Patent Application
20240011883
This disclosure relates to methods for determining interaction between cellular bodies and a functionalized wall surface based on a sequence of images. In particular to such methods wherein an interaction is determined based on a determined speed of a cellular body. This disclosure further relates to data processing systems, computer programs and systems for determining interaction between cellular bodies and a functionalized wall surface.
The study of cell interactions, e.g. the binding strength between cells or between cells and biomolecules is a highly relevant and active research area in biosciences. For example, the avidity characterizes the cumulative effect of multiple individual binding interactions between cells. Similarly, the affinity characterizes the strength with which one molecule binds to another molecule, e.g. the strength with which a receptor on the cell membrane of an immune cell binds to an antigen on the target cell. The avidity and affinity are examples of parameters that play an essential role in the study and development of therapies in medicine, e.g. immune oncology.
A known technique for studying cell adhesion to biomolecules and for studying interaction strengths between cells is referred to as acoustic force spectroscopy, AFS wherein interactions between cells and a functionalized surface can be studied by applying a force to the cells. For example, Kamsma et al. in their article Single-cell acoustic force spectroscopy: resolving kinetics and strength of T cell adhesion to fibronectin, 2018, Cell Reports 24, 3008-3016, Sep. 11, 2018 study the adhesion of T Cells to fibronectin using an acoustic force spectroscopy AFS system. Similarly, WO2018/083193 describes an AFS system including a microfluidic cell comprising a so-called functionalized wall surface which may include target cells. A plurality of unlabelled effector cells, e.g. T-cells, can be flushed into the microfluidic cell, so that they can settle and bind to target cells. Thereafter, an acoustic source is used to exert a ramping force on the bound effector cells so that effector cells will detach from the target cells at a certain force. During this process, the spatiotemporal behavior of the effector cells in the microfluidic cell is imaged using an imaging microscope. The interaction between cells, e.g. the force at which the effector cells detach, may be determined by analysing the captured video images. For example, the cell avidity of the effector cells can be determined this way.
The imaging microscope may have a focal plane essentially parallel to the functionalized wall surface so that camera acquired images will typically show effector cells in the foreground against a background representing the functionalized wall that comprise the target cells. The analysis of these captured images may include detecting cells and tracking detected cells in two or three dimensions. During a typical AFS experiment, a large amount of effector cells needs to be detected, accurately localized and tracked during the settling of the cells onto the functionalized wall, the binding of the effector cells to target cells (incubation) and/or the detachment of the effector cells from the target cells.
Automatic detection and 3D tracking of a multitude, e.g. thousands or even tens of thousands of cells against a background of a highly dynamic, “living” functionalized wall surface, comprising for example a layer of target cells, is not a trivial problem. During a typical AFS experiment, the software needs to determine for each a cell the interaction between the cell and a functionalized wall surface which may also comprise cells. To that end, the software should be able to accurately determine among others if and when a cell is detached from the functionalized wall surface.
In order for the system to determine the interaction, such as the avidity, as accurate as possible it may be important that only cells that are truly detached should be taken into account in the analysis. However, the dynamics of effector cells attached to target cells in a functionalized wall surface is complex and events detected in the images could be identified as detached cells while in reality they are not. Hence, it is important that such false positives are recognized and properly classified for determining certain parameters such as the avidity.
Hence, from the above, it follows that there is a need in the art for an accurate and robust automated determining of interactions between a cellular body and a functionalized wall surface, preferably in dependence of an applied force.
The invention aims to improve the analysis of cell interactions using force spectroscopy. Herein the term force spectroscopy is used to indicate any system or method in which a force is applied on particles of interest while a response of the particles to the force is monitored e.g. by imaging the particles with a microscope. The inventors have recognized that the dynamics of cells attached to the functionalized wall surface often is complex and that cells do not always detach from the functionalized wall surface in the same simple manner. The inventors have realized that it is incorrect to identify every cellular body that moves with respect to the functionalized wall surface as a cellular body that has detached from the functionalized wall surface during the application of a force ramp. The inventors in particular found that there are interactions between cellular bodies, wherein a cellular body moves with respect to the functionalized wall surface while still being attached to the functionalized wall surface. This may for example occur when a cellular body is attached at a single site to the functionalized wall surface at a point which is displaced laterally with respect to the center of mass of the cellular body. In such case, the cellular body may “hinge” around the point of attachment due to applied forces and may thus move relative to the functionalized wall surface even if it still attached to the functionalized wall surface. Also, the inventors have found examples where cellular bodies, upon being pulled away from the functionalized wall surface, form so-called tethers, such as membrane tubes, which cause the cellular bodies to remain attached to the functionalized wall surface. Such tethers can be elongated significantly which means that the cellular bodies can travel relatively far away relative to the functionalized wall surface while still remaining attached to it. It should be appreciated that classifying such moving cellular bodies as being detached does not correspond to the physical reality and would distort analyses of binding characteristics, e.g. would yield inaccurate avidity curves.
In an aspect, the invention may relate to a method for determining interaction between cellular bodies and a functionalized wall surface. The method may comprise obtaining, e.g. determining or receiving, a sequence of images representing manipulating cellular bodies in a holding space, the holding space including a functionalized wall surface configured to bind the cellular bodies, the manipulating including applying a force. The method may also comprise a step of tracking first locations of first pixel groups in respective first images out of the sequence of images, each first pixel group in the first images representing a first cellular body out of the cellular bodies, the first locations defining a first trajectory of the first cellular body moving relative to the functionalized wall surface. The method may further comprise determining one or more first speed values of the first cellular body at one or more locations of the first trajectory, the one or more speed values being higher than zero and the method may comprise the step of classifying that the first cellular body is attached to the functionalized wall surface based on the one or more first speed values and at least one threshold speed value.
In an embodiment, the classifying may include determining that the one or more first speed values are lower than the at least one threshold speed value.
In an embodiment, a force ramp may be applied to the cellular bodies. In a further embodiment, the force may have a direction away from the functionalized wall surface
Hence, the method determines a detachment event based on the speed at which a cell moves relative to the wall surface during a force spectroscopy experiment. This way, the method allows a more accurately study of binding characteristics of cellular bodies. The method enables to obtain more accurate information from images captured during for example a force spectroscopy measurement as known in the art.
Preferably this method is a computer-implemented method.
The term cellular body used in this application may include cell portions like subcellular organelles, cell nuclei, and/or mitochondria. A cellular body may be unicellular or pluricellular, such as small clumped cell groups, plant or animal biopts, dividing cells, budding yeast cells, colonial protists, etc. A cellular body may also be an animal embryo in an early stage of development (e.g. the morula-stadium of a mammal, possibly a human embryo). In particular cases different types of cellular bodies may be studied together. E.g., cellular bodies from a mucosal swab, blood sample, or other probing techniques could be used. A cellular body may also be one or more immune cells, one or more tumor cells, one or more cells that have been infected, for example by a virus.
The one or more cellular bodies may include at least one of: lymphocytes, monocytic cells, granulocytes, T cells, natural killer cells, B-Cells, CAR-T cells, dendritic cells, Jurkat cells, bacterial cells, red blood cells, macrophages, TCR Tg T-cells, OT-I/OT-II cells, splenocytes, thymocytes, BM derived hematopoietic stem cells, TILs, tissue derived macrophages, innate lymphoid cells.
