outlet port, for harvesting or waste removal, respectively 75 and 65 described later. The fluid return section 101 connects the two ends. It is worth noting that both elevation and radius can be varied, combining embodiment in FIG.11 and FIG.12.

[0100] FIG. 13 shows an embodiment of the container 100 where two spiroidal paths, with either different vertical elevations, different radii, or both, as described before, are joined in a symmetrical container, which avoids the need for a return section.

[0101] FIG. 14 shows an embodiment of the container 100 where the spiroidal does not have a return, and the fluid is recirculated back and forth. 18MF-361080369Attorney Docket No.328202000440

[0102] The top area of the central cavity 118 is closed with a ceiling top surface 125. The top surface can be equipped with a filter 126 that allows exchange of gasses, such as oxygen, with the external atmosphere.

[0103] The container 100 is also equipped with a surface 200 which has provisions, such as teeth, protrusions or friction surfaces to be rotated along the axis 210 of the surface 200. This can be coincident with the axis of the spiroidal container. The rotation is made possible by the nest 400, shown in FIG.3, which has actuation means 410 with surfaces 415 matching to surface 200 that can rotate the container 100 along the axis 210.

[0104] While the inner surface of the container may not have the same elevation or distance from the rotation axis, it is worth noticing that the outer container surfaces 200 is at a constant distance and election from the rotation axis.

[0105] The rotation is monitored by optical sensors, such as encoders, 460 and 461 that can track and measure the rotation of the container 100 along the axis 210. These can be optical encoders tracking tacks or marks formed or imprinted on a corresponding area of the outset surface of the container 100, which, similarly to surface 200, is designed to be concentric to the rotation axis and at a constant elevation during the rotation.

[0106] Other sensors such as magnetic, induction, optical flow or other standard measuring systems can be used. The use of two sensing areas allows redundancy as well as the measurement of the specific angle of rotation of the container 100 relative to the nest in order to identify the location of specific areas on the container body as it rotates along axis 210. Actuation means 410 can also be equipped with rotation sensors, such as incremental encoders, for controlling the rotation speed.

[0107] By controlling the speed of rotation, the cells can be exposed to a force in addition to gravity which pulls them more toward the slanted walls 110. Sinusoidal rotations can be used to gently resuspend the cells. Different speeds of rotations can be used to distribute the mixture in the fluid according to their mass properties, for example when using beads or viral vectors. This allows the 19MF-361080369Attorney Docket No.328202000440 bioreactor to also perform other functions in addition to expansion, such as activation, transfection, enrichment and others.

[0108] The bioreactor is equipped with a surface 140 which creates small cavities 160, also called micro-cavities, in which the fluid with cells can be pushed by rotating the bioreactor over a certain minimum speed, called Minimum Sampling Speed (MSS). By controlling the time and speed pattern needed to reach the MSS, the user can control the fluid mixture and composition entering the small cavity 160, selected based on the mass properties of the particles. With a quick acceleration after resuspension for example, viscosity effects would limit motion of the particles in the fluid based on their mass, while with a slower acceleration over time, the fluid entering the small cavity 160 would mostly have the heavier, and / or lower viscosity, particles. The width, shape elevation and distance from the rotation axis of the small cavity 160 cross-section can be adjusted based on the properties of the fluid and particles of interest and can vary between different sections of the circumference, creating a selection by size and fluid properties for each section, in order to perform different functions.

[0109] For example, FIG. 5 shows an embodiment where the nest 400 is equipped with a magnetic system 440 that can perform magnetic functions to specific sections of the small cavities 160 as the bioreactor container 100 is rotated. These magnetic functions can be activation, beads handling and separation, magnetic transduction to mention a few.

[0110] Sections of the surface 140 are made of a transparent or translucent material so that an image capturing system 300, shown in FIG.3, positioned externally to the small cavity 160 can capture high-resolution images of the fluid entering the small cavity 160. The image capturing system 300 can be a high speed camera, microscope, or other imaging systems. The inner surface 161 opposite to the image capturing system can be coated with a reflective membrane or other filters to enable specific measurements and light capturing technologies in the system 300. In this way, several behaviors and key parameters of the particles in the fluid can be captured and observed without removing a sample and while keeping the system closed, thus preserving the cell culture from 20MF-361080369Attorney Docket No.328202000440 potential contamination risks and allowing in-line frequent measurements that can be digitally stored as time series of data.

[0111] The cavity 160 is connected to the central cavity 118 via channels 165 that ensure the same air pressure is maintained between cavity 160 and 118. Air filter 126 is connected to the cavity 118 and allows air exchange between the central cavity 118 and the incubator where the spiroidal bioreactor is housed.

[0112] The container can be equipped with an optical surface 170 that allows sensors 470 housed in the nest (FIG.5) to perform optical measurements on the cell growth such as standard optical sensors for pH, DO and other parameters that can be captured optically with an external detector placed radially, similarly to the imaging system 300.

[0113] FIG. 4 shows a section of the bioreactor assembly 10 including the frame 20, with fluid 30 inside the bioreactor container 100. At the beginning of the cycle, the fluid is inserted in the container either manually, by removing the top surface 125 or in a closed manner via a central pivoting connector 40 which can rotate relative to the bioreactor container 100, mounted along the axis 210. The fluid inserted through the connector 40 reaches to the inside of the bioreactor container via one or multiple input channels 45.

[0114] On the input side, the input channel 21 part of the frame 20 allows the fluid to reach connector 40 from the external connector 22. Connector 22 is an aseptic-connection connector, such as a needle or needle-free connector, which mates with the corresponding receptacle in the nest 400 which will be described later in FIG. 7. Through connector 22, fluid is delivered automatically such as the initial cell seeding, or other in-process fluids, such as media, reagents, and other fluids for either spot delivery or continuous perfusion.

[0115] Connector 40 is equipped with standard components such as rotating gaskets 47 and bearing surfaces 46 to allow it to perform its fluid connecting function between two rotating bodies without leaks, similar to a standard pivoting connector. 21MF-361080369Attorney Docket No.328202000440

[0116] Fluid can also be removed though connectors 60 and 70 which are connected to the bottom of the container respectively with one more channels 65 and 75. These can be equipped with a filter 114 to maintain cells out, for example when used for the waste channel of perfusion, or used without a filter for harvesting or extra sampling. In this embodiment, connector 70 can be used for perfusion waste removal, and the filter 114 is placed on the inside of the bottom portion of the container 100. In this way, gentle rotations can be used to clear the filter from cells during perfusion and prevent clogging.

[0117] Similarly to connector 40, connectors 60 and 70 are pivoting fluid connectors, with standard means to allow them to perform their functions. These include rotating gaskets 67 and 77, and bearing surfaces. Here a larger bearing system 66 supports both the pivoting connectors as well as takes radial and axial loads that are generated during the rotation of the container 100 relative to the frame 20.

[0118] On the output side, the channels 61 and 71 part of the frame 20 allow the fluid coming respectively from connector 60 and 70 to reach the external connectors 62 and 72. These connectors, similar to connector 22, are aseptic-connection connectors which mate with the corresponding receptacles in the nest 400, part of a disposable set.

[0119] FIG. 5 shows the handling plate 23 of the frame 20 which is used for moving the bioreactor in and out of the nest. This is designed for automated robotics handling or manual handling. A tag 26 such as a barcode or QR code allows traceability by providing a unique ID as well as features for robotics image and pose recognition. Locking features 24 and centering features 25 allow a robotic gripper to precisely pick and place the bioreactor.

[0120] FIG. 6A – FIG. 6D show an embodiment of a bioreactor container 100 with specialized sections of the small cavity 160 for the selection of small quantities of fluids, like the ones otherwise handled by pipetting. This enables the handling of small volumes of fluids (i.e. < 1ml), as well as larger volumes of fluids in the same closed system without the need to operate in an open-container fashion. 22MF-361080369Attorney Docket No.328202000440

[0121] In this case the micro-cavity 160 cross-section and length are sized appropriately to contain a set volume of fluid. Excess fluid would flow back in the container through the channel 165 described before. A baffle or screen 163 could facilitate channeling the fluid into the micro-cavity 160 and prevent fluid from entering 165 inadvertently. A valve system 180 allows the selective opening of micro-cavity 160 and the opening / closing of the output channel 162 which would deliver the selected amount of fluid outside of the container through channels and rotating connections. This can be similar to what described before or can be formed by the channels 167 and 29, respectively on the container body and the frame, that overlap at a specific angular rotation of the container body relative to the frame, as shown in FIG. 6A. By controlling the air pressure in the container’s central cavity 118 via the input port 22 relative to the air pressure in the output channel 162, even small amounts of fluids can be moved through the channels, which would be coated with the state of the art coating and treatments to allow the fluid to easily advance the channel.

[0122] While this embodiment shows three output channels, either more outputs can be used in the same container, or a single central one can be used, thus simplifying the base of the container, for example in the case of a container used solely to dispense reagents in small volumes rather than for cell growth. In this case the spiroidal bioreactor would be paired with reagents housed in the same shape containers, and connected through the consumables set.

[0123] When in need to deliver different amounts of fluids, multiple micro-cavities 160 could be designed to have different set volumes and could be activated as needed by operating the respective valve systems 180.

[0124] FIG. 16 shows an embodiment of the bioreactor container 100 where the channels 166, in a similar fashion to micro-cavity 160, are used for fluid recirculation. These can be placed at different heights along the bioreactor container, for example according to the floor elevation relative to gravity or according to the median radius of the cross section relative to the rotation axis, or both, and can have different lengths and opening cross-sectional areas. 23MF-361080369Attorney Docket No.328202000440

[0125] FIG. 6B – FIG.6D show an embodiment of the valve system 180 where a moving body 181, in this case a spherical or cylindrical body, selectively closes the fluid input channel 164 (FIG.6B) or the output channel 162 (FIG.6C) by sitting respectively in the sealing area 185 or 186. The moving body 181 has a preferred resting position in the sealing area 185. This equilibrium position is held by a force that can be created by a spring, an elastic element or by connecting the moving body 181 to the body of the container with a live hinge or preloaded plastic piece. In this embodiment, the moving body 181 is composed of a ferromagnetic core material that is attracted by a magnet 182 in its resting position against the sealing area 185, closing the channel 164. When there is the need to extract and dispense the small volume of fluid, the container is spun as described before. The rotation of the container body causes the fluid to push against the moving body 181 under centrifugal force, creating a pressure p that acts against the sealing force of channel 164. The moving body 181 itself is also subject to the centrifugal force, until channel 164 is opened and the fluid can fill the micro-cavity 160. Conversely, the moving body 181 moving radially outward also closes the output channel 162. This is a second equilibrium position of the moving body 181 against the output sealing area 186, subject to the centrifugal force and pressure p. Gravity is omitted for simplicity. Once the centrifugal force is reduced or stopped, the moving body 181 would return to the first resting position closing again the input channel 164 and opening the output channel 162 thus dispensing the fluid that occupied the cavity 160 to the output channel.

[0126] FIG. 6D shows an example of the forces on the moving body 181 in this embodiment. In this case F1 is the force keeping the ball or moving body 181 against the sealing area 185 thanks to the attraction to magnet 182. The fluid pressure is indicated as p, while the centrifugal force is indicated as F2. In this embodiment an additional force F3 is used to make the ball snap quickly between the two equilibrium positions, thus creating a true bi-stable mechanism that works in conjunction with the spinning of the container body. The force F3 is a magnetic force generated by an electromagnet situated in the nest, similar to 440 shown before. In order to quickly open channel 164, the force F3 snaps the ball out of the first resting position, i.e. against the sealing area 185, into the second resting position, i.e. against sealing area 186. Here the pressure and the centrifugal force overcome the force F1, which is inversely proportional to the distance between the ball or moving body 181 24MF-361080369Attorney Docket No.328202000440 and the magnet 182. In this position force F3 is not needed anymore but can be kept for additional design margin. Since the container body is rotating, and the electromagnet is localized in the nest, the force F3 may be seen as pulsating by the ball 181, depending on the extension of the electromagnet along the circumference of the bioreactor. The force F3 would thus be the RMS value of the force seen along the rotation and the peak magnetic force exerted by the electromagnet can be designed accordingly. As soon as the rotational speed is reduced, and F3 turned off, the ball is magnetically attracted back by magnet 182 in the initial position. This can happen by design at a speed higher than MSS, i.e. a rotational speed that still maintains the fluid in the micro-cavity 160.

[0127] While in this embodiment the moving body 181 acts as a valve to open and close both the input channel 164 and output channel 162, it is possible to have a moving body for each channel, for example with a flap of materials or spring-loaded body for each channel that are subject to similar forces thus obtaining the same results.

