Method and system for identifying the position of bacterial colonies on a culture plate

Abstract

This device configures a culture plate to accurately assign coordinates to selected colonies by assigning fiducials to the culture plate using a simple mechanical technique. The fiducials correspond to the center of the plate and the center of a barcode label applied to the side of the culture plate by the device. The device then deploys a mechanism to apply coordinates to the colonies identified by the user relative to the fiducials. One such mechanism is a webcam aimed at the culture plate, allowing a technician to mark colonies on the display using a computer mouse or equivalent cursor. Another mechanism deploys a laser pointer aimed at the colony, and the device assigns coordinates to the location of the colony at which the laser pointer is aimed. In a third mechanism, the user views the surface of the culture plate through a viewfinder and manually aligns the coordinates when the viewfinder's crosshairs are over the target colony. The selected colony is assigned precise coordinates by referencing the two fiducials. Software is provided so that pixels in the image of the culture plate correspond to coordinates on the culture plate relative to the fiducials.

Description

Technical Field

[0001] Cross - References to Related Applications This application claims the benefit of U.S. Provisional Application No. 62 / 867,560, filed Jun. 27, 2019, which is hereby incorporated by reference herein in its entirety.

Background Art

[0002] For various reasons, from determining whether a patient is infected with a microorganism to determining whether a food is contaminated with a microorganism, products and samples are routinely tested for microbial contamination. Since such tests are performed everywhere, large - scale laboratories have been developed that can test hundreds or thousands of such samples. To provide high throughput and low overhead in the laboratory, these laboratories are highly automated, reducing the number of technicians required to perform such tests. One such automated platform is described in WO2016 / 191646, entitled "Automated Methods and Systems for Obtaining and Preparing Microbial Samples for Both Identification and Antibiotic Susceptibility Testing", published on Dec. 1, 2016, and assigned to the assignee of the present application. Such a platform supports the goal of Total Laboratory Automation (TLA) by providing Work Cell Automation (WCA) of the functions performed by the automated platform. That application describes an automated system for preparing a portion of a microbial colony collected for a specific test. Microbial colonies are collected from culture plates inoculated with biological samples (e.g., blood samples, urine samples, fecal samples, saliva samples, etc.). The inoculated culture plates are cultured to promote the growth of one or more colonies of microorganisms that may be present in the biological sample. The automated system locates the target colony from the inoculated culture plate, then an automated sampling tool moves to the location of the target colony and collects the colony. Next, the automated system prepares the collected colony for tests to determine the identity and antibiotic susceptibility of the microorganism that makes up the colony.

[0003] Automation of the picking requires determining the coordinates of the target colonies on the culture plate and transmitting those coordinates to a picking tool used to obtain a portion of the colonies from the culture plate. In a fully automated system, these coordinates can be obtained from a digital image of the culture plate where the positions of the target colonies in the image are identified. These coordinates are provided with reference to a fiducial attached to the culture plate. Such fiducials can be markings on the culture plate, markings on the medium itself, and barcodes on the culture plate. A machine vision device can be used to detect another reference point, such as the center of the dish, from which the coordinates of the dish can be determined. The position of a colony on the dish can be determined with reference to the relative distance from the center and the angular offset to a zero offset from one or more of the other reference markings. Once the relative position of the colony is determined, the dish can be moved to another system and the next two steps can be performed. First, the dish is centered either manually or by mechanical means. The reference zero offset is detected, for example, by rotating the dish with a fixed sensor to detect the presence of a barcode label reference and scanning the barcode with a barcode scanner. At this point, the center of the dish is known and the zero offset of the barcode is known. Therefore, it is stored as the distance to the center of the dish and the angular offset to the barcode label, so that the previously referenced position of the colony can be easily calculated.

[0004] The above method does not require a camera or computer vision system in a colony picking system or any other system where colony position information is required. The automation device determines the coordinates from the reference fiducials on the culture plate or is applied by the user to identify the coordinates of the target colonies in the coordinate space on the plate. However, such a device requires determining the colony coordinates from an image of the culture plate. Therefore, there is a need for an apparatus and method for localizing colonies on a culture dish without the need for a prior digital image to provide such position coordinates. SUMMARY OF THE INVENTION

