CULTURE IMAGING SYSTEM

• US 20180129864A1
• Filed: 04/21/2016
• Published: 05/10/2018
• Est. Priority Date: 04/21/2015
• Status: Active Grant

• Current Assignee: Purdue Research Foundation (The Trustees of Purdue University (d/b/a Purdue University))
• Original Assignee: Purdue Research Foundation (The Trustees of Purdue University (d/b/a Purdue University))
• Inventors: Robinson, Joseph Paul, Rajwa, Bartlomiej P., Ragheb, Kathryn E., Holdman, Cheryl M., Patsekin, Valery P., Bae, Euiwon, Sturgis, Jennifer
• Granted Patent: US 10,719,691 B2
• Time in Patent Office: Days
• CPC Class Codes: C12M 41/36 of biomass, e.g. colony counters or by turbidity measurements electrooptical investigation of individual particles G01N15/14, flow cytometers G01N15/1404
• CPC Class Codes: G02B 21/365 Control or image processing arrangements for digital or video microscopes G02B21/361, G02B21/362 take precedence
• CPC Class Codes: G06T 2207/10056 Microscopic image
• CPC Class Codes: G06T 2207/30024 Cell structures in vitro; Tissue sections in vitro
• CPC Class Codes: G06T 7/0012 Biomedical image inspection
• CPC Class Codes: G06V 20/693 Acquisition
• CPC Class Codes: G06V 20/695 Preprocessing, e.g. image segmentation
• CPC Class Codes: G06V 20/698 Matching; Classification

Abstract

A system for the characterization of a colony of microorganisms includes a coherent light source configured to provide coherent light of one or more wavelengths along a common optical path. A holder is configured to operationally arrange a substrate so that the colony of microorganisms on a surface of the substrate is positioned to receive the coherent light. Scattered light is generated from the colony of microorganisms receiving coherent light. A first image capture device is configured to receive the scattered light and generate a scatter image from the microorganism colony irradiated by the coherent light. The system also includes a magnifying lens configured to magnify the colony of microorganisms. A second image capture device is configured to capture a light image of the colony of microorganisms magnified by the magnifying lens. Methods of assigning organisms to categories with like organisms without necessarily identifying the organisms are also described.

Claims

1. A system for the characterization of a colony of microorganisms, the system comprising:

a coherent light source configured to provide coherent light;

a holder configured to operationally arrange a substrate so that the colony of microorganisms on a surface of the substrate is positioned to receive the coherent light and generate scattered light from the colony of microorganisms receiving the coherent light;

a first image capture device configured to receive the scattered light and generate a scatter image associated with the scattered light;

a magnifying lens; and

a second image capture device configured to capture a light image of the colony of microorganisms magnified by the magnifying lens.

2. The system according to claim 1, wherein the holder is further configured to operationally arrange the substrate so that the magnifying lens occupies an optical path between the colony of microorganisms on the substrate and the second image capture device.

3. The system according to claim 1, wherein the first image capture device is arranged on a first side of the substrate and the coherent light source, the magnifying lens, and the second image capture device are arranged on a second side of the substrate.

4. The system according to claim 1, further comprising a third image capture device configured to capture a plate image of substantially the entire surface of the substrate.

5. The system according to claim 4, wherein the second image capture device is configured to capture the light image at a first level of magnification and the third image capture device is configured to capture the plate image at a second level of magnification less than the first level of magnification.

6. The system according to claim 5, wherein the second image capture device is further configured to capture an additional light image at a second level of magnification greater than first level of magnification.

7. The system according to claim 1, further comprising a filtering unit configured to modify the light image.

8. A computer-implemented method for identifying a number of microorganism types in a set of multiple colonies of microorganisms, the method comprising:

receiving a plurality of images, each image associated with a different single colony of microorganisms from the set of multiple colonies of microorganisms;

determining, using a processor, a first set of image features, the first set of image features including at least one image feature for each image of at least a portion of the plurality of images; and

determining, using the processor and based at least in part on the first set of image features, a first group of colonies including at least a first colony of the multiple colonies of microorganisms and a second group of colonies including at least a second, different colony of the multiple colonies of microorganisms.