[0128] FIG. 7 shows the main components of nest 400, which have been previously described. The bioreactor container is secured to the nest through features 24 in the frame 20 that mate with locking features 420 to secure the bioreactor in place. Actuation means 410, such as servo motors, rotate the bioreactor container 100 via surfaces 415, which can be friction surfaces, gears or systems to transmit motion. Encoders 460 and 461 measure the rotation of the bioreactor container. The imaging system 300 is used to observe the fluid and its particles, and optical sensors in 470 capture many of the key parameters such as pH, DO and others. The system 440 is a magnetic actuator that can be used for specialized purposes, such as transduction of the cells in the microcavities 160, magnetic beads processing and removal, and other applications. A system similar to 440, such as an electromagnet, can also be included for operating the valve system 180 to dispense small amounts of fluids. The disposable cartridge 430 houses the mating aseptic connectors that engage with the corresponding ports on the bioreactor frame. These can be needle-free ports with push-pull or lock- tab connectors, rotating luer lock, needle and membrane connectors or other fluid connectors used for these applications. Multiple of these nests can be located in a bioreactor that controls the environmental parameters, such as temperature, humidity, CO2, pressure. The disposable cartridge 430 is connected to a set of reagents through tubings operated by pinch valves in order to dispense 25MF-361080369Attorney Docket No.328202000440 the desired amounts of fluids per the prescribed protocol, such as perfusion feed for example. These reagents can also be contained in simplified spiroidal containers 100 for the delivery of small amounts of fluids, for example in the case of cytokines or CRISPR reagents, as described before.

[0129] FIG. 8A – FIG. 8D show an embodiment of the bioreactor container 100 with multiple compartments for the selective growth or fluid handling under different conditions. Each of the compartments can make use of the features described above, replicated for each of the compartments.

[0130] FIG. 8A shows the container with the top surface 130 segmented into multiple surfaces, separated by rigid walls 132. The individual top surfaces 131 can be air filters, membrane, transparent covers or other materials with specialized functions.

[0131] In FIG.8B the top surface and top components are removed to show an embodiment of the container with the compartments. Here the slanted surfaces are sectioned by radial surfaces 117 which mate with the top walls 132 creating a sealed separation for each individual compartment. The slanted surfaces are thus split into smaller sections 111 and 116, and the bottom surface into sections 121 (shown in FIG.9B). Each section can be equipped with the features described before, such as the channels 165 for aliquoting, collecting sensory data or imaging and performing specific functions.

[0132] FIG. 8C and FIG. 8D show how the fluid can be delivered to each compartment. The same description holds for the output fluid, either waste, sampling and / or harvesting. Differences in air pressure between the input, the container and the output can be used to facilitate the flow of the fluid to be delivered. In this embodiment, the input channel 21 is connected to a plunger 53 which in turns mate with each individual channel 48 for each of the compartments. The channels 48 are distributed along a circumference, so that as the container 100 is rotated, different channels 48 are brought in connection with 53. The mating between 53 and the selected channel 48 can be passive, and the connection maintained by compression of a sealing element 51, or it can aided by a spring or actuation that compressed the plunger 53 head to mate with a corresponding surface on the top area 26MF-361080369Attorney Docket No.328202000440 of channel 48. A solenoid, linear actuator or similar means, housed in the nest can be used for that purpose, and a bellow or gasket 52 can allow motion while maintaining the system closed. A bearing 46 is used to maintain alignment between these features rotating relative to each other, and a seal 47 maintain the connection sealed. In order to provide the necessary compression of the seal 51, as well as to allow ease of assembly and manufacture, a separate head piece 50 can be used to complete the assembly with the frame 20. In this embodiment, the head piece 50 is provided with means to counter the torsional torque caused by friction, such as a double D profile, fins or spline, that mate with the frame 20, as well as features for securing and preloading the bearing arrangement 46 and rotating seal 47. The compression force for the gasket 51, as well as the axial force to maintain the assembly together, can be provided by features between the head piece 50 and the frame 20 such as snap features, as shown here, or screws and bosses, threaded surfaces, bonding or other standard means of retention.

[0133] A similar description applies for the output of fluids, with the same apparatus mirrored on the bottom of the container. Similarly, multiple circumferences of channels 48 and multiple plungers 53 can be used to allow multiple input and output channels.

[0134] FIG. 9A shows an embodiment of the container 100 where the slanted surfaces are equipped with features specifically designed for organoid growth. In this embodiment, these features are small cavities or indentations, such as of pyramidal, or hemispherical shape, where cells can cluster and form organoids.

[0135] These features often are in small sizes (below 100s of micrometers) and require specific manufacturing methods, such as precision injection molding, stereolithography or others. They may also require specific coatings. For these reasons, insert 610 is designed as a separate piece which get inserted into place in the container 100 using standard method such as bonding, pressing, fastening, locking features or others. A number of inserts 610 can be used in an array for each compartment, and have different features, size and shape for performing different functions. By being on the side of the container, centrifugal force can be used to push the cells, beads or materials inside the cavities, and be held there by maintaining the rotation, and thus the centrifugal force, for the time 27MF-361080369Attorney Docket No.328202000440 required for performing the task. After that, changes in rotational speed can induce different behaviors, such as adding layers of other materials, or if the rotation is reduced or stopped gradually, the assembled granules can be released in the container and the media added in order to expand the cell growth or maintain the granules or organoids in suspension.

[0136] Inserts 610 can be made of optically transparent materials, and imaging capturing systems such as 300 can be placed radially in the nest in order to capture images of the cavities and corresponding granules or organoids in them.

[0137] FIG. 9B shows an embodiment where similar inserts 650 are inserted at the bottom of the container rather than the sides. These cavities can have similar characteristics and allow the selection or growth of specific materials or cells, such as adherent cells. Gel or other coatings can be used on inserts 650 or 610 in order to facilitate the growth of cells or the performing of specific functions. Similarly to insert 610, insert 650 can be made of optically transparent materials or other filtering materials for imaging purposes, by placing imaging systems under the container 100 in the nest 400.

[0138] FIG. 10 shows an example of the imaging system, where multiple imaging sensors 310 and 320 can be placed in different orientations to capture the details of the inserts cavities and how the content grow or changes over time. This would enable real time monitoring without disturbing the culture.

[0139] In some aspects, provided is a bioreactor comprising: a container comprising a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses an axis of rotation of the bioreactor, wherein not all cross-sectional profiles of the series are the same and / or not all cross-sectional profiles’ lowest point is at the same elevation and / or wherein the path is not equidistant from the axis of rotation at all points along the path; and at least one fluid port configured to provide fluid communication with the internal volume of the container.

[0140] In some embodiments, at least one fluid port is configured to provide fluid communication between a stationary external fluid source and the internal volume of the container as the bioreactor 28MF-361080369Attorney Docket No.328202000440 rotates about its axis. In other embodiments, at least one fluid port is configured to provide fluid communication between the interior volume of the container and a stationary exterior fluid reservoir as the bioreactor rotates about its axis.

[0141] In some embodiments, the cross-sectional profiles of the series comprise a cross-section of a top plate, a first side-wall, and a second side-wall. In some variations, the bioreactor further comprises a bottom plate. In other variations, the bioreactor further comprises at least one micro cavity feature integrated with the first side-wall and configured to sample an aliquot of fluid contained within the container. In certain variations, at least one micro cavity feature is integrated with a top edge of the first side-wall. In other variations, at least one micro cavity feature is configured to sample an aliquot of fluid contained within the container when an actuation force is applied to the at least one micro cavity feature. In yet other variations, at least one micro cavity feature is configured to deliver the fluid aliquot to a stationary external fluid sample container.

[0142] In one variation, at least one micro cavity features comprises: a sample fluid inlet configured to provide fluid communication between an interior volume of the micro cavity feature and a fluid contained within the container; a valve mechanism integrated with the sample fluid inlet and configured to open when an actuation force is applied; the interior volume of the micro cavity feature; a return fluid outlet configured to vent air and / or excess fluid from the interior volume of the micro cavity feature; and a sample fluid outlet configured to provide fluid communication between the interior volume of the micro cavity feature and a stationary external fluid sample container.

[0143] In some variations, the valve mechanism of the at least one micro cavity feature comprises a moveable component configured to toggle the valve between: (i) an open sample fluid inlet / closed sample fluid outlet configuration, and (ii) a closed sample fluid inlet / open sample fluid outlet configuration, upon application of the actuation force. 29MF-361080369Attorney Docket No.328202000440

[0144] In some variations, the actuation force comprises a centrifugal force applied when an angular velocity for rotation of the container about its axis exceeds a specified minimum angular velocity threshold. In certain variations, the actuation force comprises a magnetic force.

[0145] In some variations, the moveable component comprises a rolling element that rolls between a first indent and a second indent, wherein the first indent and second indent correspond to the open sample fluid inlet / closed sample fluid outlet configuration and the closed sample fluid inlet / open sample fluid outlet configuration, respectively.

[0146] In other embodiments of the bioreactor, the intersection of the first side-wall with a first imaginary plane parallel to a plane of the top plate defines a first diameter of the container. In some variations, the intersection of the second side-wall with a second imaginary plane parallel to the plane of the top plate defines a second diameter of the container; and wherein the second diameter is smaller than the first diameter. In certain variations, the first diameter ranges from about 2 cm to about 35 cm. In certain variations, the second diameter ranges from about 1 cm to about 30 cm.

[0147] In other embodiments, the first side-wall and the second side-wall are slanted so as to converge at a third imaginary surface that defines an angle between the first side-wall and the second side-wall. In some variations, at least one of the first side-wall or the second side-wall is curved rather than planar.

[0148] In some embodiments, the bioreactor further comprises a bottom plate that intersects with the first side-wall and the second side-wall and is parallel to the top plate. In some variations, at least a portion of the top plate, the first side-wall, and / or the second side-wall is composed of a gas permeable membrane. In some variations, the first side-wall is an exterior side-wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable high speed imaging of particles suspended in a fluid contained within the container as the container rotates about its axis. In some variations, the first side-wall is an exterior side-wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable high speed imaging of particles attached to an interior surface of the first side-wall as the container rotates about its axis. In 30MF-361080369Attorney Docket No.328202000440 other variations, the first side-wall is an exterior side-wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable optical sensing of at least one of pH, dissolved oxygen (DO), O2, N2, CO2, metabolomic profile, glutamate, glutamine, lactate, glucose, volume, flow rate, pressure, and temperature in a fluid contained within the container as the container rotates about its axis. In one variation, the particles comprise cells, virus particles, beads, or any combination thereof.

[0149] In certain embodiments, the angle between the first side-wall and the second side-wall ranges from about 5 degree to about 160 degrees. In one embodiment, the angle between the first side-wall and the second side-wall ranges from about 30 degrees to about 120 degrees. In another embodiment, the angle between the first side-wall and the second side-wall is designed to optimize gas exchange between a fluid contained within the container and an overlaying gas contained within the container. In yet another embodiment, the angle between the first side-wall and the second side- wall is designed to maximize a surface area-to-fluid volume ratio for the container. In another embodiment, at least one of the first side-wall or the second side-wall that is curved has a shape configured to provide different interfacial surface area-to-fluid volume ratios for a gas-fluid interface within the container for different volumes of fluid contained within the container.

[0150] In some variations, at least one fluid port provides fluid communication between a stationary external fluid source and the interior volume of the container through a rotating fluid connector. In other variations, at least one fluid port provides fluid communication between the interior volume of the container and a stationary exterior fluid reservoir through a rotating fluid connector. In another variation, the at least one fluid port comprises a filtration membrane and is configured for periodic or continuous removal of a fluid contained within the container.

[0151] In some variations, the path that encompasses the axis of rotation of the bioreactor is confined to a plane that is perpendicular to the axis of rotation. In certain variations, the path that encompasses the axis of rotation of the bioreactor is not confined to a plane that is perpendicular to the axis of rotation. In certain variations, the path is offset in a first perpendicular direction with respect to the plane at some points along the path. In another variation, the path is offset in a second 31MF-361080369Attorney Docket No.328202000440 perpendicular direction with respect to the plane at some points along the path. In another variation, the path is a closed path. In yet other variations, a portion of the path is an open path. In certain variations, the path further comprises a return section to close the open portion of the path. In one variation, at least a portion of the path comprises a spiral path. In another variation, the path has a different radial distance from the axis of rotation of the bioreactor at different points along the path. In another variation, the path has a different radial distance from a central axis of symmetry at different points along the path, and wherein the central axis of symmetry is different from the axis of rotation of the bioreactor.

[0152] In some embodiments, some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series. In certain embodiments, some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series. In some variations, a height (or depth) of the internal volume of the container at each point along the path is defined by a distance between the top fluid level and an inner surface of a bottom plate (e.g., the inner surface of the bottom of the container). In certain variations, the height varies along at least a portion of the path. In other variations, the height increases as a function of position along at least a portion of the path. In other variations, the height decreases as a function of position along at least a portion of the path.

[0153] In some variations, a length of the portion of the path for which the height increases is the same as a length of the portion of the path for which the height decreases. In certain variations, a length of the portion of the path for which the height increases is different from a length of the portion of the path for which the height decreases.

[0154] In certain embodiments, an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. In other embodiments, an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. 32MF-361080369Attorney Docket No.328202000440

[0155] In some embodiments, the bioreactor further comprises at least one fluid channel configured to recirculation of a fluid contained within the internal volume of the container.

[0156] In another aspect, provided is a system comprising at least one container comprising: a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses an axis of rotation of the container, wherein not all cross-sectional profiles of the series are the same and / or wherein the path is not equidistant from the axis of rotation at all points along the path; and at least one fluid inlet port configured to provide fluid communication with the internal volume of the container; and at least one drive mechanism comprising: a frame for mounting the container, wherein the frame is configured to allow the container to spin around its rotational axis; and at least one drive motor; wherein the drive mechanism is configured to control an angular velocity of the container as a function of time.