[0005] What is described herein is an apparatus that allows a user to manually mark a target colony to associate the position of the colony within a coordinate space, or to enable viewing of an imaging device such as a web camera directed at a culture plate, and allows the user to mark or otherwise align the coordinates of the colonies on the plate that are directly visible to the user in the displayed image of the plate via the web camera. Marking of colonies and alignment of their coordinates can be achieved by various mechanisms, such as aligning colony coordinates using a laser pointer directly on the plate or on an image of the plate, or by moving a cursor over an image of the colony and clicking the mouse to align the coordinates of the cursor (and thus to the colony over which the cursor is overlaid). Thus, the actual coordinates of the plate need to correspond to the coordinates of either the user's view of the plate or the web camera video of the plate. The coordinates are related to two references, and each coordinate is captured in relation to each reference. For example, one reference is the midpoint of a barcode label affixed to the side of the plate, and the second reference is the midpoint of the plate. The apparatus applies the barcode label to the plate in a repeatable manner such that the midpoint of each label on each culture plate is fixed. The apparatus determines the radius and angle of the culture plate in radians. The angle is between two lines, where the first line is an imaginary line between two references (e.g., the label and the center of the dish), and the second line is a line from one of the references (e.g., the center of the dish) to the position of the colony (i.e., the coordinates of the colony relative to the position of the reference). The allowable error in the placement of the colony collection tool is approximately ±1 mm. A small allowable error is necessary to prevent the collection tool from missing a colony or collecting from a colony without an adjacent mark. The size of the colony greatly affects the placement accuracy required for the collection tool. After the apparatus positions the plate at the center and positions the barcode at a fixed position on the dish, the apparatus determines the coordinates of the target colony. These coordinates are then associated with a system within the apparatus that determines the coordinates of the target colony within the dish coordinate space, or stored and saved in a memory or database that is connected.The diameter of the plate that can be used in the device described in this specification is from about 85 mm to about 90 mm.

[0006] When the device determines the position of the colonies on the dish taken with respect to the reference markings (i.e., the plate center and the label), the coordinates of the colonies in the plate coordinate space are stored in the database. When the plate is loaded into the device from which the colonies are taken (i.e., the following sampling tool), the barcode on the plate is scanned, and the coordinates of the colonies to be taken are transferred to the sampling tool (or, if manually sampling the coordinates for the technician to convey, to the user interface). After the coordinates are provided to the sampling tool or the user interface, the sampling tool contacts the marked colonies and the colonies are taken.

[0007] Described herein is a device having a table on which a dish clamp is disposed, the dish clamp including a platform supported by the table on which a culture dish is manually placed and a chuck for fixing the culture dish on the platform. This table also includes a colony marking device including a viewfinder through which a user can view the colonies and assign coordinates to the colonies with respect to at least two reference marks. The device has a label dispenser. The label dispenser includes a wheel mount for receiving a roll of substrate carrying a plurality of labels, the plurality of labels having an adhesive applied to the outer surface of the labels not attached to the substrate strip. The label dispenser also includes at least one tension roller for applying tension to the substrate strip pulled from the roll. The label dispenser also includes a biasing roller assembly that urges the roller to engage the back side of the substrate strip, thereby urging the outer surface of the label to which the adhesive is applied to contact the side of the culture dish. This table also includes a processor for assigning the coordinates of the selected colonies with respect to the label of the culture dish and the center of the culture dish.

[0008] The viewfinder includes an angled mirror and crosshairs on the focal plane of the viewfinder. The apparatus further includes a label sensor proximate to the biasing roller assembly, and the label sensor identifies the edge of a label carried by a substrate strip as a reference mark. A controller is communicatively coupled to the label sensor and the biasing roller assembly. The biasing roller assembly is biased to a first position away from the culture dish and, when the label sensor detects a label carried by the substrate strip, prompts the label to contact the culture dish. A memory is provided, and the memory stores the coordinates of selected colonies with respect to the label affixed to the culture dish. A coordinate map of the culture dish is stored in the memory. The coordinates within the map are related to the label of the culture dish and the center of the culture dish. The apparatus further includes an imaging device, and the imaging device acquires an image of the culture dish and colonies are selected from the image of the culture dish. A camera is an example of the imaging device. In one embodiment, the image of the culture dish is provided on a touch screen display or a point-and-click display.

[0009] The device can be used in a method for assigning coordinate positions to colonies of microorganisms on a culture plate. In one embodiment of this method, the culture dish is placed in a chuck for fixing the culture dish to a table or platform. An imaging device including an image sensor is provided to capture an image of the culture dish placed on a platform to which the imaging device is coupled to a display for displaying the image of the culture dish captured by the imaging device. This method includes dispensing a label onto the culture dish using a label dispenser. The label dispenser has a wheel mount for receiving a roll of substrate strips carrying a plurality of labels. The plurality of labels have an adhesive applied to the outer surface of the labels not attached to the substrate strip. The label dispenser also includes at least one tension roller for applying tension to the substrate strip pulled from the roll. The label dispenser also includes a biasing roller assembly that urges the roller to engage the back side of the substrate strip, thereby urging the outer surface of the label with the adhesive applied to contact the side of the culture dish. This method includes assigning coordinates of a selected colony from the display relative to the label of the culture dish and the center of the culture dish. The user selects the target colony on the display, and the processor associates the user's selection with the coordinates of the culture dish relative to the center of the dish and the edge of the label.

