Interactive tree plot for flow cytometry data

• US 10,215,685 B2
• Filed: 09/10/2009
• Issued: 02/26/2019
• Est. Priority Date: 09/16/2008
• Status: Active Grant

• Current Assignee: Beckman Coulter Incorporated (Danaher Corporation)
• Original Assignee: Beckman Coulter Incorporated (Danaher Corporation)
• Inventors: Zigon, Robert, Vanwinkle, Rachel, Smith, Jeremy Alan, Myers, Larry
• Primary Examiner(s): Ng, Amy
• Assistant Examiner(s): Wong, William
• Application Number:
  US12/557,144
• Publication Number:
  US 20100070904A1
• Time in Patent Office: 3,456 Days
• Field of Search: 715771, 715853-855, 702 21
• CPC Class Codes: G01N 15/14 Optical investigation techniques, e.g. flow cytometry
• CPC Class Codes: G01N 15/147 the analysis being performed on a sample stream
• CPC Class Codes: G01N 2015/1477 Multiparameters
• CPC Class Codes: G01N 2015/1488 Methods for deciding
• CPC Class Codes: G06F 18/231 Hierarchical techniques, i.e. dividing or merging pattern sets so as to obtain a dendrogram
• CPC Class Codes: G06F 18/40 Software arrangements specially adapted for pattern recognition, e.g. user interfaces or toolboxes therefor
• CPC Class Codes: G06V 10/7625 Hierarchical techniques, i.e. dividing or merging patterns to obtain a tree-like representation; Dendograms
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Abstract

Methods, systems, and computer program products can be used for displaying and analyzing data. A method operates by receiving and displaying flow cytometry data in a tree plot, which represents multiple variations of classified flow cytometry data within an interface of computer that includes an input device. The interface permits a user to select, using the input device, portions of the tree plot associated with characteristics and sub-sets of the data. In an example, one or more histograms, contour plots, density plots, radar plots, and scatter plots representing the data are displayed within the interface. The interface permits a user to select, using the input device, portions of the histograms, contour plots, density plots, radar plots, and scatter plots, corresponding to characteristics and sub-sets of the data. In an example, updated histograms and plots are displayed in the interface substantially immediately based upon selected characteristics and subsets of the data.

Claims

1. A method for analyzing cell populations in a sample, the method comprising:

generating, with a flow cytometer, measured values for a plurality of parameters for each of a plurality of cells in the sample, the plurality of parameters for each cell including a first subset of parameters and a second subset of parameters, the second subset of parameters being different than the first subset of parameters;

for each of the plurality of cells in the sample, determining whether that cell is positive or negative for each parameter in the first subset of parameters;

displaying an interactive tree plot including a root, levels, branches and leaves, wherein each of the levels corresponds to a respective parameter in the first subset of parameters, wherein each of the levels divides the plurality of cells into a first subset of the plurality of cells which are determined to be positive for the respective parameter and a second subset of the plurality of cells which are determined to be negative for the respective parameter, wherein a path from the root to a first leaf defines a first phenotype based on a branch making up the path, and wherein a height of the first leaf corresponds to a count of cells determined to have the first phenotype;

receiving a first user input on the interactive tree plot to select or deselect a first parameter from the first subset of the parameters;

responsive to the first user input, selecting or deselecting the first parameter from the first subset of the parameters;

responsive to selecting or deselecting the first parameter from the first subset of the parameters, altering the interactive tree plot to reflect an addition or removal of a level corresponding to the first parameter;

receiving a second user input to select the first leaf of the interactive tree plot; and

responsive to the second user input, identifying a subpopulation of cells associated with the first leaf, the subpopulation including each cell of the plurality of cells determined to have the first phenotype, analyzing the subpopulation of cells on a second tree plot including second levels to determine a second phenotype for each of the cells in the subpopulation based on the second subset of parameters associated with the second levels, and displaying the second tree plot.

2. The method of claim 1, further comprising:

measuring a first value for a first measured parameter from the first subset of parameters with a first sensor of the flow cytometer;

measuring a second value for a second measured parameter from the second subset of parameters with a second sensor of the flow cytometer, the second sensor being different than the first sensor.

3. The method of claim 1, wherein determining whether each cell is positive or negative for a parameter is based, at least in part, on a gate for the parameter.

4. The method of claim 3, wherein each cell is determined to be positive for the parameter when a measured value for the parameter is inside the gate.

5. The method of claim 3, further comprising:

displaying a third plot of parameters for a plurality of cells in the sample; and

receiving a third user input indicating a boundary for a gate for one or more of the parameters on the third plot.

6. The method of claim 5, wherein the third plot is a histogram or scatter plot.

7. The method of claim 1, wherein the second tree plot includes a level corresponding to a parameter of the second subset of parameters.

8. The method of claim 1, wherein at least one of the plurality of parameters is a presence of a marker.

9. The method of claim 8, wherein the marker is a cell-surface protein detectable using a labeled antibody, and wherein generating measured values for the plurality of parameters includes measuring fluorescence of the labeled antibody.

10. The method of claim 1, wherein determining whether each cell is positive or negative for a parameter is based, at least in part, on a gate for the parameter, and wherein the cell is determined to be positive for the parameter when the measured value of the parameter is inside the gate.