The functionalized wall surface may have provided thereon one or more target cellular bodies (e.g. tumor cells, stem cells, epithelial cells, B16 melanoma, fibroblasts, endothelial cells, HEK293, HeLa, 3T3, MEFs, HuVECs, microglia, neuronal cells) that are configured to bind the one or more cellular bodies. A functionalized wall surface as referred to herein may be provided with one or more primers. The primers may comprise one or more types of interaction moieties. In particular a functionalized wall surface may be provided with one or more substances comprising at least one of antibodies, peptides, biological tissue factors, biological tissue portions, bacteria, antigens, proteins, ligands, cells, tissues, viruses, (synthetic) drug compounds, lipid (bi)layers, fibronectin, cellulose, nucleic acids, RNA, small molecules, allosteric modulators, (bacterial) biofilms, “organ-on-a-chip”, etc., and/or specific atomic or molecular surface portions (e.g. a gold surface) to which at least part of the cellular bodies tends to adhere with preference relative to other surfaces.
An image as used herein may be understood to comprise a plurality of pixels that may be arranged in a raster to form the image. A pixel may be understood to be characterized by its position in the image. Further, when reference is made to a pixel in one image and the same pixel in a different image, then this may be understood to refer to the two pixels having the same position within their respective images, thus the position of the pixel within said one image being the same as the position of the “same pixel” in the different image. Further, pixels groups and regions of interest may be understood to consist of pixels. Likewise, reference may be made to a pixel group or region of interest in one image and the same pixel group or the same region of interest in another image. This may be then understood in that two pixel group or two regions of interest are meant each having the same position in their respective image, thus one pixel group or region of interest having a certain position within said one image and the other pixel group or region of interest having the same certain position within the other image.
A sequence of images may also be referred to as a video. Each image out of the sequence of images may be associated with a time instance, e.g. time-stamped, in the sense that it depicts the situation at that time instance. A “next”, “subsequent”, or “later” image in the sequence may be understood to be associated with a later time instance, i.e. depicts the situation at a later time instance. “Earliest” image in (a part of) the sequence may refer to the image depicting the earliest situation in that (part of the) sequence.
The detected pixel groups may consist of pixels that are valued such that they distinguish from the background in the images out of the sequence of images. In an example, the detected pixel groups consist of pixels having a relatively high intensity with respect to other pixels in the images. Such other pixels for example represent the background of the image, which may be formed by the functionalized wall surface. The one or more cellular bodies, at the time when the sequence of images was captured, may have been labelled, e.g. fluorescently labelled, so that the one or more cellular bodies stand out from the background.
Detecting pixel groups in respective images, which pixel groups represent a movement relative to the functionalized wall surface of a cellular body may be performed by detecting in each subsequent image the pixel group that represents the cellular body. This may also be referred to as tracking the cellular body. Due to the movement of the cellular body, in principle, each pixel group in an image representing the cellular body has a different position within its image. The speed of the movement relative to the functionalized wall surface is for example determined based on pixel distances as further detailed below.
For a particular cellular body represented by a plurality of pixel groups in respective images, its movement may be understood to be represented by the different position that the pixel groups have within their respective images.
The threshold speed is preferably selected such that it correctly discriminates between cellular bodies attached to the functionalized wall surface and cellular bodies not attached to the functionalized wall surface. The threshold speed may be defined in terms of a number of pixels per second. In such case, the threshold speed in pixels per frame also depends on the frame rate used for capturing the sequence of images, i.e. the time difference between two time instances respectively associated with two subsequent images. The threshold speed may also depend on the magnitude of the applied force and, for example, the viscosity of the sample medium. An appropriate value for the threshold depends on the above-mentioned conditions. For a particular set of conditions, the threshold (or any other means of classification) can be determined from an annotated experimental dataset. This dataset will describe the classification for each cellular body (depending on the image frame), the cellular bodies can be tracked and their speed determined (or other features). The optimal/appropriate threshold can then be determined by finding the value that agrees best with the annotated dataset.
Further, the threshold may vary, for example in dependence of one or more parameters, such as in dependence of an applied force to the cellular bodies or any other parameter. The threshold value may be different for each pair of subsequent images of the sequence of images.
The sequence of images depicts the spatiotemporal response of the one or more cellular bodies while a force is applied to them. In an example, such force may be ramped up, in order to determine the amount of cellular bodies that detached from the functionalized wall surface as a function of the applied force. The movements of the one or more cellular bodies are thus preferably caused by the application of such force. Such force may be applied to the one or more cellular bodies using, for example, a centrifuge system and/or an acoustic wave generator.
In an embodiment, the method comprises determining an avidity curve based on the determination that the first cellular body is attached to the functionalized wall surface e.g. by plotting the number of attached cells as a function of applied force and classifying the first cellular body as attached or excluding the first cellular body from the analysis based on a speed of movement of the first cellular body.
In an embodiment, the method may include tracking second locations of second pixel groups in respective second images out of the sequence of images, each second pixel group in the second images representing a second cellular body out of the cellular bodies, wherein the second locations define a second trajectory of the second cellular body moving relative to the functionalized wall surface; determining one or more second speed values of the second cellular body at one or more positions of the second trajectory; and, classifying that the second cellular body is detached from the functionalized wall surface based on the one or more second speed values and the at least one threshold speed, preferably the classifying including determining that the one or more second speed values are higher than the at least one threshold speed.
This embodiment is advantageous in that the same threshold is used for determining whether a cellular body has detached from the functionalized wall surface. Also, in this embodiment, multiple cellular bodies are analyzed. The first images and second images may refer to the same images.
In an embodiment, the method may further include tracking third locations of third pixel groups in respective third images out of the sequence of images, the third images being later in the sequence of images than the first images, each third pixel group representing the first cellular body, wherein the third locations define a further part of the first trajectory; determining one or more further speed values of the first cellular body relative to the functionalized wall surface at one or more points of the further trajectory; and, classifying that first cellular body is detached from the functionalized wall surface based on the one or more further speed values, preferably the classifying including determining that the further speed is higher than the at least one threshold speed.
This embodiment enables to first classify cellular bodies as being attached to the functionalized wall surface, and then as being detached from the functionalized wall surface.
Preferably, the speed of the movement of the first cellular body is monitored in the sense that the speed of the movement is repeatedly calculated based on different sets of two or more images out of the sequence of images. In early images, depicting the situation at the beginning of an experiment for example, this speed may be lower than the threshold speed, as a result of which the cellular body is determined to be attached to the functionalized wall surface. In later images in the sequence of images, depicting the situation later in the experiment, the movement of the cellular body may be higher than the threshold speed, as a result of which the cellular body may be determined to be detached from the functionalized wall surface.
In an example, the speed is updated for every subsequent image for example in the sense that the speed is determined for each image based on the image and the preceding image.