[0010] In one exemplary embodiment, the imaging device is a web camera. The device further includes an adjustable mounting arm supported by a table and including a holder carrying the web camera. The label dispenser can further include a label sensor proximate to the biasing roller assembly, and the label sensor detects the edge of the label carried by the substrate strip. The device includes a controller communicatively coupled to the label sensor and the biasing roller assembly. The biasing roller assembly is biased to a first position away from the culture dish and, when the label sensor detects a label carried by the substrate strip, urges the label into contact with the culture dish.

Brief Description of the Drawings

[0011]

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Embodiments for Carrying Out the Invention

[0012]

Table 1

[0013] What is described in this specification is a device that accurately indicates the position of microbial colonies on a culture plate. As described above, biological samples (e.g., animal body fluids (e.g., blood, urine) and tissues, environmental samples (e.g., water, air), food samples, etc.) are often evaluated to determine whether the sample is contaminated or, in the case of a patient, infected with microorganisms (e.g., bacteria, viruses, yeast, fungi, parasites). Usually, biological samples obtained from an animal subject are tested for bacterial infection.

[0014] Biological samples arrive at the laboratory in various forms (body fluids such as urine, blood, sputum, pus, feces, cerebrospinal fluid, tissue samples, etc.) and formats (sample tubes, swabs, etc.). The sample is inoculated onto the medium placed on the plate. Next, the inoculated plate is cultured to ensure the time for the microorganisms to grow if they are present in the sample. The cultured culture plate 100 is shown in FIG. 1A. The culture plate has microbial colonies 110 growing on the medium 120.

[0015] BD Kiestra (trademark) InoqulA (trademark) helps rationalize workflows by automating the processing of both liquid and non-liquid bacteriological specimens, enabling a standardized process and ensuring a consistent high-quality streak for inoculation of solid growth medium 120. The medium is inoculated with the sample by any conventional means such as depositing the sample on the medium and traversing the surface of the medium with a magnetically controlled metal ball. Methods for inoculating the sample into the medium are well known to those skilled in the art and are not described in detail herein. Different inoculation patterns are used for different types of samples.

[0016] After the colonies 110 have grown to a size sufficient to provide an appropriate amount of colonies for downstream testing, the colonies are taken from the culture plate. This may seem like a fairly simple task for a laboratory technician, but manually taking colonies is actually very difficult because accuracy is required to take accurate colonies. As a result, the sampling is subject to errors and is certainly time-consuming. Therefore, automating such a process is beneficial because it requires less human labor and improves accuracy and efficiency. However, automating the colony localization process can be costly because expensive imaging devices and software are required. Once the colony localization information is obtained, it is shared with other devices that actually obtain a portion of the colony from the plate. This requires the imaging device not only to identify the colonies to be taken, but also to communicate the positions of the target colonies to an automated device that obtains the colonies from the culture plate. As described above, some laboratories do not have the advantage of imaging devices and software that acquire images of culture plates, evaluate the images, and identify the positions of target colonies within the images and those target colonies within the coordinate space of the plate.

[0017] In these systems, since the colony coordinates are not provided from an image of the plating culture on which the colony lies, a reference needs to be present on the culture dish before the colony is marked. In embodiments where one of the references is a label, the label is affixed using the apparatus described herein. The midpoint of the label is used together with the center of the plate to determine the radius and angle of the marked colony relative to these references. In one embodiment, the apparatus secures the label to the side of the plate. In further embodiments, since the colonies are not marked from an image of the culture dish, the apparatus has a store of labels disposed on the culture plate provided to the apparatus for colony marking.

[0018] Before applying the label to the culture dish, the plate must first be centered in the apparatus. One of ordinary skill in the art will appreciate that there are many different apparatuses having a chuck for centering a circular article therein. One such apparatus is described in U.S. Patent Application No. 62 / 697,197, filed July 12, 2018, entitled "System and Method for Centering a Circular Object," which is assigned to the assignee of the present application and incorporated herein by reference.

[0019] Figures 2(a)-(b) show a system for centering a circular object described in U.S. Patent Application No. 62 / 697,197. As shown, the system 200 includes a platform 210, pins 220, 230, 240, a cover 250, sensors 262, a reader 264, a robot 280, and an automated pipettor 290. The cover 250 includes slits 252, 254, and 256. Under the cover 250, the system 200 may include motors, pulleys, belts, and / or other components.