9. The computer-implemented method according to claim 8, further comprising imaging at least some colonies of the set of multiple colonies of microorganisms through a magnifying lens using an image capture device to provide respective light images.

10. The computer-implemented method according to claim 8, further comprising capturing, using an image capture device, a plurality of scatter patterns created by coherent light passing through respective colonies of the set of multiple colonies of microorganisms.

11. The computer-implemented method according to claim 8, wherein each image of the plurality of images is an image of a scatter pattern representing light scattered by a respective colony of microorganisms under coherent illumination, the method further comprising:

receiving a plurality of light images, each light image showing a magnified view of a respective colony of the set of multiple colonies of microorganisms;

determining, using the processor, a second set of image features, the second set of image features including at least one light image feature for the individual ones of at least the portion of the plurality of images; and

determining the first group of colonies and the second group of colonies based at least in further part on the second set of image features.

12. The computer-implemented method according to claim 8, wherein the determining the first group of colonies and the second group of colonies identities includes clustering the set of image features based on least in part on at least one of a parametric clustering technique or a nonparametric clustering techniques.

13. The computer-implemented method according to claim 12, wherein the clustering is based at least in part on the parametric clustering technique and the method further comprises:

performing multiple instances of the parametric clustering technique using a different numbers of clusters for each of the multiple instances to provide respective clustering result sets;

determining, using the processor, a respective level of cluster compactness associated with each of the clustering result sets;

determining, using the processor, a one of the clustering result sets having a level of cluster compactness greater than any of the other clustering result sets to determine a most compact clustering result set; and

determining that the number of microorganism types is the number of clusters associated with the most compact clustering result set.

14. The computer-implemented method according to claim 8, further comprising:

receiving a plate image of substantially the entire surface of a substrate, the set of multiple colonies of microorganisms being disposed upon the surface of the substrate; and

generating a colony map from at least a portion of the plate image, the colony map indicating individual colonies of the first group of colonies with respective first markings and indicating individual colonies of the a second group of colonies with respective second markings.

15. A system comprising:

a coherent light source configured to provide coherent light;

a first image capture device configured to capture a scatter image from a scatter pattern generated by the coherent light impinging on a colony of microorganisms associated with a substrate;

a magnifying lens;

a second image capture device configured to generate a light image depicting the colony of microorganisms; and

a positioning system configure to change relative positioning of at least two of the substrate, the coherent light source, and the magnifying lens.

16. The system of claim 15, wherein the positioning system is configured to change the relative positioning between a first position in which the coherent light passes through the colony of microorganism and a second position in which the magnifying lens occupies an optical path between the colony of microorganisms and the second image capture device.

17. The system of claim 15, wherein the substrate is further associated with multiple colonies of microorganisms and the system further comprises:

a processor;

a memory; and

computer program instructions stored in the memory or implemented in hardware to;

determine a first set of image features from the scatter image;

determine a second set of image features from the light image;

group, at least a portion of the multiple colonies of microorganism into a plurality of groups; and

associate the colony of microorganisms with a first group of the plurality of groups based at least in part on the first set of image features and the second set of image features.

18. The system of claim 17, wherein the second set of image features includes at least one of form, size, border, surface, opacity, polarization state, or color.

19. The system of claim 17, wherein the computer program instructions are further implemented to present a user interface that includes a colony map graphically depicting:

a position of the colony of microorganisms;

respective positions of a plurality of other colonies of microorganisms of the multiple colonies of microorganisms;

an indication of an association of the colony of microorganisms with the first group; and

indications of respective associations between the plurality of groups and individual colonies of the plurality of other colonies of microorganisms.

20. The system of claim 15, further comprising:

a processor;

a memory; and

computer program instructions stored in the memory or implemented in hardware to;

determine a first set of image features from the scatter image;

determine that the first set of image features is insufficient to determine a group classification associated with the colony of microorganisms;

determine a second set of features from the light image; and

determine, based at least in part on the first set of features and the second set of features, the group classification of the colony of microorganisms.