In an embodiment, the method comprises determining that the first cellular body sits in a cluster, a cluster being an aggregation of cellular bodies, in the images when a force is applied to the first cells, and refraining from classifying the first cellular body in the cluster as attached to the functionalized wall surface and refraining from classifying the first cellular body in the cluster as detached from the functionalized wall surface.
Typically, the cellular bodies in the clusters are not bound to the functionalized wall surface.
The inventors have realized that a cellular body may be driven to such cluster and that it cannot be determined with certainty whether such cellular body is still attached to the functionalized wall surface or not. Therefore, classifying such cellular body as attached or not attached to the functionalized wall surface may introduce errors.
In such embodiment, determining that the first cellular body sits in a cluster comprises determining an intensity of a pixel group out of said pixel groups representing movement of the first cellular body, and determining that the intensity of the pixel group is higher than a threshold intensity, and based on the intensity being higher than the threshold intensity, determining that the first cellular body sits in a cluster.
Additionally or alternatively, determining that a cellular body has ended up in such cluster may also be performed by receiving one or more locations where such clusters are expected and/or identified (e.g. based on close proximity of many cellular bodies) and determining that the cellular body has reached such location. The locations of the clusters may also be determined simply at the end of the force application when the clusters have been actually formed.
In an embodiment, said first images comprise a first particular image and a second particular image, wherein the first particular image comprises a first particular pixel group out of said pixel groups at a first location in the first particular image and the second particular image comprises a second particular pixel group out of said pixel groups at a second location in the second particular image, wherein the first and second locations are different, and wherein the first particular image is associated with a first time instance and the second particular image is associated with a second time instance, and wherein the speed of the movement of the first cellular body relative to the functionalized wall surface is determined based on a time difference between the first and second time instance and a distance between said first location and second location.
In an embodiment, the determining a first speed of the first cellular body at a location at the first trajectory may comprise: determining or receiving time instances associated with two or more images, preferably two or more subsequent images, in which the first cellular body is located at or around one of the one or more locations of the first trajectory; and, determining the first speed based on the time instances and the locations of the first cellular body in the two or more images.
These embodiments provide a convenient manner for determining the speed. The distance between the first and second location may be expressed by an amount of pixels. The distance is for example 2.25 pixels. In particular, the first particular pixel group may have a center, such as a center of mass, and the second particular pixel group may also have a center, such as a center of mass. The distance between the first and second location may be the distance between the respective centers of the first and second particular pixel group. Information of more than two images may also be combined in order to achieve more accurate and/or less noisy results.
In an embodiment, said sequence of images comprises an initial image representing an initial situation in which the first cellular body is bound to the functionalized wall surface. In such embodiment, the method comprises detecting a pixel group at an initial location in the initial image representing the first cellular body being attached to the functionalized wall surface, preferably while the first cellular body does not move.
In an embodiment, the sequence of images may include one or more images of the holding space before applying the force to the cellular bodies, wherein the method may further comprise: detecting the location of the first cellular body in at least one of the one or more images of the holding space before applying the force to the cellular bodies, the location defining an initial location of the first cellular body bound to the functionalized wall.
The initial image may be understood to depict the initial situation in which preferably no force is actively applied, e.g. using an acoustic wave generator, to the one or more cellular bodies.
In an embodiment, said first images comprise a particular image, wherein the particular image comprises a particular pixel group out of said pixel groups at a particular location in the particular image. In such embodiment, the method comprises determining a distance between the particular location and the initial location, and determining that the determined distance is higher than a threshold distance, and, based on the determined distance being higher than the threshold distance, determining that the first cellular body is attached to the functionalized wall surface by means of a tether, such as a membrane tube.
In an embodiment, a distance between the initial location and a further location on the first trajectory and/or a shape of the first trajectory may be used to determine that the first cellular body is attached to the functionalized wall surface by means of a tether, such as a membrane tube.
These embodiments enable to more precisely determine a binding interaction between cellular bodies in that it enables to determine what type of binding is still present between the cellular bodies.
It should be appreciated that for the first cellular body to be determined at some time instance as being attached by means of a tether, such as a membrane tube, preferably both the speed is lower than the threshold speed and the distance between the particular location and the initial location is higher than a threshold distance.
The distances may be expressed as number of pixels.
If the distance is lower than said threshold distance, then the first cellular body may be determined to be a hinge cell referred to above.
It should be appreciated that a cellular body that has first been classified as attached by means of a tether may later, based on later images in the sequence of images, be classified as detached. Also, it should be appreciated that a cellular body may first be classified as a hinge cell, but later, based on later images in the sequence of images, as attached by means of a tether and/or as detached. Further, it should be appreciated that based on methods described herein, cellular bodies that have detached from the functionalized wall surface may be further classified in (i) detached cellular bodies that have been first classified as hinge cellular bodies, and/or (ii) detached cellular bodies that have been first classified as attached by means of a tether, or (iii) as detached cellular bodies that have not been classified as attached by means of a tether and have not been classified as a hinge cellular body.
In an embodiment, the sequence of images comprises initialization images representing the one or more cellular bodies binding to the functionalized wall surface, and wherein detecting a pixel group at an initial location in the initial image comprises
The detected pixel groups in the respective first images are detected at different locations in the respective first images, the different locations forming a tracking path, the tracking starting point of the tracking path defining a pop-up location in a tracking starting image out of the first images, the tracking starting image being associated with a tracking starting time instance. In such embodiment, the method comprises determining the distance between the initial location and the pup-up location, and determining a time difference between the tracking starting time instance and an force application time instance indicating a time instance at which a force was applied to the first cellular body, determining a speed based on the time difference between the tracking starting time instance and the force application time instance and on the distance between the initial location and the pop-up location, determining that this speed is lower than a second threshold speed and/or higher than a third threshold speed, and, based on this determination, determining that the first cellular body is associated with the initial location, e.g. determining that the first cellular body is attached to the functionalized wall surface at the initial location.
Since the initialization images represent the one or more cellular bodies binding to the functionalized wall surface and the first images, which comprise the tracking starting image, are used to classify that one or more cellular bodies are attached to the wall surface, the initialization images may be understood to come before the first images, and thus before the tracking starting image, in the sequence of images. In other words, the initialization images may be understood to represent the situation at an earlier time than the first images, and, consequently, than the tracking starting image.
In an embodiment, the method comprises determining detachment images out of the sequence of images, the detachment images being the earliest images in the sequence of images that comprise pixel groups representing a speed of movement of the first cellular body that is higher than said threshold speed.
This embodiment enables to accurately determine when during an experiment the first cellular body detached from the functionalized wall surface.
Determining the detachment images may be performed by monitoring the speed of the cellular body throughout the sequence of images, and determining in which images the speed of the cellular body exceeds the threshold speed for the first time.
The detachment images are for example comprised in said third images. The detachment images may thus be later in the sequence of images than the first images (and, consequently, than the tracking starting image) and later in the sequence than the initialization images.
Preferably, each image out of the sequence of images is associated with a value of a force applied to the first one or more cellular bodies and/or with a state of a force application system configured to apply a force to the first one or more cellular bodies. As a result, based on the determined detachment images, the force and/or state of the force application system can be determined at which the first cellular body detached from the functionalized wall surface.