[0020] As shown in FIGS. 2(a)-(b), slits 252, 254, and 256 are curved and sized such that the diameters of slits 252, 254, and 256 correspond to the diameters of pins 210, 220, and 230. As a result, pins 220, 230, and 240 can traverse substantially the entire length of slits 252, 254, and 256. Further, in this embodiment, slits 252, 254, and 256 extend 15 millimeters away from platform 210. However, in other embodiments, the lengths of slits 252, 254, and 256 can be increased or decreased. For example, the lengths of slits 252, 254, and 256 can be selected such that a Petri dish can be placed on platform 210 and rotated without substantial interference from pins 220, 230, and 240. As another example, the lengths of slits 252, 254, and 256 can be significantly greater (e.g., more than twice) than the length necessary to rotate a Petri dish placed on platform 210 without substantial interference from 220, 230, and 240.

[0021] During the operation of placing at the center, slits 252, 254, and 256 guide pins 210, 220, and 230 as they advance towards platform 210. As shown, slits 252, 254, and 256 are curved and have a consistent diameter corresponding to the diameters of pins 210, 220, and 230. In other embodiments, slits 252, 254, and 256 can have different shapes. For example, slits 252, 254, and 256 can generally be straight and have a consistent diameter corresponding to the diameters of pins 210, 220, and 230. As another example, slits 252, 254, and 256 can have a conical shape with a variable diameter. In such an embodiment, slits 252, 254, and 256 can have a constricted portion near platform 210 having a diameter corresponding to the diameters of pins 210, 220, and 230.

[0022] As shown in FIG. 2(b), the Petri dish 270 can be placed on the platform 210 by the robot 280. When on the platform 210, the pins 220, 230, and 240 can be used to center the Petri dish 270 on the platform 210. After the Petri dish 270 is centered, the sensor 262 can also be used to orient the Petri dish 270. After the Petri dish 270 is centered and oriented, the reader 264 can be used to read the label 280 of the Petri dish 270. When the reader 264 measures high contrast, it interprets the high contrast as the label edge. From the position of the edge, the device can determine the midpoint of the label 280 that is used as a reference point for colony positions, as described elsewhere in this specification. By scanning the barcode, the module can recognize the coordinates and, after correctly positioning the plate, can pick the colonies. The reader 264 can also be used to further orient the Petri dish 270. After the Petri dish 270 is centered and / or oriented, the automated pipettor 290 can be used to pick one or more colonies of bacteria within the Petri dish 270.

[0023] An example of a manual method of using the apparatus of the present invention is shown in FIG. 3. Using the above apparatus, a Petri dish can be oriented to place a label thereon. This method begins with a plating culture as shown in FIG. 1. The plating culture is cultured and microbial colonies grow thereon at step 300. At step 305, the lid is removed from the culture dish and the laboratory user places the dish (with the lid) on the apparatus described herein (step 310). Once received by the apparatus, the dish is labeled (step 311). By labeling, the barcode number is paired with the dish in the database that supports the apparatus (step 312). The barcode number is saved in a file and is referenced when the colonies are harvested and tested (step 313). After labeling the plate, position the plate as described above (step 315). The technician observes either the plate in the first embodiment or the real-time image of the plate in the second embodiment of step 320 (e.g., via a web camera), marks the colonies to be harvested, and at that point, the x-y coordinates of the target colonies are measured (step 316) and the radius and angle are calculated (step 317). The position of the colonies is combined with the barcode information (step 313) and the file containing that information is sent to a database that supports the harvesting tool and any downstream testing of the harvested colonies (i.e., ID AST at step 335) (step 318). At step 325, the technician removes the culture plate from the marking machine. At step 330, the technician replaces the lid of the culture dish, and then the plate is ready to be used in the ID / AST test at step 335.

[0024] By using the dish clamp 710 (FIG. 7) and the label applicator 725 (FIG. 7) together with the label detection sensor 760 (FIG. 12), it becomes possible to generate a reference for providing the coordinates of the colony marking using simple mechanical and electrical methods. The dish clamp generates a central reference, and the label detection sensor generates a label (center) reference. When determining these two positions, it is only necessary to determine the position of the colony. The positions of these colonies can be marked in three ways.

[0025] In the first embodiment, the position of the colony can be marked using a laser pointing device directed at either the surface of the culture dish or an image of the culture dish. An example of a method for locating colonies using a laser pointing device will be described in detail below.

