Interpolated image response

• US 20050246105A1
• Filed: 01/27/2005
• Published: 11/03/2005
• Est. Priority Date: 01/28/2004
• Status: Abandoned Application

• Current Assignee: Becton, Dickinson & Co
• Original Assignee: Becton, Dickinson & Co
• Inventors: Elling, John W., Faber, Vance
• Application Number:
  US11/044,395
• Publication Number:
  US 20050246105A1
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G01N 33/5026 on cell morphology
• CPC Class Codes: G01N 33/5091 for testing the pathological state of an organism
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Systems and methods are provided for characterizing a multidimensional distribution of responses from the objects in a populations subject to a perturbation. The methods enable the creation of a “degree of response” scale interpolated from non-perturbed and perturbed reference populations. The methods enables, using the interpolated degree of response scale, the quantitation of a degree of response of a test compound subject to a given level of perturbation, and enables the generation of a dose-response curve for a test compound. The methods are useful in a wide range of applications, such cellular analysis and high-content screening of compounds, as carried out in pharmaceutical research.

Claims

1. A method of generating a degree of response scale for a population subject to multiple levels of a perturbation, wherein a response is a representation of the multidimensional state of a population, said method comprising the steps of:

a) determining a fingerprint of a first sample of said population subjected to a first level of perturbation, thus obtaining a low-response reference fingerprint that is a representation of the multidimensional state of a low-response population;

b) determining a fingerprint of a second sample of said population subjected to a second level of perturbation greater than said first level of perturbation, thus obtaining a high-response reference fingerprint that is a representation of the multidimensional state of a high-response population;

c) determining a set of interpolated fingerprints from said low-response reference fingerprint and said high-response reference fingerprint, wherein each interpolated fingerprint is a representation of the multidimensional state of a population exhibiting a degree of response intermediate to that of the low-response and high-response populations;

wherein said degree of response scale consists of said set of interpolated fingerprints, said low-response reference fingerprint, and said high-response reference fingerprint, each indexed by a corresponding degree of response.

2. The method of claim 1, wherein the population is a biological population.

3. The method of claim 2, wherein said population is a population of cells.

4. The method of claim 3, wherein determining each of said fingerprints comprises measuring a plurality of features of said cells, wherein at least one of said features is selected from the set of features consisting of length, width, height, perimeter, area, volume, orientation, shape, texture, perimeter, moments, mean, variance, skewness, kurtosis, centroid, color, luminescence, total luminescence, average luminescence, and optical density, wherein each feature is measured independently from either the entire cell or a subregion of said cell.

5. The method of claim 1, wherein said perturbation is chemical, biological, mechanical, thermal, electromagnetic, gravitational, nuclear, or temporal.

6. The method of claim 3, wherein said perturbation is a bioactive compound.

7. The method of claim 1, wherein each interpolated fingerprint of said set of interpolated fingerprints is determined as a linear combination of said low-response reference fingerprint and said high-response reference fingerprint.

8. A method of analyzing the response of a test population subjected to a known level of a test perturbation, relative to a reference perturbation, wherein a response is a representation of the multidimensional state of a population, said method comprising the steps of:

a) determining a degree of response scale by

i) determining a fingerprint of a first sample of said population subjected to a first level of said reference perturbation, thus obtaining a low-response reference fingerprint that is a representation of the multidimensional state of a low-response population;

ii) determining a fingerprint of a second sample of said population subjected to a second level of said reference perturbation greater than said first level of perturbation, thus obtaining a high-response reference fingerprint that is a representation of the multidimensional state of a high-response population;

iii) determining a set of interpolated fingerprints from said low-response reference fingerprint and said high-response reference fingerprint, wherein each interpolated fingerprint is a representation of the multidimensional state of a population exhibiting a degree of response intermediate to that of the low-response and high-response populations;

wherein said degree of response scale consists of said set of interpolated fingerprints, said low-response reference fingerprint, and said high-response reference fingerprint, each indexed by a corresponding degree of response;

b) determining a fingerprint of said test population subjected to said known level of a test perturbation, thus obtaining a test fingerprint that is a representation of the multidimensional state of said test population; and

c) determining a degree of response of said test population by determining from among said degree of response scale a fingerprint most similar to said test fingerprint and identifying a degree of response corresponding to said most similar fingerprint.

9. The method of claim 8, wherein said reference and test populations are biological populations.

10. The method of claim 9, wherein said reference and test populations are populations of cells.

11. The method of claim 10, wherein determining each of said fingerprints comprises measuring a plurality of features of said cells, wherein at least one of said features is selected from the set of features consisting of length, width, height, perimeter, area, volume, orientation, shape, texture, perimeter, moments, mean, variance, skewness, kurtosis, centroid, color, luminescence, total luminescence, average luminescence, and optical density, wherein each feature is measured independently from either the entire cell or a subregion of said cell.

12. The method of claim 8, wherein said perturbation is chemical, biological, mechanical, thermal, electromagnetic, gravitational, nuclear, or temporal.

13. The method of claim 9, wherein said perturbation is a bioactive compound.

14. The method of claim 8, wherein said test perturbation and said reference perturbation are the same.

15. The method of claim 8, wherein said test perturbation and said reference perturbation are different.

16. The method of claim 8, wherein each interpolated fingerprint of said set of interpolated fingerprints is determined as a linear combination of said low-response reference fingerprint and said high-response reference fingerprint.

18. A method of generating a dose-response curve for a population subjected to a perturbation, wherein said method comprises generating a dose-response relationship for said population according to the method of claim 15, and fitting a curve to the results obtained.

17. A method of generating a dose-response relationship for a population subjected to a perturbation, wherein a response is a representation of the multidimensional state of a population, said method comprising the steps of:

a) determining a degree of response scale by

i) determining a fingerprint of a first sample of said population subjected to a first level of perturbation, thus obtaining a low-response reference fingerprint that is a representation of the multidimensional state of a low-response population;

ii) determining a fingerprint of a second sample of said population subjected to a second level of perturbation greater than said first level of perturbation, thus obtaining a high-response reference fingerprint that is a representation of the multidimensional state of a high-response population; and

iii) determining a set of interpolated fingerprints from said low-response reference fingerprint and said high-response reference fingerprint, wherein each interpolated fingerprint is a representation of the multidimensional state of a population exhibiting a degree of response intermediate to that of the low-response and high-response populations;

wherein said degree of response scale consists of said set of interpolated fingerprints, said low-response reference fingerprint, said high-response reference fingerprint, each indexed by a corresponding degree of response;

b) determining a plurality of fingerprints of a plurality of test samples of said population, each subjected a different known level of said test perturbation, thus obtaining a test fingerprint corresponding to each of a plurality of levels of perturbation;

c) determining a degree of response for each test fingerprint by determining from among said degree of response scale a fingerprint most similar to said test fingerprint and identifying a degree of response corresponding to said most similar fingerprint;

wherein said dose-response relationship is represented by said degree of response obtained for each of said plurality of levels of perturbation.