Robust stain detection and quantification for histological specimens based on a physical model for stain absorption

A method for analyzing a color image of a stained tissue specimen, wherein the color image comprises points, wherein each point is represented by a triple of numbers, comprising the steps of

• transforming the color image to a colorspace representation in which points are represented by triplets of numbers wherein a triplet of numbers represents a color;
• defining a stain curve defined in terms of a light source and a certain point in the color image;
• calculating the distance in colorspace along the stain curve from the triplet representing the light source to the triplet representing the certain point;
• and
• calculating the amount of stain.

A method for measuring an amount of a tissue feature on a tissue specimen comprising a stain, using a color image of the tissue specimen, wherein the color image comprises points, wherein each point is represented by a triple of numbers, comprising the steps of

• randomly sampling a fixed number of points from the color image;
• performing a principal component analysis on the fixed number of points to obtain a new coordinate system;
• and
• using the new coordinate system to define a transformation matrix to convert the triple of numbers into a triple of values, wherein a component of the triple of values is proportional to the amount of stain at that point and wherein the amount of stain at that point is proportional to the amount of the tissue feature.

A method for measuring an amount of tissue feature on a tissue specimen comprising a stain, using a color image of the tissue specimen, wherein the color image comprises points, wherein each point is represented by a triple of numbers, comprising the steps of

• transforming the color image to a colorspace representation in which points are represented by triplets of numbers wherein a triplet of numbers represents a color;
• defining a stain curve defined in terms of a light source and a certain point in the color image;
• calculating the distance in colorspace along the stain curve from the triplet representing the light source to the triplet representing the certain point;
• and
• calculating the amount of stain wherein the amount of stain at that point is proportional to the amount of the tissue feature.

A method for analyzing an amount of stain on a tissue specimen comprising a stain, comprising the steps of

• capturing a color image of the tissue specimen, wherein the color image comprises points, wherein each point is represented by a triple of numbers;
• randomly sampling a fixed number of points from the color image;
• performing a principal component analysis on the fixed number of points to obtain a new coordinate system;
• and
• using the new coordinate system to define a transformation matrix to convert the triple of numbers into a triple of values, wherein a component of the triple of values is proportional to the amount of stain at that point.

A method for analyzing the amount of stain on a tissue specimen comprising a stain, comprising the steps of

• capturing a color image of the tissue specimen;
• transforming the color image to a colorspace representation in which points are represented by triplets of numbers wherein a triplet of numbers represents a color;
• defining a stain curve defined in terms of a light source and a certain point in the color image;
• calculating the distance in colorspace along the stain curve from the triplet representing the light source to the triplet representing the certain point;
• and
• calculating the amount of stain.

A method for measuring the amount of a tissue feature on a tissue specimen comprising a stain, comprising the steps of

• capturing a color image of a tissue specimen, wherein the color image comprises points, wherein each point is represented by a triple of numbers;
• randomly sampling a fixed number of points from the color image;
• performing a principal component analysis on the fixed number of points to obtain a new coordinate system;
• and
• using the new coordinate system to define a transformation matrix to convert the triple of numbers into a triple of values, wherein a component of the triple of values is proportional to the amount of stain at that point and wherein the amount of stain at that point is proportional to the amount of the tissue feature.

A method for measuring the amount of a tissue feature on a tissue specimen comprising a stain, comprising the steps of

• capturing a color image of a tissue specimen;
• transforming the color image to a colorspace representation in which points are represented by triplets of numbers wherein a triplet of numbers represents a color;
• defining a stain curve defined in terms of a light source and a certain point in the color image;
• calculating the distance in colorspace along the stain curve from the triplet representing the light source to the triplet representing the certain point;
• and
• calculating the amount of stain wherein the amount of stain at that point is proportional to the amount of the tissue feature.

A method for analyzing the amount of two stains on a stained tissue specimen, comprising the steps of

• staining a tissue specimen with two stains, a first and a second stain;
• capturing a color image of the tissue specimen, wherein the color image comprises points, wherein each point is represented by a triple of numbers;
• randomly sampling a fixed number of points from the color image;
• performing a principal component analysis on the fixed number of points to obtain a new coordinate system;
• and
• using the new coordinate system to define a transformation matrix to convert the triple of numbers into a triple of values, wherein a component of the triple of values is proportional to the amount of the first stain at that point and a component of the triple of values is proportional to the amount of the second stain at that point.

A method for analyzing the amount of three stains on a stained tissue specimen, comprising the steps of

• staining a tissue specimen with three stains, a first stain, a second stain and a third stain;
• capturing a color image of the tissue specimen, wherein the color image comprises points, wherein each point is represented by a triple of numbers;
• randomly sampling a fixed number of points from the color image;
• performing a principal component analysis on the fixed number of points to obtain a new coordinate system;
• and
• using the new coordinate system to define a transformation matrix to convert the triple of numbers into a triple of values, wherein a component of the triple of values is proportional to the amount of the first stain at that point, a component of the triple of values is proportional to the amount of the second stain at that point and a component of the triple of values is proportional to the amount of the third stain at that point.