[0026] In the second embodiment, a viewfinder with crosshairs (i.e., a pair of thin wires or lines that intersect at right angles in the focal plane) is used to assign colony coordinates relative to the reference. This embodiment is shown in FIG. 14. In this embodiment, the viewfinder is used with an angled mirror (about 45 degrees in one embodiment), such that the user can look into the viewfinder in a direction substantially parallel to the surface on which the colony is located. The angled mirror reorients the user's field of view by about 90 degrees, allowing the user to look into the viewfinder in a substantially horizontal direction and view the surface on which the colony is located from a vertical direction. As will be described in more detail below, the viewfinder is used to allow the user to manually view the colony and align its coordinates with reference to the reference of the center of the plate and the center of the label. Such coordinate alignment can be achieved, for example, by using a laser pointer that aligns the position of the beam in the coordinate space of the culture dish. When the user positions the beam on the selected colony, the user can use a button or switch provided to the user to align the coordinates of its position relative to the reference.

[0027] In the third example, the user can locate the colony coordinates using a web camera. The use of the web camera in this method will be described in detail below. In embodiments where the web camera is deployed to locate colony coordinates, the need for computer vision to determine the plate center, barcode center, or colony location is eliminated. By eliminating the need for computer vision, the setup of the device becomes easier and simpler. Also, when computer vision is not required, the system is not affected by ambient light. Therefore, in embodiments that do not require computer vision, the device does not need to be shielded from ambient light sources. When not using computer vision, the possibility of software errors that could result in incorrect positions is eliminated. All image interpretation is done by the user. When not using computer vision, there is no need to shield the dish, and the user can continue to view the culture dish on which the colony is located. This is advantageous because the user can view the dish when the reference markings are created and then, if the reference markings on the screen are not clear enough, the user can view the actual dish. The plate center and barcode center are determined mechanically and electronically as described above, and the coordinates are determined in relation to those references. When using a web camera, the location of the colony is determined by manually interpreting the image and then identifying the target colony to which coordinates are assigned relative to the reference.

[0028] An example of a web camera image of a culture plate on which colonies are formed that can be used by a technician to mark the target colonies is shown in FIG. 4. FIG. 4 shows an image 405 of a culture dish viewed through a display 410. The display 410 has a field 415 for barcodes and fields for the x and y coordinates 420 of the colonies marked by the technician. One advantage of the web camera is that there is no need to direct a laser or light beam at the target colonies for marking.

[0029] As an alternative solution to the web camera in the system described in this specification, laser beams and light beams are contemplated. For example, a laser pointing device is used to record the coordinates of colony candidates. In this exemplary embodiment, the culture plate is placed on the marking machine as described in this specification. The marking machine is centered on the culture plate and rotates the label on the side of the culture dish to detect the edge of the label (label 280 in FIG. 2(b)) on the side of the culture plate (Petri dish 270 in FIG. 2(b)). Referring to FIG. 14, the pointer device 901 is used to operate the laser pointer to obtain the coordinates of the target colony. The pointer device is either automated or controlled by the user 905. The pointer device cooperates with a viewfinder 910 having a 45-degree mirror 915. Laser light or LED light 920 enters the pointer 910 through the first aperture 925, is reflected downward, exits the pointer 910 through the aperture 930, and is transmitted to the surface of the culture plate 937. The viewfinder 910 having a target 935 with a crosshair 936 is provided with a pointer device for the user to orient the laser pointer in the coordinate space of the culture dish. Such viewfinders are well known to those skilled in the art and are not described in detail herein. The viewfinder is provided with an adjustable magnification for viewing the culture dish at a magnification sufficient to identify the target colony. Next, the light beam is directed at the colony, and the coordinates where the light beam impinges on the culture dish are recorded. In a more manual operation, the user 905 can view the colony through the viewfinder 910. When viewing the target colony, the user can activate the laser and cause it to strike the target colony. Positioning the laser in this way aligns the coordinates where the laser light strikes the target colony. The light beam and the culture dish can move relative to each other in x, y, and z. As described elsewhere in this specification, since the culture dish is supported by a rotatable platform, the culture dish can be rotated to place the target colony in a better position for marking its location.Note that the coordinates of a specific pixel are fixed relative to the position of the label and the center of the dish. Even if the culture dish is rotated, the coordinates of a specific pixel within the coordinate space of the culture dish do not change.