[0157] In some embodiments, the cross-sectional profiles of the series comprise a cross-section of a top plate, a first side-wall, and a second side-wall. In some variations, at least one container comprises at least one micro cavity feature integrated with the first side-wall and configured to sample an aliquot of fluid contained within the container. In certain variations, at least one micro cavity feature is integrated with a top edge of the first side-wall. In certain variations, at least one micro cavity feature is configured to sample an aliquot of fluid contained within the container when an actuation force is applied to the at least one micro cavity feature. In other variations, at least one micro cavity feature is configured to deliver the fluid aliquot to a stationary external fluid sample container.

[0158] In one variation, at least one micro cavity feature comprises: a sample fluid inlet configured to provide fluid communication between an interior volume of the micro cavity feature and a fluid contained within the container; a valve mechanism integrated with the sample fluid inlet and configured to open when an actuation force is applied; the interior volume of the micro cavity feature; a return fluid outlet configured to vent air and / or excess fluid from the interior volume of the micro cavity feature; and a sample fluid outlet configured to provide fluid communication 33MF-361080369Attorney Docket No.328202000440 between the interior volume of the micro cavity feature and a stationary external fluid sample container.

[0159] In some variations, the valve mechanism of the at least one micro cavity feature comprises a moveable component configured to toggle the valve between: (i) an open sample fluid inlet / closed sample fluid outlet configuration, and (ii) a closed sample fluid inlet / open sample fluid outlet configuration, upon application of the actuation force.

[0160] In other variations, the actuation force comprises a centrifugal force applied when an angular velocity for rotation of the container about its axis exceeds a specified minimum angular velocity threshold. In certain variations, the actuation force comprises a magnetic force.

[0161] In some embodiments, the moveable component comprises a rolling element that rolls between a first indent and a second indent, wherein the first indent and second indent correspond to the open sample fluid inlet / closed sample fluid outlet configuration and the closed sample fluid inlet / open sample fluid outlet configuration, respectively.

[0162] In some embodiments, the frame comprises a self-centering engagement mechanism for attachment to a robotic actuator.

[0163] In another embodiment, at least one drive motor of the drive mechanism comprises a servo motor. In some variations, at least one drive mechanism further comprises a self-centering engagement mechanism for attachment to a robotic actuator. In other variations, at least one drive mechanism further comprises a self-centering engagement mechanism for attachment to a rack configured to hold a plurality of drive mechanisms. In certain variations, at least one drive mechanism further comprises at least one optical encoder for monitoring the angular velocity of the container as a function of time. In certain variations, at least one drive mechanism is configured to vary the angular velocity of the container as a function of time in a programmable fashion. 34MF-361080369Attorney Docket No.328202000440

[0164] In some embodiments, a variation in the angular velocity of the container as a function of time is used to control a composition of a fluid mixture that enters the at least one micro cavity feature.

[0165] In some variations, at least one drive mechanism, or a housing thereof, further comprises at least one optical imaging camera configured to perform high speed imaging of particles suspended in the fluid contained within the container. In other variations, at least one drive mechanism, or a housing thereof, further comprises at least one optical imaging camera configured to perform high speed imaging of particles attached to an interior surface of the first side-wall of the container. In other variations, at least one drive mechanism, or a housing thereof, further comprises at least one optical sensor configured to perform optical sensing of at least one of pH, dissolved oxygen (DO), and temperature in a fluid contained within the container.

[0166] In some embodiments, the system further comprises a gas controller configured to provide control of the flow rate for at least one gas flowing into the container. In some embodiments, the system further comprises a housing configured to provide temperature control for the container.

[0167] In some variations, a geometry of the at least one micro cavity feature is configured to modify a shape of a cell that enters therein. In some variations, a geometry of the at least one micro cavity feature is configured to lyse a cell that enters therein.

[0168] In some embodiments, the system further comprises an electromagnetic device configured to modify a cell that enters the at least one micro cavity feature. In other embodiments, the system further comprises an electronic device configured to electroporate a cell that enters the at least one micro cavity feature.

[0169] In some variations, the path that encompasses the axis of rotation of the container is confined to a plane that is perpendicular to the axis of rotation. In some variations, the path that encompasses the axis of rotation of the container is not confined to a plane that is perpendicular to the axis of rotation. In some variations, the path is offset in a first perpendicular direction with respect to the plane at some points along the path. In certain variations, the path is offset in a second 35MF-361080369Attorney Docket No.328202000440 perpendicular direction with respect to the plane at some points along the path. In one variation, the path is a closed path. In another variation, a portion of the path is an open path. In yet another variation, the path further comprises a return section to close the open portion of the path. In another variation, at least a portion of the path comprises a spiral path. In certain variations, the path has a different radial distance from the axis of rotation of the container at different points along the path. In certain variations, the path has a different radial distance from a central axis of symmetry at different points along the path, and wherein the central axis of symmetry is different from the axis of rotation of the container.

[0170] In some embodiments, some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series. In certain embodiments, some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series.

[0171] In some embodiments, a height of the internal volume of the at least one container at each point along the path is defined by a distance between an inner surface of the top plate and an inner surface of a bottom plate . In one variation, the height varies along at least a portion of the path. In another variation, the height increases as a function of position along at least a portion of the path. In yet another variation, the height decreases as a function of position along at least a portion of the path. In other variations, a length of the portion of the path for which the height increases is the same as a length of the portion of the path for which the height decreases. In other variations, a length of the portion of the path for which the height increases is different from a length of the portion of the path for which the height decreases.

[0172] In some embodiments, an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. In other embodiments, an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

[0173] In some embodiments, the system further comprises: at least one fluid channel configured to recirculation of a fluid contained within the internal volume of the container. In some variations, at 36MF-361080369Attorney Docket No.328202000440 least one fluid port is configured to provide fluid communication between a stationary external fluid source and the internal volume of the container as the container rotates about its axis. In other variations, at least one fluid port is configured to provide fluid communication between the interior volume of the container and a stationary exterior fluid reservoir as the container rotates about its axis.

[0174] In other aspects, provided is a method for culturing cells using any of the bioreactors and systems described herein. In some embodiments, the method comprises: introducing cells into a fluid contained within the bioreactor; aerating and / or agitating the fluid contained within the container by rotating the container about its axis at a specified angular velocity; and monitoring cell growth within the fluid by at least one of: performing high speed imaging of cells suspended in the fluid, performing high speed imaging of cells attached to an interior surface of the first side-wall of the container, or performing high speed imaging of cells contained in the at least on micro cavity feature; and sampling an aliquot of the fluid using the at least one micro cavity feature by increasing an angular velocity for rotation of the container so that it exceeds a specified minimum angular velocity threshold, and delivering the aliquot of the fluid to a stationary external sample container for testing.

[0175] In some embodiments, the method further comprises using different angular velocity settings to perform different cell culture functions. In some variations, the different cell culture functions comprise mixing, resuspension, temperature control, cluster prevention, delivery of an aliquot of fluid to the at least one micro cavity for cell analysis and / or modification, or any combination thereof.

[0176] In certain embodiments, the method further comprises monitoring at least one of pH, dissolved oxygen (DO), and temperature within the fluid as a function of time.

[0177] In some variations, prior to the sampling step, an angular velocity for rotation of the container is adjusted to select a subset of cells for sampling by the at least one micro cavity feature. In other variations, prior to the sampling step, an external force is applied to select a subset of cells 37MF-361080369Attorney Docket No.328202000440 for sampling by the at least one micro cavity feature. In one variation, the cells are attached to magnetic beads and the external force is a magnetic force.

[0178] In some embodiments, the path that encompasses the axis of rotation of the container is confined to a plane that is perpendicular to the axis of rotation. In some variations, the path that encompasses the axis of rotation of the bioreactor is not confined to a plane that is perpendicular to the axis of rotation. In some variations, the path is offset in a first perpendicular direction with respect to the plane at some points along the path. In certain variations, the path is offset in a second perpendicular direction with respect to the plane at some points along the path. In one variation, the path is a closed path. In another variation, a portion of the path is an open path. In certain variations, the path further comprises a return section to close the open portion of the path. In another variation, at least a portion of the path comprises a spiral path. In yet another variation, the path has a different radial distance from the axis of rotation of the container at different points along the path. In other variations, the path has a different radial distance from a central axis of rotation at different points along the path, and wherein the central axis of rotation is different from the axis of rotation of the container.

[0179] In some embodiments, some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series. In other embodiments, some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series.

[0180] In some embodiments, a height of the internal volume of the container at each point along the path is defined by a distance between an inner surface of the top plate and an inner surface of a bottom plate. In some variations, the height varies along at least a portion of the path. In other variations, the height increases as a function of position along at least a portion of the path. In yet other variations, the height decreases as a function of position along at least a portion of the path.

[0181] In some variations, a length of the portion of the path for which the height increases is the same as a length of the portion of the path for which the height decreases. In certain variations, a 38MF-361080369Attorney Docket No.328202000440 length of the portion of the path for which the height increases is different from a length of the portion of the path for which the height decreases.

[0182] In some embodiments, an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. In other embodiments, an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

[0183] In some embodiments, the method further comprises recirculating a fluid contained within the internal volume of the container. In some variations, this is accomplished by at least one fluid channel.

[0184] In another aspect, provided is a bioreactor comprising: a container comprising a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses a central axis of the bioreactor, wherein not all cross-sectional profiles of the series are the same and / or wherein the path is not equidistant from the central axis at all points along the path; and at least one fluid port configured to provide fluid communication with the internal volume of the container.

[0185] In some variations, the bioreactor is configured to rotate about a rotation axis. In other variations, the rotation axis coincides with the central axis.

[0186] Bioreactor container design: The disclosed bioreactor containers may comprise a plurality of compartments (e.g., cell growth compartments, sample compartments and / or reagent storage compartments), micro-cavities and / or fluid channels.

[0187] In some instances, the overall dimensions of the bioreactor container may comprise an outer diameter ranging from about 100 mm to about 400 mm, an inner diameter ranging from about 30 mm to about 110 mm, and an overall height ranging from about 30 mm to about 100 mm.

[0188] In some instances, the outer diameter of the bioreactor container may be at least 100 mm, at least 120 mm, at least 140 mm, at least 160 mm, at least 180 mm, at least 200 mm, at least 220 mm, 39MF-361080369Attorney Docket No.328202000440 at least 240 mm, least 260 mm, at least 280 mm, at least 300 mm, at least 320 mm at least 340 mm, at least 360 mm, at least 380 mm, or at least 400 mm. In some instances, the outer diameter of the bioreactor container may be at most 400 mm, at most 380 mm, at most 360 mm, at most 340 mm, st most 320 mm, at most 300 mm, at most 280 mm, at most 260 mm, at most 240 mm, at most 220 mm, at most 200 mm, at most 180 mm, at most 160 mm, at most 140 mm, at most 120 mm, or at most 100 mm. Any of the lower and upper values described in this paragraph may be combined to form a range included within the present disclosure, for example, the outer diameter of the bioreactor container may range from about 220 mm to about 320 mm. Those of skill in the art will recognize that the outer diameter of the bioreactor container may have any value within this range, e.g., about 254 mm.

[0189] In some instances, the inner diameter of the bioreactor container may be at least 30 mm, at least 35 mm, at least 40 mm, at least 45 mm, at least 50 mm, at least 55 mm, at least 60 mm, at least 65 mm, at least 70 mm, at least 75 mm, at least 80 mm, at least 85 mm, at least 90 mm, at least 95 mm, at least 100 mm, at least 105 mm, or at least 110 mm. In some instances, the inner diameter of the bioreactor container may be at most 110 mm, at most 105 mm, at most 100 mm, at most 95 mm, at most 90 mm, at most 85 mm, at most 80 mm, at most 75 mm, at most 70 mm, at most 65 mm, at most 60 mm, at most 55 mm, at most 50 mm, at most 45 mm, at most 40 mm, at most 35 mm, or at most 30 mm. Any of the lower and upper values described in this paragraph may be combined to form a range included within the present disclosure, for example, the inner diameter of the bioreactor container may range from about 85 mm to about 105 mm. Those of skill in the art will recognize that the inner diameter of the bioreactor container may have any value within this range, e.g., about 96 mm.

[0190] In some instances, the overall height of the bioreactor container may be at least 30 mm, at least 35 mm, at least 40 mm, at least 45 mm, at least 50 mm, at least 55 mm, at least 60 mm, at least 65 mm, at least 70 mm, at least 75 mm, at least 80 mm, at least 85 mm, at least 90 mm, at least 95 mm, or at least 100 mm. In some instances, the overall height of the bioreactor container may be at most 100 mm, at most 95 mm, at most 90 mm, at most 85 mm, at most 80 mm, at most 75 mm, at most 70 mm, at most 65 mm, at most 60 mm, at most 55 mm, at most 50 mm, at most 45 mm, at 40MF-361080369Attorney Docket No.328202000440 most 40 mm, at most 35 mm, or at most 30 mm. Any of the lower and upper values described in this paragraph may be combined to form a range included within the present disclosure, for example, the overall height of the bioreactor container may range from about 45 mm to about 55 mm. Those of skill in the art will recognize that the overall height of the bioreactor container may have any value within this range, e.g., about 48 mm.