In an embodiment, detecting the pixel groups in the respective first images comprises detecting a pixel group in an image out of the first images, the detected pixel group comprising pixels representing the first cellular body, said pixels having respective pixel values that distinguish them from pixels representing a background of the image, e.g. said pixels having a high intensity value. This embodiment further comprises determining a region of interest in the image, the region of interested comprising the pixels representing the first cellular body and pixels representing the background of the image, and analyzing said region of interest in a subsequent image out of the first images, and identifying in said region of interest pixels having respective pixel values that distinguish them from pixels representing a background of the subsequent image, determining said distinct pixels in the region of interest to represent at least part of the first cellular body, and, based on the identified pixels in the region of interest in the subsequent image, determining a further pixel group in the subsequent image representing the first cellular body.
This embodiment provides a convenient manner for tracking the movement of cellular bodies.
In an embodiment, the method comprises updating, e.g. shifting, the region of interest such that it comprises the further pixel group in the subsequent image, and analyzing said updated region of interest in a further subsequent image, subsequent to the subsequent image, out of the first images, and identifying in the updated region of interest pixels having respective pixel values that distinguish them from pixels representing a background of the further subsequent image, and determining said distinct pixels in the updated region of interest to represent at least part of the first cellular body, and, based on the identified pixels in the region of interest in the subsequent image, determining an even further pixel group in the further subsequent image representing the first cellular body.
This method also provides a convenient way for tracking the movement of cellular bodies throughout several images. This embodiment may namely be repeatedly performed in the sense that the region of interest is updated for every image.
Preferably, updating the region of interest is performed such that the updated region of interest comprises at its center the center of mass of the further pixel group.
One aspect of this disclosure relates to a method for determining interaction between cellular bodies, the method comprising for each of a plurality of cellular bodies represented in the sequence of images,
Another aspect of the disclosure relates to a method for determining interaction between cellular bodies, wherein the method may comprise: obtaining, e.g. determining or receiving, a sequence of images representing manipulating cellular bodies in a holding space, the holding space including a functionalized wall configured to bind the cellular bodies, the manipulating including applying a force on the settled cellular bodies away from the functionalized holding space; for each of a plurality of cellular bodies represented in the sequence of images: tracking locations of pixel groups in respective images out of the sequence of images, each pixel group in the images representing a cellular body out of the cellular bodies, the locations in the respective images defining a trajectory of the cellular body moving relative to the functionalized wall surface; determining one or more first speed values of the cellular body at one or more locations of the trajectory, the one or more speed values being higher than zero; and, classifying that the cellular body is attached to or detached from the functionalized wall surface based on the one or more speed values and at least one threshold speed value.
In yet another aspect, the disclosure may relate to a method for determining interaction between cellular bodies comprising: receiving a sequence of images representing cellular bodies bound to a functionalized wall of a flow cell and subsequent application a force on the cellular bodies; determining initial locations of cellular bodies that are bound to the functionalized in images representing the cellular bodies bound to the functionalized wall; tracking positions of the detected cellular bodies in images representing the application of a force on the cellular bodies, the tracked positions of a cellular body defining a trajectory of the cellular body moving in the flow cell; determining the travelling speed of a tracked cellular body for different positions on its trajectory; and, classifying a tracked cellular body based on the travelling speed and a speed threshold value, and, optionally, other parameters such as the initial position or the shape of the trajectory.
Of course, the methods described herein may be performed in parallel on many cellular bodies that are present in a single sequence of images. Thousands of cellular bodies may be analyzed in a single experiment.
This embodiment may comprise determining an avidity curve based on the respective determinations whether the cellular bodies are attached to the functionalized wall surface or not in relation to a force being applied to the cellular bodies.
One aspect of this disclosure relates to a method for determining interaction between cellular bodies comprising providing a sample holder comprising a holding space, wherein the holding space comprises, e.g. is substantially filled with, a fluid medium and comprises the functionalized wall surface, and the one or more cellular bodies in the fluid medium, wherein the one or more cellular bodies are bound the functionalized wall surface, and applying a force to the one or more cellular bodies for separating at least some of the one or more cellular bodies from the functionalized wall surface, and capturing a sequence of images from the one or more cellular bodies while said force is applied, and determining interaction between the one or more cellular bodies and functionalized wall surface based on the captured images in accordance with any of the preceding claims.
One aspect of this disclosure relates to a data processing system comprising a
One aspect of this disclosure relates to a computer program or suite of computer programs comprising at least one software code portion or a computer program product storing at least one software code portion, the software code portion, when run on a computer system, being configured for executing any of the methods described herein.
One aspect of this disclosure relates to a system for determining interaction between cellular bodies and a functionalized wall surface, the system comprising a sample holder comprising a holding space for holding a fluid medium, a functionalized wall surface and one or more cellular bodies, and a force generator for providing a force to the one or more cellular bodies in the holding space, and an imaging system for capturing images of the one or more cellular bodies in the holding space, and a data processing system as described herein.
The data processing system may be configured to control the force generator as well.
One aspect of this disclosure relates to a non-transitory computer-readable storage medium storing at least one software code portion, the software code portion, when executed or processed by a computer, is configured to perform any of the methods described herein.
As will be appreciated by one skilled in the art, aspects of the present invention may be embodied as a system, a method or a computer program product. Accordingly, aspects of the present invention may take the form of an entirely hardware embodiment, an entirely software embodiment (including firmware, resident software, micro-code, etc.) or an embodiment combining software and hardware aspects that may all generally be referred to herein as a “circuit,” “module” or “system.” Functions described in this disclosure may be implemented as an algorithm executed by a processor/microprocessor of a computer. Furthermore, aspects of the present invention may take the form of a computer program product embodied in one or more computer readable medium(s) having computer readable program code embodied, e.g., stored, thereon.
Any combination of one or more computer readable medium(s) may be utilized. The computer readable medium may be a computer readable signal medium or a computer readable storage medium. A computer readable storage medium may be, for example, but not limited to, an electronic, magnetic, optical, electromagnetic, infrared, or semiconductor system, apparatus, or device, or any suitable combination of the foregoing. More specific examples of a computer readable storage medium may include, but are not limited to, the following: an electrical connection having one or more wires, a portable computer diskette, a hard disk, a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or Flash memory), an optical fiber, a portable compact disc read-only memory (CD-ROM), an optical storage device, a magnetic storage device, or any suitable combination of the foregoing. In the context of the present invention, a computer readable storage medium may be any tangible medium that can contain, or store, a program for use by or in connection with an instruction execution system, apparatus, or device.
A computer readable signal medium may include a propagated data signal with computer readable program code embodied therein, for example, in baseband or as part of a carrier wave. Such a propagated signal may take any of a variety of forms, including, but not limited to, electro-magnetic, optical, or any suitable combination thereof. A computer readable signal medium may be any computer readable medium that is not a computer readable storage medium and that can communicate, propagate, or transport a program for use by or in connection with an instruction execution system, apparatus, or device.