[0030] It is advantageous when the device is calibrated to ensure the correspondence between the coordinates of the marked colonies within the device and the coordinates used to pick the colonies for ID / AST. It is also advantageous when the device is calibrated in the same way as any other tool that can process the culture plate downstream of the device described herein. In one embodiment, the downstream device is an automated picking tool. An example of such a calibration dish 500 is shown in FIG. 5. The dish contains nine fiducial points. Fiducial point 501 is the midpoint of the label position 505 on the side of the dish. Fiducial point 510 is the center of the dish. The angles and radii of the remaining fiducial points 511 are known. The positioning software is calibrated using these points. This provides a map of the coordinate space of the culture dish, and that coordinate space is saved in memory. When an image of the culture dish is displayed via a webcam or a display, the user selects the colony of interest, and the coordinates of that colony are saved in memory relative to the culture plate reference (e.g., fiducial points 501 and 510). The coordinates of the colony can be obtained by the user in various conventional ways. In one embodiment, a touch screen is provided, and the user can save the coordinates of the object of interest by touching the touch screen. In another embodiment, the user interface is a point-and-click monitor, and the user can save the coordinates by placing the cursor over the colony of interest and selecting that colony.

[0031] The device links the coordinates of the marked colonies to the barcode of the label affixed to the culture plate within the device. So, when the plate barcode is scanned as the plate enters the ID / AST module, the ID / AST module knows where the marked colonies are and can "find" them. The ID is performed, for example, using MALDI-TOF MS. MALDI-TOF MS is a well-known device for performing ID tests on microorganisms and is not described in detail herein. AST is a well-known technique for determining the MIC of antibiotics against specific microorganisms. The systems and methods of AST are well known to those skilled in the art and are not described in detail herein.

[0032] As described above, the barcode is on the label affixed to the side of the culture plate before the colonies are marked by the technician using the device. As described above, the midpoint of the affixed label is used as one reference point for the radius and angle of the bacteria, and the midpoint of the plate is used as a second such reference point. The user can provide the device with a roll of pre-printed barcoded labels. The device does not need to print barcodes on the labels (or on the plates themselves).

[0033] As described above, the device can be used in combination with a mechanism (e.g., the web camera and display described above) that can assign coordinates to the target colonies on the culture dish and transmit those coordinates to a device for collecting the test target colonies. Automated collection tools are known to those skilled in the art and are not described in detail herein. In one example, the automated collection tool is integrated with an automated device that performs ID and AST tests. Such a system includes a controller that communicates with the robotic collection tool and instructs the robotic collection tool to obtain a pipette (or other suitable consumable of the collection tool such as a wire loop), and then moves the pipette or other collection tool to a position above the target colony. Remove the top of the plate before colony collection. Next, the robotic collection tool lowers the pipette or other consumable so that the consumable contacts the target colony.

[0034] In another embodiment, fiducial markings on the agar surface or in the culture dish can be used to orient the sampling tool to acquire the target colony. These fiducial markings can be embedded in the plate during manufacture, applied by the user, or by organic growth, or incorporated into the dish or agar surface by any suitable means. Using a machine vision device, another fiducial point such as the center of the dish can be detected, from which the coordinates of the dish can be determined. As described above, the barcode is one example of a fiducial. Also, as described above, the position of the colony on the dish is determined with reference to the relative distance from the center and the angular offset relative to the barcode zero offset. Once the relative position of the colony is determined by the apparatus described herein, the dish is transferred to another system where the next two steps are performed. The dish is centered, for example, by mechanical means (such as the three-pinch chuck described herein). The barcode zero offset is detected, for example, by rotating the dish with a fixed sensor to detect the presence of the barcode label and scanning the barcode with a barcode scanner. At this point, the center of the dish is known and the barcode zero offset is known. Thus, it is stored as the distance to the center of the dish and the angular offset to the barcode label, so that the previously referenced position of the colony can be easily calculated. The methods and apparatus described herein do not require the camera or computer vision system of a second system (in this example, the colony sampling system), or any other system that requires colony position information. The zero offset used in this example is relative to the barcode label, but this can be any unique fiducial function of the dish or applied to the dish as described above.

[0035] As described above, once the colony coordinates within the plate coordinate space are determined by the device, those coordinates are saved and communicated to the device used to pick colonies from the plate. The plate is transported to the device where the colonies are to be picked. One automated method and apparatus for picking microorganisms from the surface of a medium is described in U.S. Patent No. 9,677,044 to Botma et al., entitled "Method for Picking Cellular Material and Assembly for Performing Said Method". This is generally owned and is incorporated herein by reference. One of ordinary skill in the art will understand that the methods and apparatus described herein can be used to provide the colony coordinates within the plate coordinate space to various devices that can use the coordinates determined according to the apparatus and methods described herein.