[0191] In some instances, the total internal fluid volume of the bioreactor container may range from about 1 ml to about 5,000 ml. In some instance, the total internal fluid volume of the bioreactor container may be at least 1 ml, at least 5 ml, at least 10 ml, at least 20 ml, at least 30 ml, at least 40 ml, at least 50 ml, at least 60 ml, at least 70 ml, at least 80 ml, at least 90 ml, at least 100 ml, at least 200 ml, at least 300 ml, at least 400 ml, at least 500 ml, at least 600 ml, at least 700 ml, at least 800 ml, at least 900 ml, at least 1,000 ml, at least 2,000 ml, at least 3,000 ml, at least 4,000 ml, or at least 5,000 ml. In some instances, the total internal fluid volume of the bioreactor container may be at most 5,000 ml, at most 4,000 ml, at most 3,000 ml, at most 2,000 ml, at most 1,000 ml, at most 900 ml, at most 800 ml, at most 700 ml, at most 600 ml, at most 500 ml, at most 400 ml, at most 300 ml, at most 200 ml, at most 100 ml, at most 90 ml, at most 80 ml, at most 70 ml, at most 60 ml, at most 50 ml, at most 40 ml, at most 30 ml, at most 20 ml, at most 10 ml, at most 5 ml, at most 1 ml. Any of the lower and upper values described in this paragraph may be combined to form a range included within the present disclosure, for example, the total internal fluid volume of the bioreactor container may range from about 10 ml to about 2,000 ml. Those of skill in the art will recognize that the total internal fluid volume of the bioreactor container may have any value within this range, e.g., about 3,560 ml.

[0192] In some instances, the fluid channels of the bioreactor container may have a substantially square, rectangular, and / or circular cross-section. In some instances, the dimensions of the fluid channels of the bioreactor container may comprise a width (or diameter) ranging from about 0.1 mm to about 10 mm in width, a height (or depth) ranging from about 0.1 mm to about 10 mm, and a length ranging from about 0.1 mm to about 100 mm. 41MF-361080369Attorney Docket No.328202000440

[0193] In some instances, the width (or diameter) of the fluid channels may be at least 0.1 mm, at least 0.2 mm, at least 0.4 mm, at least 0.6 mm, at least 0.8 mm, at least 1.0 mm, at least 2.0 mm, at least 4.0 mm, at least 6.0 mm, at least 8.0 mm, or at least 10 mm. In some instances, the width (or diameter) of the fluid channels may be at most 10 mm, at most 8 mm, at most 6 mm, at most 4 mm, at most 2 mm, at most 1 mm, at most 0.8 mm, at most 0.6 mm, at most 0.4 mm, at most 0.2 mm, or at most 0.1 mm. Any of the lower and upper values described in this paragraph may be combined to form a range included within the present disclosure, for example, the width (or diameter) of the fluid channels may range from about 0.6 mm to about 8 mm. Those of skill in the art will recognize that the width (or diameter) of the fluid channels of the bioreactor container may have any value within this range, e.g., about 5.5 mm.

[0194] In some instances, the height (or depth) of the fluid channels may be at least 0.1 mm, at least 0.2 mm, at least 0.4 mm, at least 0.6 mm, at least 0.8 mm, at least 1.0 mm, at least 2.0 mm, at least 4.0 mm, at least 6.0 mm, at least 8.0 mm, or at least 10 mm. In some instances, the height (or depth) of the fluid channels may be at most 10 mm, at most 8 mm, at most 6 mm, at most 4 mm, at most 2 mm, at most 1 mm, at most 0.8 mm, at most 0.6 mm, at most 0.4 mm, at most 0.2 mm, or at most 0.1 mm. Any of the lower and upper values described in this paragraph may be combined to form a range included within the present disclosure, for example, the height (or depth) of the fluid channels may range from about 0.6 mm to about 8 mm. Those of skill in the art will recognize that the height (or depth) of the fluid channels of the bioreactor container may have any value within this range, e.g., about 2.8 mm.

[0195] In some instances, the length of the fluid channels may be at least 0.1 mm, at least 0.5 mm, at least 1 mm, at least 5 mm, at least 10 mm, at least 20 mm, at least 30 mm, at least 40 mm, at least 50 mm, at least 60 mm, at least 70 mm, at least 80 mm, at least 90 mm, or at least 100 mm. In some instances, the length of the fluid channels may be at most 100 mm, at most 90 mm, at most 80 mm, at most 70 mm, at most 60 mm, at most 50 mm, at most 40 mm, at most 20 mm, at most 10 mm, at most 5 mm, at most 1 mm, at most 0.5 mm, or at most 0.1 mm. Any of the lower and upper values described in this paragraph may be combined to form a range included within the present disclosure, for example, the length of the fluid channels may range from about 1 mm to about 50 mm. Those of 42MF-361080369Attorney Docket No.328202000440 skill in the art will recognize that the length of the fluid channels of the bioreactor container may have any value within this range, e.g., about 32 mm.

[0196] In some instances, the bioreactor container may comprise from about 1 to about 36 compartments (e.g., sample compartments, cell growth compartments, and / or fluid storage compartments, etc.) In some instances, the bioreactor container may comprise at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, at least 14, at least 16, at least 18, at least 20, at least 22, at least 24, at least 26, at least 28, at least 30, at least 32, at least 34, at least 36 compartments.

[0197] In some instances, the volume of the compartments in the bioreactor container may all be the same. In some instances, the volume of the compartments in the bioreactor container may differ. In some instances, the volume of the compartments in the bioreactor container may range from about 0.1 ml to about 100 ml. In some instance, the volume of the compartments may be at least 0.1 ml, at least 0.5 ml, at least 1.0 ml, at least 5 ml, at least 10 ml, at least 20 ml, at least 30 ml, at least 40 ml, at least 50 ml, at least 60 ml, at least 70 ml, at least 80 ml, at least 90 ml, or at least 100 ml. In some instances, the volume of the compartments may be at most 100 ml, at most 90 ml, at most 80 ml, at most 70 ml, at most 60 ml, at most 50 ml, at most 40 ml, at most 30 ml, at most 20 ml, at most 10 ml, at most 5 ml, at most 1 ml, at most 0.5 ml, or at most 0.1 ml. Any of the lower and upper values described in this paragraph may be combined to form a range included within the present disclosure, for example, the volume of the compartments may range from about 10 ml to about 40 ml. Those of skill in the art will recognize that the volume of the compartments may have any value within this range, e.g., about 12 ml.

[0198] In some instances, the bioreactor container may comprise from about 1 to about 36 micro- cavities configured for withdrawing a sample from a compartment. In some instances, the bioreactor container may comprise at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, at least 14, at least 16, at least 18, at least 20, at least 22, at least 24, at least 26, at least 28, at least 30, at least 32, at least 34, at least 36 microcavities. 43MF-361080369Attorney Docket No.328202000440

[0199] In some instances, the bioreactor container may comprise 1, 2, 3, or 4 microcavities per compartment (e.g., per sample compartment, per cell growth compartment, and / or per fluid storage compartment, etc.).

[0200] In some instances, the volume of the micro-cavities in the bioreactor container may all be the same. In some instances, the volume of the micro-cavities in the bioreactor container may differ. In some instances, the volume of the micro-cavities in the bioreactor container may range from about 0.01 ml to about 1 ml. In some instances, the volume of the micro-cavities may be at least 0.01 ml, at least 0.05 ml, at least 0.1 ml, at least 0.5 ml, or at least 1 ml. In some instances, the volume of the micro-cavities may be at most 1 ml, at most 0.5 ml, at most 0.1 ml, at most 0.05 ml, or at most 0.01 ml. Any of the lower and upper values described in this paragraph may be combined to form a range included within the present disclosure, for example, the volume of the micro-cavities may range from about 0.05 ml to about 0.5 ml. Those of skill in the art will recognize that the volume of the micro-cavities may have any value within this range, e.g., about 0.035 ml.

[0201] In addition to a plurality of compartments (e.g., cell growth compartments, sample compartments and / or reagent storage compartments), micro-cavities and / or fluid channels, the disclosed bioreactor containers, in some instances, may further comprise a variety of micro-valves, filtration membranes, gas-permeable membranes, optically transparent windows, etc.

[0202] Polymeric materials: The disclosed bioreactor containers may be fabricated from any of a variety of materials (or combinations thereof) known to those of skill in the art including, but not limited to, glass (e.g., borosilicate glass, soda lime glass, etc.), fused silica (quartz), polymer (e.g., polystyrene (PS), tissue culture-treated polystyrene (TCPS), macroporous polystyrene (MPPS), polymethylmethacrylate (PMMA), polycarbonate (PC), polypropylene (PP), polyethylene (PE), high density polyethylene (HDPE), cyclic olefin polymers (COP), cyclic olefin copolymers (COC), polyethylene terephthalate (PET), polydimethylsiloxane (PDMS), etc.), porous polytetrafluoroethylene (PTFE) or other gas permeable membranes, polyetherimide (PEI) and perfluoroelastomer (FFKM) as more chemically inert alternatives, or any combination thereof. FFKM is also known as Kalrez. 44MF-361080369Attorney Docket No.328202000440

[0203] Fabrication techniques: The disclosed bioreactor containers may be fabricated using any of a variety of techniques (or combinations thereof) known to those of skill in the art, where the choice of fabrication technique is often dependent on the choice of material used, and vice versa. Examples of suitable fabrication techniques include, but are not limited to, injection molding, casting, extrusion, drawing, precision computer numerical control (CNC) machining and boring, laser photoablation, micro-molding, embossing, 3D-printing, thermal bonding, ultrasonic welding, adhesive bonding, anodic bonding, and the like.

[0204] Optical sensing and / or imaging modules: The disclosed bioreactor containers and / or systems may comprise optical sensing and / or imaging instrumentation. In some instances, the optical sensing and / or imaging instrumentation may comprise one or more light sources, one or more objective lenses, one or more image sensors or cameras, one or more processors or controllers, one or more additional optical components (e.g., lenses, mirrors, prisms, beam-splitters, optical filters, colored glass filters, narrowband interference filters, broadband interference filters, dichroic reflectors, diffraction gratings, apertures, shutters, optical fibers, optical waveguides, acousto-optic modulators, auto-focus sub-systems, and the like), or any combination thereof. In some instances, the optical sensing and / or imaging instrumentation may comprise a focus mechanism, e.g., an autofocus mechanism. In some instances, the optical sensing and / or imaging instrumentation may be configured to perform multichannel imaging, e.g., multichannel fluorescence imaging comprising the use of excitation light at one or more excitation wavelengths, and imaging the emitted fluorescence at two or more different emission wavelengths. In some instances, the optical sensing may comprise a laser emitter and fiber optics sensors, fiber optics grating or other laser-based measuring systems.

[0205] Any of a variety of image sensors may be used for imaging purposes, including but not limited to, photodiode arrays, charge-coupled device (CCD) sensors or cameras, complementary metal–oxide–semiconductor (CMOS) image sensors or cameras, or negative-channel metal-oxide semiconductor (NMOS) image sensors or cameras. Image sensors may be used with any of a variety of different types of illumination sources and emitters (such as light emitting diodes (LEDs) or lasers emitting at specific wavelengths) may be used to create labeled or label-free sensing systems 45MF-361080369Attorney Docket No.328202000440 including, but not limited to, bright-field optical microscopy, flow cytometry, Raman spectroscopy or fluoroscopy sensory systems. Imaging sensors may be one-dimensional (linear) or two- dimensional array sensors. Imaging sensors may be monochrome image sensors (i.e., configured to capture greyscale images) or color image sensors (i.e., configured to capture RGB or color images).

[0206] The image sensor may be used to capture a single image or a series of images (e.g., a single image, a series of single images, or video data) of the sample or object plane. The series of images and spectral data may comprise images (or video frames) that correspond to images captured before, during, and / or after an event (for example before, during, and / or after addition of a reagent to a cell sample). The series of images may comprise at least 1 image, at least 2 images, at least 3 images, at least 4 images, at least 5 images, at least 10 images, at least 20 images, at least 30 images, at least 40 images, at least 50 images, at least 100 images, at least 200 images, at least 300 images, at least 400 images, at least 500 images, at least 1000 images, at least 2000 images, at least 3000 images, at least 4000 images, at least 5000 images, at least 10,000 images, or more.

[0207] The image sensor may capture the series of image frames at a predefined capture or image acquisition rate. For example, the image acquisition rate may range from about 1frame per minute to about 100 frames per second.

[0208] Image sensors may vary in terms of pixel size and pixel count. The image resolution may depend on the pixel size and pixel count. Image sensors may have a pixel count of about or more than 0.5 mega pixels, 1 mega pixels, 4 mega pixels, 10 mega pixels, 20 mega pixels, 50 mega pixels, 80 mega pixels, 100 mega pixels, 200 mega pixels, or 500 mega pixels. The pixel size corresponding to the image sensor may be about or less than 5 microns, 3.5 microns, 2 microns, 1 micron, 0.5 microns, or 0.1 micron.

[0209] Fluidics modules and components: The disclosed bioreactor containers and / or systems may comprise one or more fluidics modules (or fluidics controllers) configured to control the delivery of fluids (e.g., gasses and / or liquid) to the internal volume of the toroidal container. In some instances, the one or more fluidics controllers may be configured to control volumetric flow rates for one or 46MF-361080369Attorney Docket No.328202000440 more gasses and / or liquids, linear flow velocities for one or more gasses and / or liquids, mixing ratios for one or more gasses and / or liquids, or any combination thereof. Fluid flow may be generated by pressure differences in the respective containers, by adding or removing gas (air), or by fluid pumps. Fluidics modules may comprise one or more gas and / or liquid flow sensors (e.g., flow rate sensors, pressure sensors, etc.), pressure sensors, one or more gas and / or liquid flow actuators (e.g., pumps), one or more fluid flow control devices (e.g., valves), one or more processors (and associated electronics), tubing and connectors to connect the one or more fluidics modules to one or more toroidal containers, or any combination thereof.

