Automated measurement of concentration and/or amount in a biological sample

1. A computer implemented method of quantifying a color in a sample comprising multiple colors, the method comprising:

measuring a first color channel value in a plurality of pixels from a plurality of separate control samples, each separate control sample comprising a single color of interest;

defining a vector for each of the plurality of separate control samples, wherein each vector comprises an average of each first color channel value present in the plurality of separate control samples;

defining a matrix based upon control measurements comprising each of the averages for each of the first color channels;

defining a conversion matrix comprising the inverse of the matrix based upon the control measurements;

measuring second color channel values in an image of an experimental sample comprising a plurality of colors of interest, each pixel of the image of the experimental sample comprising a plurality of second color channels; and

calculating an amount of a color in the experimental sample by converting the second color channel values in the experimental sample using the conversion matrix.

2. The method of claim 1 , wherein the second color channels comprise red, green, and blue.

3. The method of claim 1 , wherein each separate control sample is stained with a single staining reagent to generate the color of interest.

4. The method of claim 1 , wherein the experimental sample is stained with a plurality of stains to generate a plurality of colors of interest.

5. The method of claim 1 , wherein the number of stains in an experimental sample are less than or equal to the number of color channels.

6. The method of claim 1 , wherein an image of the experimental sample is displayed as a monochrome image.

7. The method of claim 1 , further comprising setting all but one of the color channel values to zero (0), thereby determining the amount of a single color in the experimental sample.

8. The method of claim 1 , further comprising rendering a digital display of the experimental sample.

9. A computer program on a non-transitory computer readable medium comprising instructions to cause a computer to:

measure a first color channel value in a plurality of pixels from a plurality of separate control samples, each separate control sample comprising a single color of interest;

define a vector for each of the plurality of separate control samples, wherein each vector comprises an average of each first color channel value present in the plurality of separate control samples;

define a matrix based upon control measurements comprising each of the averages for each of the first color channels;

define a conversion matrix comprising the inverse of the matrix based upon the control measurements;

measure second color channel values in an image of an experimental sample comprising a plurality of colors of interest, each pixel of the image of the experimental sample comprising a plurality of second color channels;

calculate an amount of a color in the experimental sample by converting the second color channel values in the experimental sample using the conversion matrix; and

outputting the amount of the color in the experimental sample.

10. The computer readable program of claim 9 , wherein the second color channels comprise red, green, and blue.

11. The computer readable program of claim 9 , wherein each separate control sample is stained with a single staining reagent to generate a color of interest.

12. The computer readable program of claim 9 , wherein the experimental sample is stained with a plurality of stains to generate a plurality of colors of interest.

13. The computer readable program of claim 9 , wherein the number of stains in an experimental sample are less than or equal to the number of color channels.

14. The computer readable program of claim 9 , wherein an image of the experimental sample is displayed as a monochrome image.

15. The computer readable program of claim 9 , further comprising setting all but one of the color channel values to zero (0), thereby determining the amount of a single color in the experimental sample.

16. The computer readable program of claim 9 , further comprising rendering a digital display of the experimental sample.

17. A machine vision system for automated analysis of a biological sample on a slide comprising:

a computer comprising:

a system processor;

a computer program on a nontransitory computer readable medium, the computer program comprising an image algorithm comprising instructions to cause the computer to:

measure a first color channel value in a plurality of pixels from a plurality of separate control samples, each separate control sample comprising a single color of interest;

define a vector for each of the plurality of separate control samples, wherein each vector comprises an average of each first color channel value present in the plurality of separate control samples;

define a matrix comprising each of the averages for each of the color channels;

define a conversion matrix comprising the inverse of the matrix based upon the control measurements;

measure second color channel values in an image of an experimental sample comprising a plurality of colors of interest, each pixel of the image of the experimental sample comprising a plurality of second color channels;

calculating an amount of a color in the experimental sample by converting the second color channel values in the experimental sample using the conversion matrix; and

outputting the amount of a color in the experimental sample;

a monitor in communication with the computer, and

an input device in communication with the computer;

an optical system in communication with the computer, comprising:

a stage;

an automated loading and unloading member for loading and unloading of a slide;

an identification member;

an optical sensing array in optical communication with the stage configured to acquire an image at a location on a slide and in electrical communication with the processor,

a storage member for storing the location of a candidate object or area of interest; and

a storage device for storing each image.