[0036] Referring to FIG. 6, when the dish 3 is received at the sampling station 1020, colony sampling is performed. The station 1020 includes a positioning device 8 that includes a sampling tool holder 9 for releasably holding a sampling tool such as a disposable pipette tip. The positioning device receives coordinate information from the colony localization device. The positioning device first locates a reference that is the reference frame of the colony coordinates to confirm the position of the colony. Next, the positioning device moves the sampling tool on the dish to the coordinates identified by the colony localization device. As shown, the sampling tool holder 9 holds the first sampling tool 6. The positioning device 8 positions the first sampling tool 6 at the starting position (shown by the solid line in FIG. 2) on the culture dish 3 so that it can be positioned at the position (shown by the dashed line) where it contacts the microorganism 4 and collects the sample 19 of the microorganism 4, and the positioning device 8 is arranged to automatically move the first sampling tool 6 up and down towards and away from the culture dish 3. After the first sampling tool 6 has collected the sample 19 (the first sampling tool having the held sample 19 shown as 6' in FIG. 2), the positioning device 8 raises the first sampling tool 6' and positions it at the transfer position "A" above the suspension tube 11. The positioning device 8 preferably vertically raises the sampling tool 6' to the starting position before horizontally moving it to the transfer position A along the transfer track 18. This can help prevent contamination by the mucoid strings that may form during sample collection. However, in other embodiments, the positioning device 8 can move simultaneously in both the vertical and horizontal directions towards the transfer position A (as shown by the arrow in FIG. 2).

[0037] As described above, the apparatus generates coordinates of marked colonies that reflect the radius and angle within a reference coordinate space corresponding to the coordinate space in which sampling is performed. The apparatus deploys a table that can move in the x and y directions. Referring to FIG. 7, apparatus 700 has a table 705 that can be adjusted in both the x and y directions. Apparatus 700 has a dish clamp 710 that uses three pins 715, each pin 715 facing in a locking channel 720. The apparatus further includes a roller assembly 725 for attaching a label from a label strip 740 to a dish 722. As the label advances through a series of vertical rollers 737, the roll of the label strip 740 rotates about a vertical axis 738. The label strip 740 has an adhesive surface that carries a label 739. As the label is advanced near the roller 725 by an apex roller 738, the label 739 having an adhesive on the outside is moved by the roller 725 to contact the culture dish 722. Apparatus 700 also includes a web camera holder 730 to which a web camera 735 is attached.

[0038] A view looking down from above the dish clamp 710 and the roller 725 is shown in FIG. 8. In the illustrated position, the clamp is rotated so that the dish 722 is spaced from the roller 725. When the pins 715 are in the illustrated position, the locking of the dish 722 is released. When the pins 715 are in the locked position, the plate 722 is held in place when the roller 725 attaches a label from the label strip 740 to the dish 722. The pins 715 are moved from their first position to their second position by pins 723. One of the three pins 715 is fixed to prevent the plate 722 from rotating on the clamp disk 710. The plate 722 is always fixed to the center of the clamp disk 710 for the other two pins 715.

[0039] Figure 9 is a side view of the roller assembly 725. The roller assembly 725 has a rubber roller wheel 745 disposed around a bearing 750. The dish 722 is fixed to the clamp 710. As shown in Figure 10, the roller assembly is biased near the dish 722 by a spring 755. Thereby, the roller assembly transfers the label from the label strip to the dish 722. Since the dish 722 typically has a conical shape (the bottom of the dish has a slightly smaller diameter than the top of the dish such that the walls of the dish taper inwardly downward), the roller 725 is inclined slightly outwardly in balance with the taper of the side wall of the dish.

[0040] Figure 11 shows a mounting arm 730 for a web camera 735 that transmits a real-time image of the plating culture on the plate 722. The technician uses the image of the web camera to select the colony to be sampled. This is because the dish 722 is labeled. Coordinates are assigned to the selected colony with reference to the midpoint of the applied label and the center of the dish 722.

[0041] Figure 12 shows a sensor 760 used to detect the label on the label strip 740. The sensor detects the contrast between the label and its background. When the edge of the label is detected, the roller assembly 725 and the dish clamp 710 advance and contact to transfer the label from the label strip 740 to the dish 722.

[0042] Figure 13 is a flowchart of the operation of the apparatus described in this specification. At step 800, the lid is removed from the plate. At step 805, the load button is pressed to position the clamp in the open position to receive the dish. At step 810, the dish is placed in the clamp. At step 815, the start switch is turned on, the clamp is closed over the dish, and the label is affixed. At step 820, an image of the plate is captured, and at step 821, the technician looks at the colonies, selects them, and the coordinates of the selected colonies relative to the center of the label and the center of the dish are recorded at step 822. At step 825, the apparatus is turned off, the clamp is opened, enabling the technician to remove the plate from the apparatus. At step 830, the lid is placed back over the dish.

[0043] Although the invention of this specification has been described with reference to specific embodiments, it should be understood that these embodiments are merely illustrative of the principles and applications of the invention. Accordingly, it is to be understood that numerous modifications may be made to the exemplary embodiments and other configurations may be devised without departing from the spirit and scope of the invention as defined by the appended claims.