[0210] Temperature control modules: The disclosed bioreactor containers and systems may comprise one or more temperature control modules (or temperature controllers) configured to maintain a specified temperature for the gas and liquid within one or more toroidal containers for the purpose of facilitating the accuracy and reproducibility of cell growth and / or analysis results. Examples of temperature control components that may be incorporated into the disclosed bioreactor containers and / or systems and controlled by a temperature control module include, but are not limited to, resistive heating elements, infrared light sources, Peltier heating or cooling devices, heat sinks, thermistors, thermocouples, and the like.

[0211] In some instances, the temperature control module may provide for a programmable temperature change at a specified, adjustable time prior to performing specific assay or analysis steps. In some instances, the temperature control module may provide for programmable changes in temperature over specified time intervals. In some instances, the temperature control module may further provide for cycling of temperatures between two or more set temperatures with specified frequency and ramp rates.

[0212] Motion control modules: The disclosed bioreactor containers and / or systems may comprise one or more motion control modules (or motion controllers) configured to control the angular velocity of one or more toroidal containers and / or the position of one or more toroidal containers relative to an optical sensor, relative to an objective lens of an imaging module objective lens, etc. In some instances, the motion control module may control the position of the toroidal container in 47MF-361080369Attorney Docket No.328202000440 one dimension, two dimensions, or three dimensions (e.g., in the X-, Y-, and / or Z-directions). In some instances, the motion control module may separately or additionally control a degree of rotation of the toroidal container in one, two, or three dimensions. In some instances, the motion control module may be interfaced with an imaging module to also provide control of an autofocus mechanism. For example, the motion control module may be configured to adjust the focal plane by moving the toroidal container and / or by moving an objective lens (or other optical component) of the imaging module.

[0213] In some instances, the motion control module may comprise one or more (e.g., one, two, three, or more than three) translation stages, one or more (e.g., one, two, three, or more than three) rotational stages, one or more (e.g., one, two, three, or more than three) linear encoders, one or more (e.g., one, two, three, or more than three) rotary encoders, associated motors and control electronics, or any combination thereof. In some instances, the motion control module may further control components of the imaging module such as an automated objective lens turret or slide, or a microscope turret-mounted focus adjustment mechanism.

[0214] Suitable translation stages are commercially available from a variety of vendors, for example, Parker Hannifin, Harmonic Drives, Kollmorgen, Wittenstein, Ametek, THK, Applied motion and others. Precision translation stage systems typically comprise a combination of several components including, but not limited to, linear actuators, optical encoders, servo and / or stepper motors, and motor controllers or drive units. High precision and repeatability of stage movement is required for the disclosed bioreactor containers and / or systems in order to ensure accurate and reproducible fluid control, positioning, and optical sensing and / or imaging.

[0215] System control module: The disclosed bioreactor containers and / or systems may comprise one or more system control modules (or system controllers) configured to synchronize and control data communication between other functional units of the system, e.g., the one or more optical sensing and / or imaging modules, one or more fluidics modules, one or more temperature control modules, one or more motion control modules, or any combination thereof. In some instances, a system control module may comprise one or more processors, one or more power supplies, one or 48MF-361080369Attorney Docket No.328202000440 more wired and / or wireless data communication interfaces, one or more memory storage devices, one or more user interface devices, or any combination thereof. In some instances, the system control function may be provided by an external computer or computer system. In some instances, the one or more system control modules may interface with one or more external computers or computer systems.

[0216] System control software: In some instances, the disclosed bioreactor systems may comprise a computer (or processor) and computer-readable media that includes code for providing a user interface as well as manual, semi-automated, or fully-automated control of all system functions, e.g. control of a fluid flow controller and / or fluid dispensing system (or sub-system), a temperature control system (or sub-system), an imaging system (or sub-system), etc. In some instances, the system computer or processor may be an integrated component of the instrument system (e.g. a microprocessor or mother board embedded within the instrument). In some instances, the system computer or processor may be a stand-alone module, for example, a personal computer or laptop computer. Examples of fluid flow control functions that may be provided by the instrument control software include, but are not limited to, volumetric fluid flow rates, fluid flow velocities, the timing and duration for sample and reagent additions, rinse steps, and the like. Examples of temperature control functions that may be provided by the instrument control software include, but are not limited to, specifying temperature set point(s) and control of the timing, duration, and ramp rates for temperature changes. Examples of imaging system control functions that may be provided by the instrument control software include, but are not limited to, autofocus capability, control of illumination or excitation light exposure times and intensities, control of image acquisition rate, exposure time, data storage options, and the like.

[0217] Image processing software: In some instances, of the disclosed bioreactor containers and / or systems, any of a variety of image and data processing methods known to those of skill in the art may be used for image processing / pre-processing of images and spectral data acquired of cell samples or suspensions held within the bioreactor container. Examples include, but are not limited to, Canny edge detection methods, Canny-Deriche edge detection methods, first-order gradient edge detection methods (e.g., the Sobel operator), second order differential edge detection methods, phase 49MF-361080369Attorney Docket No.328202000440 congruency (phase coherence) edge detection methods, other image segmentation algorithms (e.g., intensity thresholding, intensity clustering methods, intensity histogram-based methods, etc.), feature and pattern recognition algorithms (e.g., the generalized Hough transform for detecting arbitrary shapes, the circular Hough transform, etc.), and mathematical analysis algorithms (e.g., Fourier transform, fast Fourier transform, wavelet analysis, auto-correlation, etc.), or any combination thereof.

[0218] Computing devices and systems: FIG.17 illustrates an example of a computing device or system in accordance with one or more examples of the disclosure. Device or system 1700 can be a host computer connected to a network. Device or system 1700 can be a client computer or a server. As shown in FIG.17, device or system 1700 can be any suitable type of microprocessor-based device, such as a personal computer, workstation, server, or handheld computing device (portable electronic device), such as a phone or tablet. The device can include, for example, one or more of processor 1710, input device 1720, output device 1730, storage 1740, and communication device 1760. Input device 1720 and output device 1730 can generally correspond to those described above, and they can either be connectable or integrated with the computer.

[0219] Input device 1720 can be any suitable device that provides input, such as a touch screen, keyboard or keypad, mouse, or voice-recognition device. Output device 1730 can be any suitable device that provides output, such as a touch screen, haptics device, or speaker.

[0220] Storage 1740 can be any suitable device that provides storage, such as an electrical, magnetic, or optical memory including a RAM, cache, hard drive, or removable storage disk. Communication device 1760 can include any suitable device capable of transmitting and receiving signals over a network, such as a network interface chip or device. The components of the computer can be connected in any suitable manner, such as via a physical bus 1770 or wirelessly.

[0221] Software 1750, which can be stored in memory / storage 1740 and executed by processor 1710, can include, for example, the programming that embodies the functionality of the present disclosure (e.g., as embodied in the devices and systems described above). 50MF-361080369Attorney Docket No.328202000440

[0222] Software 1750 can also be stored and / or transported within any non-transitory computer- readable storage medium for use by or in connection with an instruction execution system, apparatus, or device, such as those described above, that can fetch instructions associated with the software from the instruction execution system, apparatus, or device and execute the instructions. In the context of this disclosure, a computer-readable storage medium can be any medium, such as storage 1740, that can contain or store programming for use by or in connection with an instruction execution system, apparatus, or device.

[0223] Software 1750 can also be propagated within any transport medium for use by or in connection with an instruction execution system, apparatus, or device, such as those described above, that can fetch instructions associated with the software from the instruction execution system, apparatus, or device and execute the instructions. In the context of this disclosure, a transport medium can be any medium that can communicate, propagate, or transport programming for use by or in connection with an instruction execution system, apparatus, or device. The transport readable medium can include, but is not limited to, an electronic, magnetic, optical, electromagnetic, or infrared wired or wireless propagation medium.

[0224] Device or system 1700 may be connected to a network, which can be any suitable type of interconnected communication system. The network can implement any suitable communications protocol and can be secured by any suitable security protocol. The network can comprise network links of any suitable arrangement that can implement the transmission and reception of network signals, such as wireless network connections, Tl or T3 lines, cable networks, DSL, or telephone lines.

[0225] Device or system 1700 can implement any operating system suitable for operating on the network. Software 1750 can be written in any suitable programming language, such as C, C++, Java, or Python. In various instances, application software embodying the functionality of the present disclosure can be deployed in different configurations, such as in a client / server arrangement or through a web browser as a web-based application or web service, for example. 51MF-361080369Attorney Docket No.328202000440 ENUMERATED EMBODIMENTS