Program code embodied on a computer readable medium may be transmitted using any appropriate medium, including but not limited to wireless, wireline, optical fiber, cable, RF, etc., or any suitable combination of the foregoing. Computer program code for carrying out operations for aspects of the present invention may be written in any combination of one or more programming languages, including an object oriented programming language such as Java™, Smalltalk, C++ or the like and conventional procedural programming languages, such as the “C” programming language or similar programming languages. The program code may execute entirely on the users computer, partly on the user's computer, as a stand-alone software package, partly on the users computer and partly on a remote computer, or entirely on the remote computer or server. In the latter scenario, the remote computer may be connected to the user's computer through any type of network, including a local area network (LAN) or a wide area network (WAN), or the connection may be made to an external computer (for example, through the Internet using an Internet Service Provider).
Aspects of the present invention are described below with reference to flowchart illustrations and/or block diagrams of methods, apparatus (systems), and computer program products according to embodiments of the present invention. It will be understood that each block of the flowchart illustrations and/or block diagrams, and combinations of blocks in the flowchart illustrations and/or block diagrams, can be implemented by computer program instructions. These computer program instructions may be provided to a processor, in particular a microprocessor or a central processing unit (CPU), of a general purpose computer, special purpose computer, or other programmable data processing apparatus to produce a machine, such that the instructions, which execute via the processor of the computer, other programmable data processing apparatus, or other devices create means for implementing the functions/acts specified in the flowchart and/or block diagram block or blocks.
These computer program instructions may also be stored in a computer readable medium that can direct a computer, other programmable data processing apparatus, or other devices to function in a particular manner, such that the instructions stored in the computer readable medium produce an article of manufacture including instructions which implement the function/act specified in the flowchart and/or block diagram block or blocks.
The computer program instructions may also be loaded onto a computer, other programmable data processing apparatus, or other devices to cause a series of operational steps to be performed on the computer, other programmable apparatus or other devices to produce a computer implemented process such that the instructions which execute on the computer or other programmable apparatus provide processes for implementing the functions/acts specified in the flowchart and/or block diagram block or blocks.
The flowchart and block diagrams in the figures illustrate the architecture, functionality, and operation of possible implementations of systems, methods and computer program products according to various embodiments of the present invention. In this regard, each block in the flowchart or block diagrams may represent a module, segment, or portion of code, which comprises one or more executable instructions for implementing the specified logical function(s). It should also be noted that, in some alternative implementations, the functions noted in the blocks may occur out of the order noted in the figures. For example, two blocks shown in succession may, in fact, be executed substantially concurrently, or the blocks may sometimes be executed in the reverse order, depending upon the functionality involved. It will also be noted that each block of the block diagrams and/or flowchart illustrations, and combinations of blocks in the block diagrams and/or flowchart illustrations, can be implemented by special purpose hardware-based systems that perform the specified functions or acts, or combinations of special purpose hardware and computer instructions.
Moreover, a computer program for carrying out the methods described herein, as well as a non-transitory computer readable storage-medium storing the computer program are provided. A computer program may, for example, be downloaded (updated) to the existing data processing systems or be stored upon manufacturing of these systems.
Elements and aspects discussed for or in relation with a particular embodiment may be suitably combined with elements and aspects of other embodiments, unless explicitly stated otherwise. Embodiments of the present invention will be further illustrated with reference to the attached drawings, which schematically will show embodiments according to the invention. It will be understood that the present invention is not in any way restricted to these specific embodiments.
Aspects of the invention will be explained in greater detail by reference to exemplary embodiments shown in the drawings, in which:
In the figures, identical reference numbers indicate identical or similar elements.
At the beginning of a measurement the cellular bodies are typically attached to the functionalized wall surface. The holding space 4 may be part of a flow cell (also referred to as a microfluidic cell). The system 2 may comprises a force generator 8 for providing a force to the one or more cellular bodies in the holding space 4. The force generator, in an embodiment, may be an acoustic wave generator based on a piezo element, connected to the sample holder 3 for generating a bulk acoustic wave in the holding space 4 so that a force is exerted on cellular bodies that may be present in the holding space 4. The force field generator 8 may be connected to a controller 10, which may be connected to a data processing system 100 as described herein, so that the force exerted on the cellular bodies can be controlled.
Further, the depicted system may comprise an imaging system configured to capture images of the one or more cellular bodies in the holding space 4. The imaging system may include a microscope 12 including optics, e.g. adjustable objective 14, and a camera 16 for capturing images, e.g. video frames, of the processes in the holding space 4. The imaging system may be connected to the data processing system 100 that is configured to perform any of methods, in particular the image analyses, as described in this application. The data processing system may also be configured to control any of the elements of the depicted system, such as the controller 10 and thus the force generator, and one or more, e.g. all, elements of the imaging system, which are further described below. An embodiment of the data processing system 100 is described in more detail with reference to
The imaging system may comprise a light source 1 for illuminating the sample, including the functionalized wall surface described herein, using any suitable optics (not shown) to provide a desired illumination intensity and intensity pattern, e.g. plane wave illumination, Köhler illumination, etc., known per se. Here, the light 22 emitted from the light source 1 may be directed through the force field generator 8 to (the sample in) the sample holder 3 and sample light 24 from the sample is transmitted through the objective 14 and through an optional tube lens 26 and/or further optics (not shown) to the camera 16. The objective and the camera may be integrated. In an embodiment, two or more optical detection systems, e.g. with different magnifications, may be used simultaneously for detection of sample light, e.g. using a beam splitter.
In another embodiment, not shown but discussed in detail in WO2014/200341, the system 2 may comprise a partially reflective reflector and light emitted from the light source is directed via the reflector through the objective and through the sample, and light from the sample is reflected back into the objective, passing through the partially reflective reflector and directed into a camera via optional intervening optics. Further embodiments may be apparent to the reader.
The sample light 24 may comprise light affected by the sample (e.g. scattered and/or absorbed) and/or light emitted by one or more portions of the sample itself e.g. by chromophores/fluorophores attached to the cellular bodies.
Some optical elements in the imaging system may be at least one of partly reflective, dichroic (having a wavelength specific reflectivity, e.g. having a high reflectivity for one wavelength and high transmissivity for another wavelength), polarization selective and otherwise suitable for the shown setup. Further optical elements e.g. lenses, prisms, polarizers, diaphragms, reflectors etc. may be provided, e.g. to configure the system 2 for specific types of microscopy.
The sample holder 3 may be formed by a single piece of material with a channel inside, e.g. glass, injection moulded polymer, etc. (not shown) or by fixing different layers of suitable materials together more or less permanently, e.g. by welding, glass bond, gluing, taping, clamping, etc., such that a holding space is formed in which the fluid and functionalized wall surface are contained, at least for the duration of an experiment. While, the system of
With the system depicted in
Further, the sample holder 3 may be connected to a fluid flow system 32 for introducing fluid and unbound cellular bodies, such as cells, into the holding space of the sample holder 3 and/or removing fluid from the holding space, e.g. for flowing fluid through the holding space (see arrows in
One or more software programs that run on the data processing system 100 of the system may be configured to control the camera, the force field generator and the flow cell to conduct different experiments. In a typical experiment, cellular bodies, e.g. effector cells, may be flushed into the holding space of the flow cell and may interact, e.g. bind, with elements provided on the functionalized wall surface, such as target cells or antigens. This interaction can be probed by analyzing the response of cellular bodies that are bound to the functionalized wall surface as a function of the applied force. As shown in the figure, an acoustic force is applied perpendicularly to the cellular bodies bound to the functionalized wall surface (indicated with upward open arrows) and one or more cellular bodies may detach from the target cells and migrate to the acoustic node at a certain applied force (migration vectors for the cellular bodies are indicated with solid black arrows in
For both hinge cells and tether cells it may be preferred not to count them as detached and/or to not count the force at which the cell first moves as a detachment force because the underlying bond at the cell-cell attachment focus has not ruptured at the moment of first movement of the cells. This way, parameters like avidity curves may be improved by not counting these events or by classifying them differently.