Claims

1. An apparatus for assigning coordinate positions to colonies of microorganisms on a culture plate, the apparatus comprising: a table; a dish clamp supported by the table, the dish clamp including a platform on which a culture dish is manually placed and a chuck for fixing the culture dish on the platform; a colony marking device including the viewfinder that enables a user to view colonies through the viewfinder and assign coordinates to the colonies with respect to at least two reference marks; a label dispenser a wheel mount for receiving a roll of a substrate strip carrying a plurality of labels, the plurality of labels having an adhesive applied to an outer surface of the labels not adhered to the substrate strip; at least one tension roller for applying tension to the substrate strip pulled out from the roll; a biasing roller assembly that urges the roller to engage the back side of the substrate strip, thereby urging the outer surface of the label having the adhesive applied thereto to contact the side surface of the culture dish; a processor for assigning coordinates of a selected colony with respect to the label of the culture dish and the center of the culture dish.

2. The apparatus according to claim 1, wherein the viewfinder includes an angled mirror and a crosshair in a focal plane of the viewfinder.

3. The apparatus according to claim 1 or claim 2, further comprising a label sensor proximate to the biasing roller assembly, the label sensor identifying an edge of the label carried by the substrate strip as a reference mark.

4. The apparatus according to claim 3, comprising a controller communicatively coupled to the label sensor and the biasing roller assembly.

5. The apparatus according to claim 4, wherein the biasing roller assembly is biased to a first position away from the culture dish and, when the label sensor detects the label, urges the label carried by the substrate strip to contact the culture dish.

6. The apparatus according to any one of claims 1 to 5, further comprising an imaging device, wherein the imaging device acquires an image of the culture dish, a colony is selected from the image of the culture dish, and the imaging device is a camera.

7. The apparatus according to any one of claims 1 to 6, wherein the image of the culture dish is provided on a display, and the display is a touch screen display.

8. The apparatus according to any one of claims 1 to 7, wherein the image of the culture dish is provided on a display, and the display is a point-and-click display.

9. The apparatus according to any one of claims 1 to 5, further comprising a memory that stores the coordinates of the selected colony with respect to the label attached to the culture dish.

10. The apparatus according to claim 9, wherein the memory stores a coordinate map of the culture dish, and the coordinate map is related to the label of the culture dish and the center of the culture dish.

11. An apparatus for assigning coordinate positions to colonies of microorganisms on a culture plate, the apparatus comprising: a table; a dish clamp supported by the table, the dish clamp including a platform on which a culture dish is manually placed and a chuck for fixing the culture dish to the platform; an imaging device including an image sensor, the imaging device being arranged to capture an image of the culture dish placed on the platform, and the imaging device being coupled to a display for displaying the image of the culture dish captured by the imaging device; a label dispenser, a wheel mount for receiving a roll of a substrate strip carrying a plurality of labels, the plurality of labels having an adhesive attached to an outer surface of the labels not attached to the substrate strip; at least one tension roller for applying tension to the substrate strip pulled out from the roll; a biasing roller assembly that urges the roller to engage the back side of the substrate strip, thereby urging the outer surface of the label having the adhesive attached to contact the side surface of the culture dish. An apparatus comprising: a processor that assigns coordinates of a colony selected from the display with respect to the label of the culture dish and the center of the culture dish.

12. The apparatus according to claim 11, wherein the imaging device is a web camera.

13. The apparatus according to claim 12, further comprising an adjustable mounting arm supported by the table, the adjustable mounting arm including a holder that carries the web camera.

14. The apparatus according to any one of claims 11 to 13, further comprising a label sensor proximate to the biasing roller assembly, the label sensor identifying an edge of the label carried by the substrate strip as a reference mark.

15. The apparatus according to claim 14, comprising a controller communicatively coupled to the label sensor and the biasing roller assembly.

16. The apparatus according to claim 14 or claim 15, wherein the biasing roller assembly is biased to a first position away from the culture dish and, when the label sensor detects the label carried by the substrate strip, urges the label into contact with the culture dish.

17. The apparatus according to claim 11, wherein the imaging device is a camera.

18. The apparatus according to any one of claims 11 to 17, wherein the display is a touch screen display.

19. The apparatus according to any one of claims 11 to 18, wherein the display is a point-and-click display.

20. The apparatus according to any one of claims 11 to 18, further comprising a memory that stores coordinates of a selected colony with respect to the label affixed to the culture dish.

21. The apparatus according to claim 20, wherein the memory stores a coordinate map of the culture dish, the coordinate map being related to the label of the culture dish and the center of the culture dish.

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