[0226] The following enumerated embodiments are representative of some aspects of the invention. 1. A bioreactor comprising: a container comprising a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses an axis of rotation of the bioreactor, wherein not all cross-sectional profiles of the series are the same and / or not all cross-sectional profiles’ lowest points have the same elevation and / or wherein the path is not equidistant from the axis of rotation at all points along the path; and at least one fluid port configured to provide fluid communication with the internal volume of the container. 2. The bioreactor of embodiment 1, wherein at least one fluid port is configured to provide fluid communication between an external fluid source and the internal volume of the container as the bioreactor rotates about its axis. 3. The bioreactor of embodiment 1 or embodiment 2, wherein at least one fluid port is configured to provide fluid communication between the interior volume of the container and a stationary exterior fluid reservoir as the bioreactor rotates about its axis. 4. The bioreactor of any one of embodiments 1 to 3, wherein the cross-sectional profiles of the series comprise a cross-section of a top plate, a first side-wall, and a second side-wall. 5. The bioreactor of embodiment 4, further comprising at least one micro cavity feature integrated with the first side-wall and configured to sample an aliquot of fluid contained within the container. 6. The bioreactor of embodiment 5, wherein the at least one micro cavity feature is integrated with a top edge of the first side-wall. 7. The bioreactor of embodiment 5 or embodiment 6, wherein the at least one micro cavity feature is configured to sample an aliquot of fluid contained within the container when an actuation force is applied to the at least one micro cavity feature. 52MF-361080369Attorney Docket No.328202000440 8. The bioreactor of any one of embodiments 5 to 7, wherein the at least one micro cavity feature is configured to deliver the fluid aliquot to a stationary external fluid sample container. 9. The bioreactor of any one of embodiments 5 to 8, wherein the at least one micro cavity feature comprises: a sample fluid inlet configured to provide fluid communication between an interior volume of the micro cavity feature and a fluid contained within the container; a valve mechanism integrated with the sample fluid inlet and configured to open when an actuation force is applied; the interior volume of the micro cavity feature; a return fluid outlet configured to vent air and / or excess fluid from the interior volume of the micro cavity feature; and a sample fluid outlet configured to provide fluid communication between the interior volume of the micro cavity feature and a stationary external fluid sample container. 10. The bioreactor of embodiment 9, wherein the interior volume of the at least one micro cavity feature is at least 5 microliters, 10 microliters, 20 microliters, 30 microliters, 40 microliters, 50 microliters, 60 microliters, 70 microliters, 80 microliters, 90 microliters, 0.1 milliliters, 0.2 milliliters, 0.3 milliliters, 0.4 milliliters, 0.5 milliliters, 0.6 milliliters, 0.7 milliliters, 0.8 milliliters, 0.9 milliliters, 1 milliliters, 2 milliliters, 3 milliliters, 4 milliliters, or 5 milliliters. 11. The bioreactor of embodiment 9 or embodiment 10, wherein the valve mechanism of the at least one micro cavity feature comprises a moveable component configured to toggle the valve between: (i) an open sample fluid inlet / closed sample fluid outlet configuration, and (ii) a closed sample fluid inlet / open sample fluid outlet configuration, upon application of the actuation force. 53MF-361080369Attorney Docket No.328202000440 12. The bioreactor of any one of embodiments 9 to 11, wherein the actuation force comprises a centrifugal force applied when an angular velocity for rotation of the container about its axis exceeds a specified minimum angular velocity threshold. 13. The bioreactor of any one of embodiments 9 to 12, wherein the actuation force comprises a magnetic force. 14. The bioreactor of any one of embodiments 11 to 13, wherein the moveable component comprises a rolling element that rolls between a first indent and a second indent, wherein the first indent and second indent correspond to the open sample fluid inlet / closed sample fluid outlet configuration and the closed sample fluid inlet / open sample fluid outlet configuration, respectively. 15. The bioreactor of any one of embodiments 1 to 14, wherein: the intersection of the first side-wall with a first imaginary plane parallel to a plane of the top plate defines a first diameter of the container; wherein the intersection of the second side-wall with a second imaginary plane parallel to the plane of the top plate defines a second diameter of the container; and wherein the second diameter is smaller than the first diameter. 16. The bioreactor of embodiment 15, wherein the first diameter ranges from about 2 cm to about 35 cm. 17. The bioreactor of embodiment 15 or embodiment 16, wherein the second diameter ranges from about 1 cm to about 30 cm. 18. The bioreactor of any one of embodiments 4 to 17, wherein the first side-wall and the second side-wall are slanted so as to intersect at an imaginary line that defines an angle between the first side-wall and the second side-wall at each cross-sectional profile of the series. 19. The bioreactor of any one of embodiments 4 to 18, wherein at least one of the first side-wall or the second side-wall is curved rather than planar. 20. The bioreactor of any one of embodiments 4 to 19, further comprising a bottom surface that intersects with the first side-wall and the second side-wall. 54MF-361080369Attorney Docket No.328202000440 21. The bioreactor of any one of embodiments 4 to 20, wherein at least a portion of the top plate, the first side-wall, and / or the second side-wall is composed of a gas permeable membrane. 22. The bioreactor of any one of embodiments 4 to 21, wherein the first side-wall is an exterior side-wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable high speed imaging of particles suspended in a fluid contained within the container as the container rotates about its axis. 23. The bioreactor of any one of embodiments 4 to 22, wherein the first side-wall is an exterior side-wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable high speed imaging of particles attached to an interior surface of the first side-wall as the container rotates about its axis. 24. The bioreactor of any one of embodiments 4 to 23, wherein the first side-wall is an exterior side-wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable optical sensing of at least one of pH, dissolved oxygen (DO), O2, N2, CO2, metabolomic profile, glutamate, glutamine, lactate, glucose, volume, flow rate, pressure, and temperature in a fluid contained within the container as the container rotates about its axis. 25. The bioreactor of any one of embodiments 20 to 24, wherein at least a portion of the bottom surface is optically transparent and configured to enable high speed imaging of particles suspended in a fluid contained within the container as the container rotates about its axis. 26. The bioreactor of any one of embodiments 20 to 25, wherein at least a portion of the bottom surface is optically transparent and configured to enable high speed imaging of particles attached to the bottom surface as the container rotates about its axis. 27. The bioreactor of any one of embodiments 20 to 26, wherein at least a portion of the bottom surface is optically transparent and configured to enable optical sensing of at least one of pH, dissolved oxygen (DO), O2, N2, CO2, metabolomic profile, glutamate, glutamine, lactate, glucose, volume, flow rate, pressure, and temperature in a fluid contained within the container as the container rotates about its axis. 55MF-361080369Attorney Docket No.328202000440 28. The bioreactor of any one of embodiments 22, 23, 25, or 26, wherein the particles comprise cells, virus particles, beads, or any combination thereof. 29. The bioreactor of any one of embodiments 18 to 28, wherein the angle between the first side- wall and the second side-wall ranges from about 5 degree to about 160 degrees. 30. The bioreactor of any one of embodiments 18 to 29, wherein the angle between the first side- wall and the second side-wall ranges from about 30 degrees to about 120 degrees. 31. The bioreactor of any one of embodiments 18 to 30, wherein the angle between the first side- wall and the second side-wall is designed to optimize gas exchange between a fluid contained within the container and an overlaying gas contained within the container. 32. The bioreactor of any one of embodiments 18 to 31, wherein the angle between the first side- wall and the second side-wall is designed to maximize a surface area-to-fluid volume ratio for the container. 33. The bioreactor of any one of embodiments 19 to 32, wherein the at least one of the first side- wall or the second side-wall that is curved has a shape configured to provide different interfacial surface area-to-fluid volume ratios for a gas-fluid interface within the container for different volumes of fluid contained within the container. 34. The bioreactor of any one of embodiments 1 to 33, wherein a total fluid volume of the container is at least 2 milliliters, 4 milliliters, 6 milliliters, 8 milliliters, 10 milliliters, 20 milliliters, 30 milliliters, 40 milliliters, 50 milliliters, 60 milliliters, 70 milliliters, 80 milliliters, 90 milliliters, 0.1 liters, 0.2 liters, 0.3 liters, 0.4 liters, 0.5 liters, 0.6 liters, 0.7 liters, 0.8 liters, 0.9 liters, 1 liters, 1.2 liters, 1.4 liters, 1.6 liters, 1.8 liters, or 2 liters. 35. The bioreactor of any one of embodiments 1 to 34, wherein the at least one fluid port provides fluid communication between a stationary external fluid source and the interior volume of the container through a rotating fluid connector. 56MF-361080369Attorney Docket No.328202000440 36. The bioreactor of any one of embodiments 1 to 35, wherein the at least one fluid port provides fluid communication between the interior volume of the container and a stationary exterior fluid reservoir through a rotating fluid connector. 37. The bioreactor of any one of embodiments 1 to 36, wherein the at least one fluid port comprises a filtration membrane and is configured for periodic or continuous removal of a fluid contained within the container. 38. The bioreactor of any one of embodiments 1 to 37, wherein the path that encompasses the axis of rotation of the bioreactor is confined to a plane that is perpendicular to the axis of rotation. 39. The bioreactor of any one of embodiments 1 to 38, wherein the path that encompasses the axis of rotation of the bioreactor is not confined to a plane that is perpendicular to the axis of rotation. 40. The bioreactor of embodiment 39, wherein the path is offset in a first perpendicular direction with respect to the plane at some points along the path. 41. The bioreactor of embodiment 39 or embodiment 40, wherein the path is offset in a second perpendicular direction with respect to the plane at some points along the path. 42. The bioreactor of any one of embodiments 1 to 41, wherein the path is a closed path. 43. The bioreactor of any one of embodiments 1 to 41, wherein a portion of the path is an open path. 44. The bioreactor of embodiment 43, wherein the path further comprises a return section to close the open portion of the path. 45. The bioreactor of embodiment 43 or embodiment 44, wherein at least a portion of the path comprises a spiral path. 46. The bioreactor of any one of embodiments 1 to 41, wherein the path has a different radial distance from the axis of rotation of the bioreactor at different points along the path. 57MF-361080369Attorney Docket No.328202000440 47. The bioreactor of any one of embodiments 1 to 41, wherein the path has a different radial distance from a central axis of symmetry at different points along the path, and wherein the central axis of symmetry is different from the axis of rotation of the bioreactor. 48. The bioreactor of any one of embodiments 1 to 47, wherein some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series. 49. The bioreactor of any one of embodiments 1 to 48, wherein some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series. 50. The bioreactor of any one of embodiments 4 to 49, wherein a height of the internal volume of the container at each point along the path is defined by a distance between an inner surface of the top plate and an inner surface of a bottom plate. 51. The bioreactor of embodiment 50, wherein the height varies along at least a portion of the path. 52. The bioreactor of embodiment 50 or embodiment 51, wherein the height increases as a function of position along at least a portion of the path. 53. The bioreactor of any one of embodiments 50 to 52, wherein the height decreases as a function of position along at least a portion of the path. 54. The bioreactor of embodiment 53, wherein a length of the portion of the path for which the height increases is the same as a length of the portion of the path for which the height decreases. 55. The bioreactor of embodiment 53, wherein a length of the portion of the path for which the height increases is different from a length of the portion of the path for which the height decreases. 56. The bioreactor of any one of embodiments 1 to 55, wherein an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. 57. The bioreactor of any one of embodiments 1 to 56, wherein an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. 58MF-361080369Attorney Docket No.328202000440 58. The bioreactor of any one of embodiments 1 to 57, further comprising at least one fluid channel configured to recirculation of a fluid contained within the internal volume of the container. 59. A system comprising: at least one container comprising: a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses an axis of rotation of the container, wherein not all cross- sectional profiles of the series are the same and / or wherein the path is not equidistant from the axis of rotation at all points along the path; and at least one fluid inlet port configured to provide fluid communication with the internal volume of the container; and at least one drive mechanism comprising: a frame for mounting the container, wherein the frame is configured to allow the container to spin around its rotational axis; and at least one drive motor; wherein the drive mechanism is configured to control an angular velocity of the container as a function of time. 60. The system of embodiment 59, wherein the cross-sectional profiles of the series comprise a cross-section of a top plate, a first side-wall, and a second side-wall. 61. The system of embodiment 60, wherein the at least one container comprises at least one micro cavity feature integrated with the first side-wall and configured to sample an aliquot of fluid contained within the container. 62. The system of embodiment 61, wherein the at least one micro cavity feature is integrated with a top edge of the first side-wall. 59MF-361080369Attorney Docket No.328202000440 63. The system of embodiment 61 or embodiment 62, wherein the at least one micro cavity feature is configured to sample an aliquot of fluid contained within the container when an actuation force is applied to the at least one micro cavity feature. 64. The system of any one of embodiments 61 to 63, wherein the at least one micro cavity feature is configured to deliver the fluid aliquot to a stationary external fluid sample container. 65. The system of any one of embodiments 61 to 64, wherein the at least one micro cavity feature comprises: a sample fluid inlet configured to provide fluid communication between an interior volume of the micro cavity feature and a fluid contained within the container; a valve mechanism integrated with the sample fluid inlet and configured to open when an actuation force is applied; the interior volume of the micro cavity feature; a return fluid outlet configured to vent air and / or excess fluid from the interior volume of the micro cavity feature; and a sample fluid outlet configured to provide fluid communication between the interior volume of the micro cavity feature and a stationary external fluid sample container. 66. The system of embodiment 65, wherein the valve mechanism of the at least one micro cavity feature comprises a moveable component configured to toggle the valve between: (i) an open sample fluid inlet / closed sample fluid outlet configuration, and (ii) a closed sample fluid inlet / open sample fluid outlet configuration, upon application of the actuation force. 67. The system of any one of embodiments 63 to 66, wherein the actuation force comprises a centrifugal force applied when an angular velocity for rotation of the container about its axis exceeds a specified minimum angular velocity threshold. 60MF-361080369Attorney Docket No.328202000440 68. The system of any one of embodiments 63 to 67, wherein the actuation force comprises a magnetic force. 69. The system of any one of embodiments 63 to 68, wherein the moveable component comprises a rolling element that rolls between a first indent and a second indent, wherein the first indent and second indent correspond to the open sample fluid inlet / closed sample fluid outlet configuration and the closed sample fluid inlet / open sample fluid outlet configuration, respectively. 70. The system of any one of embodiments 65 to 69, wherein the interior volume of the at least one micro cavity feature at least 5 microliters, 10 microliters, 20 microliters, 30 microliters, 40 microliters, 50 microliters, 60 microliters, 70 microliters, 80 microliters, 90 microliters, 0.1 milliliters, 0.2 milliliters, 0.3 milliliters, 0.4 milliliters, 0.5 milliliters, 0.6 milliliters, 0.7 milliliters, 0.8 milliliters, 0.9 milliliters, 1 milliliters, 2 milliliters, 3 milliliters, 4 milliliters, or 5 milliliters. 71. The system of any one of embodiments 59 to 70, wherein the frame comprises a self- centering engagement mechanism for attachment to a robotic actuator. 72. The system of any one of embodiments 59 to 71, wherein the at least one drive motor of the drive mechanism comprises a servo motor. 73. The system of any one of embodiments 59 to 72, wherein the at least one drive mechanism further comprises a self-centering engagement mechanism for attachment to a robotic actuator. 74. The system of any one of embodiments 59 to 73, wherein the at least one drive mechanism further comprises a self-centering engagement mechanism for attachment to a rack configured to hold a plurality of drive mechanisms. 75. The system of any one of embodiments 59 to 74, wherein the at least one drive mechanism further comprises at least one optical encoder for monitoring the angular velocity of the container as a function of time. 76. The system of any one of embodiments 59 to 75, wherein the at least one drive mechanism is configured to vary the angular velocity of the container as a function of time in a programmable fashion. 61MF-361080369Attorney Docket No.328202000440 77. The system of any one of embodiments 59 to 75, wherein a variation in the angular velocity of the container as a function of time is used to control a composition of a fluid mixture that enters the at least one micro cavity feature. 78. The system of any one of embodiments 59 to 77, wherein the at least one drive mechanism, or a housing thereof, further comprises at least one optical imaging camera configured to perform high speed imaging of particles suspended in the fluid contained within the container. 79. The system of any one of embodiments 59 to 78, wherein the at least one drive mechanism, or a housing thereof, further comprises at least one optical imaging camera configured to perform high speed imaging of particles attached to an interior surface of the first side-wall of the container. 80. The system of any one of embodiments 59 to 79, wherein the at least one drive mechanism, or a housing thereof, further comprises at least one optical sensor configured to perform optical sensing of at least one of pH, dissolved oxygen (DO), and temperature in a fluid contained within the container. 81. The system of any one of embodiments 59 to 80, wherein the system further comprises a gas controller configured to provide control of the flow rate for at least one gas flowing into the container. 82. The system of any one of embodiments 59 to 81, wherein the system further comprises a housing configured to provide temperature control for the container. 83. The system of any one of embodiments 61 to 82, wherein a geometry of the at least one micro cavity feature is configured to modify a shape of a cell that enters therein. 84. The system of any one of embodiments 61 to 83, wherein a geometry of the at least one micro cavity feature is configured to lyse a cell that enters therein. 85. The system of any one of embodiments 61 to 84, further comprising an electromagnetic device configured to modify a cell that enters the at least one micro cavity feature. 86. The system of any one of embodiments 61 to 85, further comprising an electronic device configured to electroporate a cell that enters the at least one micro cavity feature. 62MF-361080369Attorney Docket No.328202000440 87. The system of any one of embodiments 59 to 86, wherein the path that encompasses the axis of rotation of the container is confined to a plane that is perpendicular to the axis of rotation. 88. The system of any one of embodiments 59 to 87, wherein the path that encompasses the axis of rotation of the container is not confined to a plane that is perpendicular to the axis of rotation. 89. The system of embodiment 88, wherein the path is offset in a first perpendicular direction with respect to the plane at some points along the path. 90. The system of embodiment 88 or embodiment 89, wherein the path is offset in a second perpendicular direction with respect to the plane at some points along the path. 91. The system of any one of embodiments 59 to 90, wherein the path is a closed path. 92. The system of any one of embodiments 59 to 91, wherein a portion of the path is an open path. 93. The system of embodiment 92, wherein the path further comprises a return section to close the open portion of the path. 94. The system of embodiment 92 or embodiment 93, wherein at least a portion of the path comprises a spiral path. 95. The system of any one of embodiments 59 to 94, wherein the path has a different radial distance from the axis of rotation of the container at different points along the path. 96. The system of any one of embodiments 59 to 94, wherein the path has a different radial distance from a central axis of symmetry at different points along the path, and wherein the central axis of symmetry is different from the axis of rotation of the container. 97. The system of any one of embodiments 59 to 95, wherein some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series. 98. The system of any one of embodiments 59 to 97, wherein some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series. 63MF-361080369Attorney Docket No.328202000440 99. The system of any one of embodiments 60 to 98, wherein a height of the internal volume of the at least one container at each point along the path is defined by a distance between the top fluid surface and an inner surface of a bottom plate. 100. The system of embodiment 99, wherein the height varies along at least a portion of the path. 101. The system of embodiment 99 or embodiment 100, wherein the height increases as a function of position along at least a portion of the path. 102. The system of any one of embodiments 99 to 101, wherein the height decreases as a function of position along at least a portion of the path. 103. The system of embodiment 102, wherein a length of the portion of the path for which the height increases is the same as a length of the portion of the path for which the height decreases. 104. The system of embodiment 102, wherein a length of the portion of the path for which the height increases is different from a length of the portion of the path for which the height decreases. 105. The system of any one of embodiments 59 to 104, wherein an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. 106. The system of any one of embodiments 59 to 105, wherein an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. 107. The system of any one of embodiments 59 to 106, wherein the at least one container further comprises at least one fluid channel configured for recirculation of a fluid contained within the internal volume of the container. 108. The system of any one of embodiments 59 to 107, wherein at least one fluid port is configured to provide fluid communication between a stationary external fluid source and the internal volume of the container as the container rotates about its axis. 64MF-361080369Attorney Docket No.328202000440 109. The system of any one of embodiments 59 to 108, wherein at least one fluid port is configured to provide fluid communication between the interior volume of the container and a stationary exterior fluid reservoir as the container rotates about its axis. 110. A method for culturing cells, the method comprising: introducing cells into a fluid contained within a bioreactor comprising: a container comprising a continuous internal volume formed by a series of cross- sectional profiles swept along a path that encompasses an axis of rotation of the bioreactor, wherein not all cross-sectional profiles of the series are the same and / or wherein the path is not equidistant from the axis of rotation at all points along the path, and optionally, at least one micro cavity feature integrated with a first side-wall and configured to perform at least one of: (i) sampling an aliquot of fluid contained within the container when the container is rotated; and / or (ii) delivering the fluid aliquot to a stationary external fluid sample container; aerating and / or agitating the fluid contained within the container by rotating the container about its axis at a specified angular velocity; monitoring cell growth within the fluid by at least one of: performing high speed imaging of cells suspended in the fluid, performing high speed imaging of cells attached to an interior surface of the first side-wall of the container, or performing high speed imaging of cells contained in the at least on micro cavity feature; sampling an aliquot of the fluid using the at least one micro cavity feature by increasing an angular velocity for rotation of the container so that it exceeds a specified minimum angular velocity threshold, and 65MF-361080369Attorney Docket No.328202000440 delivering the aliquot of the fluid to a stationary external sample container for testing. 111. The method of embodiment 110, wherein sampling an aliquot of fluid contained within the container comprises applying a force to a valve mechanism integrated with the at least one micro cavity feature. 112. The method of embodiment 110 or embodiment 111, further comprising use of different angular velocity settings to perform different cell culture functions. 113. The method of embodiment 112, wherein the different cell culture functions comprise mixing, resuspension, temperature control, cluster prevention, delivery of an aliquot of fluid to the at least one micro cavity for cell analysis and / or modification, or any combination thereof. 114. The method of any one of embodiments 110 to 113, further comprising monitoring at least one of pH, dissolved oxygen (DO), and temperature within the fluid as a function of time. 115. The method of any one of embodiments 110 to 114, wherein, prior to the sampling step, an angular velocity for rotation of the container is adjusted to select a subset of cells for sampling by the at least one micro cavity feature. 116. The method of any one of embodiments 110 to 115, wherein, prior to the sampling step, an external force is applied to select a subset of cells for sampling by the at least one micro cavity feature. 117. The method of embodiment 116, wherein the cells are attached to magnetic beads and the external force is a magnetic force. 118. The method of any one of embodiments 110 to 117, wherein the path that encompasses the axis of rotation of the container is confined to a plane that is perpendicular to the axis of rotation. 119. The method of any one of embodiments 110 to 118, wherein the path that encompasses the axis of rotation of the bioreactor is not confined to a plane that is perpendicular to the axis of rotation. 120. The method of embodiment 119, wherein the path is offset in a first perpendicular direction with respect to the plane at some points along the path. 66MF-361080369Attorney Docket No.328202000440 121. The method of embodiment 119 or embodiment 120, wherein the path is offset in a second perpendicular direction with respect to the plane at some points along the path. 122. The method of any one of embodiments 110 to 121, wherein the path is a closed path. 123. The method of any one of embodiments 110 to 121, wherein a portion of the path is an open path. 124. The method of embodiment 123, wherein the path further comprises a return section to close the open portion of the path. 125. The method of embodiment 123 or embodiment 124, wherein at least a portion of the path comprises a spiral path. 126. The method of any one of embodiments 110 to 125, wherein the path has a different radial distance from the axis of rotation of the container at different points along the path. 127. The method of any one of embodiments 110 to 126, wherein the path has a different radial distance from a central axis of rotation at different points along the path, and wherein the central axis of rotation is different from the axis of rotation of the container. 128. The method of any one of embodiments 110 to 127, wherein some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series. 129. The method of any one of embodiments 110 to 128, wherein some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series. 130. The method of any one of embodiments 111 to 129, wherein a height of the internal volume of the container at each point along the path is defined by a distance between an inner surface of the top plate and an inner surface of a bottom plate. 131. The method of embodiment 130, wherein the height varies along at least a portion of the path. 132. The method of embodiment 130 or embodiment 131, wherein the height increases as a function of position along at least a portion of the path. 67MF-361080369Attorney Docket No.328202000440 133. The method of any one of embodiments 130 to 132, wherein the height decreases as a function of position along at least a portion of the path. 134. The method of embodiment 133, wherein a length of the portion of the path for which the height increases is the same as a length of the portion of the path for which the height decreases. 135. The method of embodiment 133, wherein a length of the portion of the path for which the height increases is different from a length of the portion of the path for which the height decreases. 136. The method of any one of embodiments 110 to 135, wherein an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. 137. The method of any one of embodiments 110 to 136, wherein an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof. 138. The method of any one of embodiments 110 to 137, wherein the container further comprises at least one fluid channel configured for recirculation of a fluid contained within the internal volume of the container. 139. A bioreactor comprising: a container comprising a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses a central axis of the bioreactor, wherein not all cross- sectional profiles of the series are the same and / or wherein the path is not equidistant from the central axis at all points along the path; and at least one fluid port configured to provide fluid communication with the internal volume of the container. 140. The bioreactor of embodiment 139, wherein the bioreactor is configured to rotate about a rotation axis. 141. The bioreactor of embodiment 140, wherein the rotation axis coincides with the central axis. 68MF-361080369Attorney Docket No.328202000440 EXAMPLES