The incubation phase may be imaged and when the cells are introduced into the holding space and move towards the functionalized wall, groups of pixels representing cells in the captured images may be detected and tracked. After the incubation phase, a force may be applied to the cellular bodies 50 that are bound to the functionalized wall surface. The force may have a direction away from the functionalized wall surface, e.g. substantially perpendicular to the functionalized wall surface. Typically, a force ramp will be applied to the cellular bodies, so that if the force becomes larger than a binding force, they will start to move away from the functionalized wall surface in the direction of the force (
When the force is sufficiently large, a cellular body will move away from the functionalized wall surface in a direction that depends on the applied force, which may have an axial component perpendicular to the functionalized wall (e.g. the z-direction) and two lateral components in the plane of the functionalized wall (e.g. the x and y direction). As discussed with reference to
Based on a measurement scheme as described with reference to
The cellular bodies are schematically depicted as black solid circles in the images. The cellular bodies are typically represented by pixel groups formed by pixels having a value that distinguishes them from pixels representing background, e.g. representing the functionalized wall surface. In an embodiment, pixels in the pixel groups representing the cellular bodies for example have a relatively high intensity. For example, cellular bodies may have been fluorescently labelled which may have caused the cellular bodies to light up against a dark background upon appropriate illumination. In another embodiment, a pixel group may have a particular features, e.g. shape and/or size, that matches features of a cellular body.
Each black solid circle in the images A-F may be understood to be a pixel group as referred to in this disclosure. To illustrate, 64 indicates a pixel group in image A, 66 indicates a pixel group in image B, 68 indicates a pixel group in image C, 70 indicates a pixel group in image D, 72 indicates a pixel group in image E, 74 indicates a pixel group in image F. Further, these pixel groups 64-74 represent the same cellular body. As such, these pixel groups 64-74 represent a movement of the cellular body relative to the sample surface. Similarly, pixel groups 76, 78, 80, 82 in respective images A, B, C, D, represent a movement relative to the functionalized wall surface of another cellular body represented in the sequence of images.
The images show that there are two clusters of cellular bodies, indicated by 84 in image A. These clusters may be formed by a standing acoustic wave generating a force that directs all separated cellular bodies to a node of the acoustic wave. This causes the cellular bodies to accumulate in regions 84. During an experiment more and more cellular bodies typically separate from the functionalized wall surface, for example due to the force applied to the cellular bodies increasing. This may result in more and more accumulation in the cluster regions. 84.
Image A may be understood to be an initial image, at least for the cellular body represented by pixel group 76 and the cellular body represented by pixel group 64 in the sense that these cellular bodies are bound to the functionalized wall surface and/or in the sense that they at the same position as they were before any force was applied to the cellular bodies, i.e. they have not moved yet during the experiment. Pixel group 76 thus defines an initial location for one cellular body and pixel group 64 another initial location for another cellular body. In fact, it can be assumed for clarity in the explanation here that each cellular body that is not in a cluster 84 at the time image A was captured is at its initial position, i.e. has not moved since the beginning of the experiment.
The pixel groups representing cellular bodies at their initial position may be detected based on the aberrant values of their pixels relative to the values representing a background of the image, e.g. representing the functionalized wall surface.
The speed of a cellular body moving along its path can be determined based on the distance between “adjacent” pixel groups on the path. To illustrate, the speed—at the beginning of the experiment—of the movement of the cellular body represented by pixel group 76 can be determined based on the distance 92 and the time difference between the time instance respectively associated with image A and image B. The distance may be expressed as a pixel distance, for example may be 3.6 pixels. The speed determined in such manner may be compared to a threshold speed. In an embodiment, the speed of cellular body represented by pixel group 76 is higher than this threshold. Based on this determination, it may be determined that this cellular body has detached from the functionalized wall surface.
Cellular body represented by pixel group 90 in image A is different in that sense. As can be seen from the figure, this cellular body has moved, yet at relatively low speed. Again, this speed may be compared, in an embodiment, to a threshold value, preferably the same threshold value as above, and it may be determined that this cellular body is still attached to the functionalized wall surface. Even further, it can be seen that this cellular body does not move further from its initial position, indicated by pixel group 90 (the solid circle) than a threshold distance. The threshold distance is indicated by circle 98. Based on determining that this cellular body has not travelled further than this threshold distance, it may be determined that this cellular body is a hinged cell, meaning that it is tightly attached to the functionalized surface at a point which is displaced laterally with respect to the center of mass of the cellular body in relation to the direction of the applied force. Cellular body represented by pixel groups 64-74 is also different. Up until image D (pixel group 70), the speed is relatively low, in this example lower than the threshold speed. Based on determining that the speed of the movement is lower than the threshold speed, it may be determined that this cellular body is attached to the functionalized wall surface, at least up until the time instance associated with image D. Even further, it can be seen that in image C (pixel group 68) this cellular body has travelled a distance 99 from its initial position 64. This distance may be determined and it may be determined that this distance 99 exceeds the threshold distance indicated by the circle around pixel group 64. Based on the latter determination, it may be determined that this cellular body is attached to the functionalized wall surface by means of a tether, such as a membrane tube, at least up until image D (pixel group 70).
After image D, the speed of the movement of cellular body represented by pixel groups 64-74, suddenly increases. This speed may be determined based on distance 96 and on the time difference between the time instances associated respectively with images D and E. As a side note, the time difference between two subsequent images is typically constant and related to a so-called frame rate of the imaging system. The speed of this “further movement” of the cellular body exceeds the threshold speed. Based on determining that this is indeed the case, it may be determined that the cellular body has detached from the functionalized wall surface.
Typically, the speed of a cellular body throughout a video is constantly monitored so that it can be determined easily when exactly the speed exceeded the threshold speed. This may provide valuable information, for example at which forces and/or at which distances from its initial position and/or at which state of the force generator the cellular body separated from the functionalized wall surface.
In an embodiment, the method may then comprise determining detachment images which are the earliest images in the sequence of images that comprise pixel groups representing a speed of movement of the first cellular body that is higher than said threshold speed. In the above example, the detachment images would then be image D (pixel group 70) and image E (pixel group 72), because these images are the first images in the video based on which the determined speed exceeds the threshold speed. As time of detachment a time between time instance associated with image D and time instance associated with image E may be selected. Alternatively, the time instance of image D or E may be regarded as time of detachment.