[0227] The following examples are included for illustrative purposes only and are not intended to limit the scope of the present disclosure. Example 1 – Jurkat Cell Cultures

[0228] Prototypes of the bioreactor described herein were tested in the lab using Jurkat cells with a number of different cell growth protocols.

[0229] The first cell growth experiment described here was performed under a fixed volume of growth medium of 20 ml, while the second experiment was performed with an incremental volume of growth medium adjusted from 2.5 ml to 80 ml, with cells seeded at a density of 0.3e6 and 0.6e6 cells / ml respectively, comparing the cell growth in the prototype bioreactor with that in flasks and G-Rex6M multi-well plates.

[0230] Under the fixed volume condition, and performing media exchange every other day, it was observed that cells grown in the prototype bioreactor continue exponential expansion up to day 15, while cells grown in flasks or G-rex6M multi-well plates plateaued at day 9 and 12 respectively. Cells expanded in the prototype bioreactor (Toro bioreactor) outperformed those expanded in flasks or G-Rex6M multi-well plates (FIG.18A) in terms of both cell density (FIG.18B) and viability (FIG.18C). Flask data: green (lower curve). G-rex6M multi-well plate data: red (middle curve). Toro bioreactor: blue (upper curve).

[0231] Tables 1 – 3 summarize the data underlying the plots shown in FIGS. 18A – 18C. 69MF-361080369Attorney Docket No. 328202000440Table 1. Fold Expansion. Table 2. Cell Density.Table 3. Cell Viability

[0232] Under the incremental volume condition, where media exchange occurred after the volumereached 80 ml, the same superior expansion of cells was observed (FIG. 19A) with higher celldensity (FIG. 19B) and viability (FIG. 19C) in two different prototypes of the disclosed bioreactor(Toro #1 and Toro #2) compared to cells grown in flasks or G-Rex 6M multi-well plates. Flask data:green (lower curve). G-rex6M multi-well plate data: red (next lowest curve). Toro #1 bioreactor70 MF-361080369Attorney Docket No. 328202000440(comprising a first spiral path): light blue (next highest curve). Toro #2 bioreactor (comprising asecond spiral path): darker blue (highest curve). The asterisks indicate timepoints at which thegrowth medium was replaced.

[0233] Tables 4 – 6 summarize the data underlying the plots shown in FIGS. 19A – 19C.Table 4. Fold Expansion.Table 5. Cell Density.MF-361080369Attorney Docket No. 328202000440Table 6. Cell Viability

[0234] These results indicate that the unique design of the disclosed bioreactor promotes cellexpansion at higher cell density with better viability.

[0235] It should be understood from the foregoing that, while particular implementations of thedisclosed methods, devices, and systems have been illustrated and described, various modificationscan be made thereto and are contemplated herein. It is also not intended that the invention be limited by the specific examples provided within the specification. While the invention has been describedwith reference to the aforementioned specification, the descriptions and illustrations of thepreferable embodiments herein are not meant to be construed in a limiting sense. Furthermore, it shall be understood that all aspects of the invention are not limited to the specific depictions, configurations or relative proportions set forth herein which depend upon a variety of conditions and variables. Various modifications in form and detail of the embodiments of the invention will be apparent to a person skilled in the art. It is therefore contemplated that the invention shall also cover any such modifications, variations and equivalents. 72 MF-361080369

Claims

Attorney Docket No.328202000440 CLAIMS What is claimed is:

1. A bioreactor comprising: a container comprising a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses an axis of rotation of the bioreactor, wherein not all cross-sectional profiles of the series are the same and / or not all cross-sectional profiles’ lowest points have the same elevation and / or wherein the path is not equidistant from the axis of rotation at all points along the path; and at least one fluid port configured to provide fluid communication with the internal volume of the container.

2. The bioreactor of claim 1, wherein at least one fluid port is configured to provide fluid communication between an external fluid source and the internal volume of the container as the bioreactor rotates about its axis.

3. The bioreactor of claim 1 or claim 2, wherein at least one fluid port is configured to provide fluid communication between the interior volume of the container and a stationary exterior fluid reservoir as the bioreactor rotates about its axis.

4. The bioreactor of any one of claims 1 to 3, wherein the cross-sectional profiles of the series comprise a cross-section of a top plate, a first side-wall, and a second side-wall.

5. The bioreactor of claim 4, further comprising at least one micro cavity feature integrated with the first side-wall and configured to sample an aliquot of fluid contained within the container.

6. The bioreactor of claim 5, wherein the at least one micro cavity feature is integrated with a top edge of the first side-wall.

7. The bioreactor of any one of claims 1 to 6, wherein: the intersection of the first side-wall with a first imaginary plane parallel to a plane of the top plate defines a first diameter of the container; 73MF-361080369Attorney Docket No.328202000440 wherein the intersection of the second side-wall with a second imaginary plane parallel to the plane of the top plate defines a second diameter of the container; and wherein the second diameter is smaller than the first diameter.

8. The bioreactor of any one of claims 4 to 7, wherein the first side-wall and the second side- wall are slanted so as to intersect at an imaginary line which defines an angle between the first side- wall and the second side-wall at each cross-sectional profile of the series.

9. The bioreactor of any one of claims 4 to 8, wherein at least one of the first side-wall or the second side-wall is curved rather than planar.

10. The bioreactor of any one of claims 4 to 9, further comprising a bottom surface that intersects with the first side-wall and the second side-wall.

11. The bioreactor of any one of claims 4 to 10, wherein at least a portion of the top plate, the bottom surface, the first side-wall, and / or the second side-wall is composed of a gas permeable membrane.

12. The bioreactor of any one of claims 4 to 11, wherein the first side-wall is an exterior side- wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable high speed imaging of particles suspended in a fluid contained within the container as the container rotates about its axis.

13. The bioreactor of any one of claims 4 to 12, wherein the first side-wall is an exterior side- wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable high speed imaging of particles attached to an interior surface of the first side-wall as the container rotates about its axis.

14. The bioreactor of any one of claims 4 to 13, wherein the first side-wall is an exterior side- wall, and wherein at least a portion of the first side-wall is optically transparent and configured to enable optical sensing of at least one of pH, dissolved oxygen (DO), O2, N2, CO2, metabolomic profile, glutamate, glutamine, lactate, glucose, volume, flow rate, pressure, and temperature in a fluid contained within the container as the container rotates about its axis. 74MF-361080369Attorney Docket No.328202000440 15. The bioreactor of any one of claims 10 to 14, wherein at least a portion of the bottom surface is optically transparent and configured to enable high speed imaging of particles suspended in a fluid contained within the container as the container rotates about its axis.

16. The bioreactor of any one of claims 10 to 15, wherein at least a portion of the bottom surface is optically transparent and configured to enable high speed imaging of particles attached to the bottom surface as the container rotates about its axis.

17. The bioreactor of any one of claims 10 to 16, wherein at least a portion of the bottom surface is optically transparent and configured to enable optical sensing of at least one of pH, dissolved oxygen (DO), O2, N2, CO2, metabolomic profile, glutamate, glutamine, lactate, glucose, volume, flow rate, pressure, and temperature in a fluid contained within the container as the container rotates about its axis.

18. The bioreactor of any one of claims 1 to 17, wherein the at least one fluid port provides fluid communication between a stationary external fluid source and the interior volume of the container through a rotating fluid connector.

19. The bioreactor of any one of claims 1 to 18, wherein the at least one fluid port provides fluid communication between the interior volume of the container and a stationary exterior fluid reservoir through a rotating fluid connector.

20. The bioreactor of any one of claims 1 to 19, wherein the at least one fluid port comprises a filtration membrane and is configured for periodic or continuous removal of a fluid contained within the container.

21. The bioreactor of any one of claims 1 to 20, wherein the path that encompasses the axis of rotation of the bioreactor is confined to a plane that is perpendicular to the axis of rotation.

22. The bioreactor of any one of claims 1 to 21, wherein the path that encompasses the axis of rotation of the bioreactor is not confined to a plane that is perpendicular to the axis of rotation.

23. The bioreactor of any one of claims 1 to 22, wherein the path is a closed path.

24. The bioreactor of any one of claims 1 to 22, wherein a portion of the path is an open path. 75MF-361080369Attorney Docket No.328202000440 25. The bioreactor of any one of claims 1 to 22, wherein the path has a different radial distance from the axis of rotation of the bioreactor at different points along the path.

26. The bioreactor of any one of claims 1 to 22, wherein the path has a different radial distance from a central axis of symmetry at different points along the path, and wherein the central axis of symmetry is different from the axis of rotation of the bioreactor.

27. The bioreactor of any one of claims 1 to 26, wherein some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series.

28. The bioreactor of any one of claims 1 to 27, wherein some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series.

29. The bioreactor of any one of claims 4 to 28, wherein a height of the internal volume of the container at each point along the path is defined by a distance between an inner surface of the top plate and an inner surface of a bottom plate.

30. The bioreactor of any one of claims 1 to 29, wherein an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

31. The bioreactor of any one of claims 1 to 30, wherein an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

32. The bioreactor of any one of claims 1 to 31, further comprising at least one fluid channel configured to recirculation of a fluid contained within the internal volume of the container.

33. A system comprising: at least one container comprising: a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses an axis of rotation of the container, wherein not all cross- sectional profiles of the series are the same and / or wherein the path is not equidistant from the axis of rotation at all points along the path; and 76MF-361080369Attorney Docket No.328202000440 at least one fluid inlet port configured to provide fluid communication with the internal volume of the container; and at least one drive mechanism comprising: a frame for mounting the container, wherein the frame is configured to allow the container to spin around its rotational axis; and at least one drive motor; wherein the drive mechanism is configured to control an angular velocity of the container as a function of time.

34. The system of claim 33, wherein the cross-sectional profiles of the series comprise a cross- section of a top plate, a first side-wall, and a second side-wall.

35. The system of claim 34, wherein the at least one container comprises at least one micro cavity feature integrated with the first side-wall and configured to sample an aliquot of fluid contained within the container.

36. The system of claim 35, wherein the at least one micro cavity feature is integrated with a top edge of the first side-wall.

37. The system of claim 35 or claim 36, wherein the at least one micro cavity feature is configured to sample an aliquot of fluid contained within the container when an actuation force is applied to the at least one micro cavity feature.

38. The system of any one of claims 35 to 37, wherein the at least one micro cavity feature is configured to deliver the fluid aliquot to a stationary external fluid sample container.

39. The system of any one of claims 33 to 38, wherein the frame comprises a self-centering engagement mechanism for attachment to a robotic actuator.

40. The system of any one of claims 33 to 39, wherein the at least one drive motor of the drive mechanism comprises a servo motor. 77MF-361080369Attorney Docket No.328202000440 41. The system of any one of claims 33 to 40, wherein the at least one drive mechanism further comprises a self-centering engagement mechanism for attachment to a robotic actuator.

42. The system of any one of claims 33 to 41, wherein the at least one drive mechanism further comprises a self-centering engagement mechanism for attachment to a rack configured to hold a plurality of drive mechanisms.

43. The system of any one of claims 33 to 42, wherein the at least one drive mechanism further comprises at least one optical encoder for monitoring the angular velocity of the container as a function of time.

44. The system of any one of claims 33 to 43, wherein the at least one drive mechanism is configured to vary the angular velocity of the container as a function of time in a programmable fashion.

45. The system of any one of claims 33 to 44, wherein a variation in the angular velocity of the container as a function of time is used to control a composition of a fluid mixture that enters the at least one micro cavity feature.

46. The system of any one of claims 33 to 45, wherein the at least one drive mechanism, or a housing thereof, further comprises at least one optical imaging camera configured to perform high speed imaging of particles suspended in the fluid contained within the container.

47. The system of any one of claims 33 to 46, wherein the at least one drive mechanism, or a housing thereof, further comprises at least one optical imaging camera configured to perform high speed imaging of particles attached to an interior surface of the first side-wall of the container.

48. The system of any one of claims 33 to 47, wherein the at least one drive mechanism, or a housing thereof, further comprises at least one optical sensor configured to perform optical sensing of at least one of pH, dissolved oxygen (DO), O2, N2, CO2, metabolomic profile, glutamate, glutamine, lactate, glucose, volume, flow rate, pressure, and temperature in a fluid contained within the container. 78MF-361080369Attorney Docket No.328202000440 49. The system of any one of claims 33 to 48, wherein the system further comprises a gas controller configured to provide control of the flow rate for at least one gas flowing into the container.

50. The system of any one of claims 33 to 49, wherein the system further comprises a housing configured to provide temperature control for the container.

51. The system of any one of claims 33 to 50, wherein a geometry of the at least one micro cavity feature is configured to modify a shape of a cell that enters therein.

52. The system of any one of claims 35 to 51, wherein a geometry of the at least one micro cavity feature is configured to lyse a cell that enters therein.

53. The system of any one of claims 35 to 52, further comprising an electromagnetic device configured to modify a cell that enters the at least one micro cavity feature.

54. The system of any one of claims 35 to 53, further comprising an electronic device configured to electroporate a cell that enters the at least one micro cavity feature.

55. The system of any one of claims 33 to 54, wherein the path that encompasses the axis of rotation of the container is confined to a plane that is perpendicular to the axis of rotation.

56. The system of any one of claims 33 to 55, wherein the path that encompasses the axis of rotation of the container is not confined to a plane that is perpendicular to the axis of rotation.

57. The system of any one of claims 33 to 56, wherein the path is a closed path.

58. The system of any one of claims 33 to 57, wherein a portion of the path is an open path.

59. The system of any one of claims 33 to 58, wherein the path has a different radial distance from the axis of rotation of the container at different points along the path.

60. The system of any one of claims 33 to 58, wherein the path has a different radial distance from a central axis of symmetry at different points along the path, and wherein the central axis of symmetry is different from the axis of rotation of the container. 79MF-361080369Attorney Docket No.328202000440 61. The system of any one of claims 33 to 60, wherein some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series.

62. The system of any one of claims 33 to 61, wherein some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series.

63. The system of any one of claims 34 to 62, wherein a height of the internal volume of the at least one container at each point along the path is defined by a distance between the top fluid surface and an inner surface of a bottom plate.

64. The system of any one of claims 33 to 63, wherein an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

65. The system of any one of claims 33 to 64, wherein an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

66. The system of any one of claims 33 to 65, wherein the at least one container further comprises at least one fluid channel configured for recirculation of a fluid contained within the internal volume of the container.

67. The system of any one of claims 33 to 66, wherein at least one fluid port is configured to provide fluid communication between a stationary external fluid source and the internal volume of the container as the container rotates about its axis.

68. The system of any one of claims 33 to 67, wherein at least one fluid port is configured to provide fluid communication between the interior volume of the container and a stationary exterior fluid reservoir as the container rotates about its axis.

69. A method for culturing cells, the method comprising: introducing cells into a fluid contained within a bioreactor comprising: a container comprising a continuous internal volume formed by a series of cross- sectional profiles swept along a path that encompasses an axis of rotation of the bioreactor, wherein not all cross-sectional profiles of the series are the same and / or wherein the path is not equidistant from the axis of rotation at all points along the path, and 80MF-361080369Attorney Docket No.328202000440 optionally, at least one micro cavity feature integrated with a first side-wall and configured to perform at least one of: (i) sampling an aliquot of fluid contained within the container when the container is rotated; and / or (ii) delivering the fluid aliquot to a stationary external fluid sample container; aerating and / or agitating the fluid contained within the container by rotating the container about its axis at a specified angular velocity; monitoring cell growth within the fluid by at least one of: performing high speed imaging of cells suspended in the fluid, performing high speed imaging of cells attached to an interior surface of the first side-wall of the container, or performing high speed imaging of cells contained in the at least on micro cavity feature; sampling an aliquot of the fluid using the at least one micro cavity feature by increasing an angular velocity for rotation of the container so that it exceeds a specified minimum angular velocity threshold, and delivering the aliquot of the fluid to a stationary external sample container for testing.

70. The method of claim 69, wherein sampling an aliquot of fluid contained within the container comprises applying a force to a valve mechanism integrated with the at least one micro cavity feature.

71. The method of claim 69 or claim 70, further comprising use of different angular velocity settings to perform different cell culture functions.

72. The method of claim 71, wherein the different cell culture functions comprise mixing, resuspension, temperature control, cell wash, cluster prevention, delivery of an aliquot of fluid to the at least one micro cavity for cell analysis and / or modification, or any combination thereof. 81MF-361080369Attorney Docket No.328202000440 73. The method of any one of claims 69 to 72, further comprising monitoring at least one of pH, dissolved oxygen (DO), carbon dioxide (CO2) and temperature within the fluid as a function of time.

74. The method of any one of claims 69 to 73, wherein, prior to the sampling step, an angular velocity for rotation of the container is adjusted to select a subset of cells for sampling by the at least one micro cavity feature.

75. The method of any one of claims 69 to 74, wherein, prior to the sampling step, an external force is applied to select a subset of cells for sampling by the at least one micro cavity feature.

76. The method of any one of claims 69 to 75, wherein the path that encompasses the axis of rotation of the container is confined to a plane that is perpendicular to the axis of rotation.

77. The method of any one of claims 69 to 76, wherein the path that encompasses the axis of rotation of the bioreactor is not confined to a plane that is perpendicular to the axis of rotation.

78. The method of any one of claims 69 to 77, wherein the path is a closed path.

79. The method of any one of claims 69 to 78, wherein a portion of the path is an open path.

80. The method of any one of claims 69 to 79, wherein the path has a different radial distance from the axis of rotation of the container at different points along the path.

81. The method of any one of claims 69 to 80, wherein the path has a different radial distance from a central axis of rotation at different points along the path, and wherein the central axis of rotation is different from the axis of rotation of the container.

82. The method of any one of claims 69 to 81, wherein some of the cross-sectional profiles of the series differ in shape from other cross-sectional profiles of the series.

83. The method of any one of claims 69 to 82, wherein some of the cross-sectional profiles of the series differ in at least one dimension from other cross-sectional profiles of the series.

84. The method of any one of claims 71 to 83, wherein a height of the internal volume of the container at each point along the path is defined by a distance between an inner surface of the top plate and an inner surface of a bottom plate. 82MF-361080369Attorney Docket No.328202000440 85. The method of any one of claims 71 to 84, wherein an interior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

86. The method of any one of claims 71 to 85, wherein an exterior surface of the container comprises a parabolic shape, a concave shape, a convex shape, or any combination thereof.

87. The method of any one of claims 71 to 86, wherein the container further comprises at least one fluid channel configured for recirculation of a fluid contained within the internal volume of the container.

88. A bioreactor comprising: a container comprising a continuous internal volume formed by a series of cross-sectional profiles swept along a path that encompasses a central axis of the bioreactor, wherein not all cross- sectional profiles of the series are the same and / or wherein the path is not equidistant from the central axis at all points along the path; and at least one fluid port configured to provide fluid communication with the internal volume of the container.

89. The bioreactor of claim 88, wherein the bioreactor is configured to rotate about a rotation axis.

90. The bioreactor of claim 89, wherein the rotation axis coincides with the central axis. 83MF-361080369

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