Cellular body represented by pixel group 84 in image A does not move in the sequence of images A-F. Hence, it may be determined that this cellular body is attached to the functionalized wall surface.
Cellular body represented by pixel group 88 in image A can first, based on images A, B, C be determined to be attached to the functionalized wall surface, in particular as a hinged cell. However, the speed determined based on images D and C, in this example, exceeds the threshold speed. Hence, it may be determined that this cellular body has detached from the functionalized wall surface.
A cellular body classified as hinge cell may move faster than a certain threshold th1 and less than a second threshold th2 (e.g. indicated as 98 in 6A). A cellular body that moves less than th1 may be classified as an attached cell (e.g. 84) and may at a later stage turn into a cell detaching directly (such as 76->78 and 86) or it may become a hinge or tether cell.
Cellular body represented by pixel group 86 immediately travels at a speed higher than the threshold speed to cluster area 84a. Hence, it may be determined as detached from the functionalized wall surface.
Cellular body represented by pixel group 120 in image A travels at relatively low speed, and further than the threshold distance. Hence, this cellular body may at first be classified as a tethered cellular body. However, the cellular body in image E has reached a cluster 84b. Based on determining that this is the case, this cellular body may be disregarded in the experiment, for example by refraining from classifying the cellular body as detached from or attached to the surface.
Then, the same region of interest 122 is analyzed in image B, i.e. an image subsequent to image A. It is then found that pixel group 76 no longer has aberrant pixel values, yet only pixels representing background. In an embodiment, the method comprises identifying pixels in region of interest 122 in image B that do have pixel values that distinguish them from pixels representing background. In this example, pixels at the bottom of region interest 122 in image B are identified.
Then, based on these identified pixels, pixel group 78 may be determined. This may comprise identifying all pixels that are adjacent the identified pixel at the bottom of region interest 122, which also have values distinguishing them from the background. Then, pixel group 78 in image B may be determined to represent the same cellular body as pixel group 76 in image A.
Then, as shown in image B at the bottom left of
Subsequently, this updated region of interest 122′ can be analyzed in a further subsequent image C and again pixels can be identified having aberrant values. These pixels may be determined to also represent the same cellular body that is tracked. Again, based on the identified pixels in the updated region of interest 122′ in image C, a pixel group 80 in image C can be determined to represent the same cellular body.
These steps may be repeated, which results in the tracking of a cellular body throughout the video wherein the locations of the cellular body in subsequent images may form a trajectory of the cellular body moving in the flow cell due to the applied force.
It should be understood that sometimes the cellular body moves so fast that its movement cannot be tracked, which may result in a tracking error. This may also be dependent on the size of the region of interest that is chosen. It should be appreciated that determining the speed of the movement of a cellular body may be performed by determining that a cellular body cannot be tracked. This may namely be understood to be determining the speed in the sense that it is determined that the speed is higher than the maximum speed at which a cellular body can be tracked.
Another tracking mechanism for tracking cellular bodies that may be used may be based on a global minimization of distances between pixel groups representing cellular bodies in subsequent images. This may allow tracking of faster cellular bodies or tracking using smaller regions of interest.
Below, a pseudo-code is provided that illustrates a tracking method according to an embodiment that is based on a similarly score, e.g. the so-called structural similarity index measure (SSIM) score. The SSIM score is well is known in the art, see for example the article by Wang et al, 2004 Apr. 1). “Image quality assessment: from error visibility to structural similarity”. IEEE Transactions on Image Processing. 13]). The SSIM comparison yields a score of 0 for no structural similarity and 1 for identical images.
Initialize ROIs and Create Reference ROI Images for SSIM Algorithm:
For a First Image in the Image Sequence
For all Images in the Sequence of Images:
For all Cellular Bodies:
Run Fixed ROI Tracker:
Run Moving ROI Tracker:
Classify Cellular Body Type (Normal Cell, Hinge Cell, Tether Cell, Cluster Error):
Classify Cellular Body Presence Based on Cellular Body Type and Presence Results of the 2 Trackers:
After Last Frame:
Filtering of Cellular Bodies Based on Cellular Body Type:
In step 1 of the code, the size of a region of interest (ROI) of a so-called “fixed tracker ROI size” parameter is set to a size of 12×12 pixels. This parameter defines the size of the area that will be used to track a cell. In step 2, the initial locations of detected cellular bodies that are bound to the functionalized wall of the flow cells are determined using a known image recognition algorithm (such as template matching or a blob selection method). In step 3, ROIs in an initial image which represent cellular bodies, are initialized at the locations determined in step 2. These ROIs comprise the pixel groups representing respective cellular bodies. An initial image may depict the situation at the beginning of an experiment when no force is actively applied to the cellular bodies. In step 4, the identified pixel groups, i.e. the cellular bodies, in the initial image are stored as ROI reference images. Thus, each cellular body is associated with its own ROI, a fixed ROI location within the image, and a ROI reference image.
In step 5, the so-called “moving tracker ROI size” is set to a predetermined size, e.g. 30×30 pixels. In step 6, the moving tracker ROIs are initialized at locations found in step 2. In step 7, the moving tracker ROI ref images are defined. This reference image that is used by the moving tracker may comprise pixels that have the same pixel value. In an embodiment, this pixel value may represent a median value of all pixel values in the initial images. In this manner, the moving tracker reference image is a homogeneous image having pixel values that are similar to the pixel values of the background of the image, e.g. similar to the functionalized wall surface. Thus, each cellular body is additionally associated with its own moving tracker ROI, moving tracker ROI location, and moving tracker ROI reference image.
Steps 8-20 are performed for all or at least a substantial part of the cellular bodies in the video frames. Steps 8 and 9 relate to the fixed tracker, which is configured to determine whether a cellular body is positioned at its initial position or not. In step 8, a similarity score, such as an SSIM score, may be determined based on the fixed tracker reference image for a cellular body in question and the fixed ROI of the image in question. If the similarity score is higher than a predetermined threshold, 0.2 in this example, then a Fixed tracker present state—True, meaning that the cellular body has not moved (significantly) from its initial position (see step 9).
Steps 10-13 relate to a so-called “moving ROI tracker” algorithm which is configured to track a cellular body as it moves relative to the functionalized wall surface. The algorithm may be configured to determine if a pixel group representing a cellular body is still present inside the moving ROI and compute the current location of the determined pixels group. Steps 11-13 are performed while Moving tracker present state is true. In step 11, the center of mass is determined of the pixel group representing the cellular body in question in the frame in question and the ROI position is updated. This may be performed as described with reference to
Steps 14-17 relate to the classification of the cellular body. This classification may be performed for each cellular body, in each frame of the video. In step 14, if both the fixed tracker presence state has been false for at least a number of frames, for example 4*framerate (i.e. for four seconds in reality), and if the moving tracker presence state is true, then the cell is preliminary classified as a hinge cell. In step 15, it is further checked whether the distance from the initial position for the cellular body in question exceeds a predetermined threshold, 30 pixels in this example. If this is the case and if the cellular body was preliminary classified as hinge cell, then, the cellular body is classified as a tethered cellular body. In step 16, it is checked whether the cellular body has reached a cluster. The algorithm may check this based on an intensity value. In this example, if the pixels values of the updated ROI have a higher mean intensity than 1.5 times the initial ROI, then a cluster error is determined. In step 17, if the cellular body has not been classified in any of steps 14, 15, 16, then it is classified as a normal cellular body.
In step 18, a presence of a normal cellular body is determined to be given by the fixed ROI tracker presence. Thus, if the value for the fixed ROI tracker is true, then the cellular body has not moved and may be counted as a cellular body that is still attached to the functionalized wall surface. In step 19, cellular bodies in clusters are excluded. These cellular bodies are not counted as attached nor as attached. In step 20, the presence of hinge cellular bodies and tethered cellular bodies is given by the moving tracker presence.
Finally, in step 21, which is performed after all frames have been analyzed, cellular bodies are filtered based on type—normal, hinge, tether. Since the type for a cellular body may be updated, and thus changes, in each new frame, it should be understood that the type based on which the cellular bodies are filtered after the experiment may be the type they were last assigned.
By filtering, a user can choose to dismiss for example tethered cellular bodies from an avidity analysis, for example in the sense that they are not counted as detached from the functionalized wall surface. The normal cellular bodies, if their presence is true, may be counted as still attached to the functionalized wall surface. The cluster error cellular bodies may preferably not be counted. The hinge cells may be counted as attached to the functionalized wall surface. The “tether” cellular bodies may be disregarded from an avidity analysis altogether, because, in spite of being still bound to the functionalized wall surface, it is doubtful whether these cellular bodies showed desired binding properties that a researcher is investigating.
It should be appreciated that the above described methods for tracking a cellular body may also be employed for tracking cellular bodies in the initialization images described herein. When a cellular body can no longer be tracked by such tracking algorithm it may be determined that the cellular body has settled onto the functionalized wall surface. In such case, the cellular body may no longer be trackable because, once settled, it may not be distinguishable anymore from the functionalized wall surface.
Thus, the above described algorithm and insights allow accurate classification of cellular bodies during force spectroscopy using an AFS system or another suitable force spectroscopy system.
Before a force is applied to the cellular bodies, initial locations of cellular bodies that are bound to the functionalized may be determined in the sequence of images using well known image recognition techniques (step 202). Thereafter, the positions of the detected cellular bodies are tracked while an increasing force (a force ramp) may be applied to the bound cellular bodies (step 204). The force may cause some of the cellular bodies to be pulled away from the functionalized wall and start moving. The positions in subsequent video frames of a tracked cellular body may define a trajectory of the cellular body moving in the holding space. During the tracking of the position of the cellular bodies in the holding space, the travelling speed of the cellular bodies may be determined and monitored (step 206). The travelling speed of a cellular body at a certain point on the trajectory may be determined based on one or more images that comprise a representation of that cellular body around that point, e.g. two or more earlier video frames.
The tracked cellular bodies may then be classified based on the determined speed (step 208). If the speed at a certain point on the trajectory is larger than a predetermined threshold value, then a cellular body may be classified as a detached cellular body. If the speed at a certain point on the trajectory is smaller than the predetermined threshold value, then the cellular body may be classified as attached (despite the fact that the cellular body is moving). Further, the class of cellular bodies which have a speed larger than zero and which are classified as attached, may be further (sub)classified on the basis of other parameters such as a distance between the initial position and a further position, the shape of the trajectory, or any other suitable parameter or combination of parameters. For example, based on the distance (or another suitable parameter), such cellular body may be either classified as a hinged cellular body or a tethered cellular body.
The memory elements 104 may include one or more physical memory devices such as, for example, local memory 108 and one or more bulk storage devices 110. The local memory may refer to random access memory or other non-persistent memory device(s) generally used during actual execution of the program code. A bulk storage device may be implemented as a hard drive or other persistent data storage device. The processing system 100 may also include one or more cache memories (not shown) that provide temporary storage of at least some program code in order to reduce the number of times program code must be retrieved from the bulk storage device 110 during execution.
Input/output (I/O) devices depicted as an input device 112 and an output device 114 optionally can be coupled to the data processing system. Examples of input devices may include, but are not limited to, a keyboard, a pointing device such as a mouse, a touch-sensitive display, or the like. Examples of output devices may include, but are not limited to, a monitor or a display, speakers, or the like. Input and/or output devices may be coupled to the data processing system either directly or through intervening I/O controllers.
In an embodiment, the input and the output devices may be implemented as a combined input/output device (illustrated in
A network adapter 116 may also be coupled to the data processing system to enable it to become coupled to other systems, computer systems, remote network devices, and/or remote storage devices through intervening private or public networks. The network adapter may comprise a data receiver for receiving data that is transmitted by said systems, devices and/or networks to the data processing system 100, and a data transmitter for transmitting data from the data processing system 100 to said systems, devices and/or networks. Modems, cable modems, and Ethernet cards are examples of different types of network adapter that may be used with the data processing system 100.
As pictured in
In one aspect of the present invention, the data processing system 100 may represent a controller 10 as described herein or a data processing system configured to perform any of the methods described herein.
Various embodiments of the invention may be implemented as a program product for use with a computer system, where the program(s) of the program product define functions of the embodiments (including the methods described herein). In one embodiment, the program(s) can be contained on a variety of non-transitory computer-readable storage media, where, as used herein, the expression “non-transitory computer readable storage media” comprises all computer-readable media, with the sole exception being a transitory, propagating signal. In another embodiment, the program(s) can be contained on a variety of transitory computer-readable storage media. Illustrative computer-readable storage media include, but are not limited to: (i) non-writable storage media (e.g., read-only memory devices within a computer such as CD-ROM disks readable by a CD-ROM drive, ROM chips or any type of solid-state non-volatile semiconductor memory) on which information is permanently stored; and (ii) writable storage media (e.g., flash memory, floppy disks within a diskette drive or hard-disk drive or any type of solid-state random-access semiconductor memory) on which alterable information is stored. The computer program may be run on the processor 102 described herein.
The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. As used herein, the singular forms “a,” “an,” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. It will be further understood that the terms “comprises” and/or “comprising,” when used in this specification, specify the presence of stated features, integers, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and/or groups thereof.
The corresponding structures, materials, acts, and equivalents of all means or step plus function elements in the claims below are intended to include any structure, material, or act for performing the function in combination with other claimed elements as specifically claimed. The description of embodiments of the present invention has been presented for purposes of illustration, but is not intended to be exhaustive or limited to the implementations in the form disclosed. Many modifications and variations will be apparent to those of ordinary skill in the art. The embodiments were chosen and described in order to best explain the principles and some practical applications of the present invention, and to enable others of ordinary skill in the art to understand the present invention for various embodiments with various modifications as are suited to the particular use contemplated.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2026548 | Sep 2020 | NL | national |
This application is a Section 371 National Stage Application of International Application No. PCT/NL2021/050573, filed Sep. 23, 2021, and published as WO 2022/066009 A1 on Mar. 31, 2022, and further claims priority to Netherlands Patent Application No. 2026548, filed Sep. 25, 2020.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/NL2021/050573 | 9/23/2021 | WO |