11. The method of claim 1, wherein a root of the second tree plot corresponds to the first leaf of the interactive tree plot.

12. The method of claim 1, wherein the plurality of parameters include at least one of cellular size, mitotic phase, cellular complexity, and cellular health.

13. The method of claim 1, further comprising:

receiving a third user input on the second tree plot to select or deselect a second parameter of the second subset of parameters;

responsive to the third user input, selecting or deselecting the second parameter from the second subset of the parameters; and

responsive to selecting or deselecting the second parameter from the second subset of the parameters, altering the second tree plot to reflect adding or removing a level corresponding to the second parameter.

14. An apparatus comprising:

a computer processor receiving measured values from a flow cytometer of a plurality of parameters for each of a plurality of cells in a sample, the plurality of parameters including a first subset of parameters and a second subset of parameters, the second subset of parameters being different than the first subset of parameters, and for each of the plurality of cells in the sample, determining whether that cell is positive or negative for each parameter in the first subset of parameters;

a display device in communication with the computer processor, under control of the computer processor, displaying an interactive tree plot including a root, levels, branches and leaves, wherein each of the levels corresponds to a respective parameter in the first subset of parameters, wherein each of the levels divides the plurality of cells into a first subset of the plurality of cells which are determined to be positive for the respective parameter and a second subset of the plurality of cells which are determined to be negative for the respective parameter, wherein a path from the root to a first leaf defines a first phenotype based on a branch making up the path, and wherein a height of the first leaf corresponds to a count of cells determined to have the first phenotype; and

a user input device in communication with the computer processor, the user input device receiving a first user input on the interactive tree plot to select or deselect a first parameter of the first subset of parameters,

wherein the computer processor is further configured to select or deselect the first parameter from the first subset of parameters responsive to the first user input and the display device is further configured to alter the interactive tree plot to reflect an addition or removal of a level corresponding to the first parameter, and

wherein the user input device further receives a second user input to select the first leaf of the interactive tree plot and the computer processor, responsive to the second user input, identifies a subpopulation of cells associated with the first leaf, the subpopulation including each cell of the plurality of cells determined to have the first phenotype, the computer processor, responsive to the second user input, analyzes the subpopulation of cells on a second tree plot including second levels to determine a second phenotype for each of the cells in the subpopulation based on the second subset of parameters associated with the second levels, and the display device displays the second tree plot.

15. The apparatus of claim 14, further comprising the flow cytometer.

16. The apparatus of claim 14, wherein:

the display device further displays a third plot of parameters for a plurality of cells in the sample;

the input device receives user inputs a boundary for a gate for the parameters on the third plot; and

the computer processor determines whether a cell is positive or negative for a parameter of the third plot based, at least in part, on the gate for the parameter.

17. The apparatus of claim 14, wherein the second tree plot includes a level corresponding to a parameter of the second subset of parameters.

18. The apparatus of claim 14, wherein at least one of the plurality of parameters is a presence of a marker, the marker being a cell-surface protein detectable using a labeled antibody, and wherein measurements of the plurality of parameters include measurements of a fluorescence of the labeled antibody.

19. The apparatus of claim 14, wherein:

the input device is further configured to receive a third user input on the second tree plot to select or deselect a second parameter of the second subset of parameters;

the processor is further configured, responsive to the third user input, to select or deselect the second parameter from the second subset of parameters; and

the display device is further configured, responsive to selecting or deselecting the second parameter from the second subset of parameters, to alter the second tree plot to reflect adding or removing a level corresponding to the second parameter.

20. An article of manufacture comprising a non-transitory computer readable storage medium having computer program code recorded thereon, that when executed by a processor, causes a method for analyzing cell populations in a sample to be carried out, the method comprising:

generating with a flow cytometer values for a plurality of parameters for each of a plurality of cells in the sample, the plurality of parameters including a first subset of parameters and a second subset of parameters, the second subset of parameters being different than the first subset of parameters;

for each of the plurality of cells in the sample, determining whether that cell is positive or negative for each parameter in the first subset of parameters;

displaying an interactive tree plot including a root, levels, branches and leaves, wherein each of the levels corresponds to a respective parameter in the first subset of parameters, wherein each of the levels divides the plurality of cells into a first subset of the plurality of cells which are determined to be positive for the respective parameter and a second subset of the plurality of cells which are determined to be negative for the respective parameter, wherein a path from the root to a first leaf defines a first phenotype based on a branch making up the path, and wherein a height of the first leaf corresponds to a count of cells determined to have the first phenotype;

receiving a first user input on the interactive tree plot to select or deselect a first parameter from the first subset of parameters;

responsive to the first user input, selecting or deselecting the first parameter from the first subset of parameters;

responsive to selecting or deselecting the first parameter from the first subset of the parameters, altering the interactive tree plot to reflect an addition or removal of a level corresponding to the first parameter;

receiving a second user input to select the first leaf of the interactive tree plot; and

responsive to the second user input, identifying a subpopulation of cells associated with the first leaf, the subpopulation including each cell of the plurality of cells determined to have the first phenotype, analyzing the subpopulation of cells on a second tree plot including second levels to determine a second phenotype for each of the cells in the subpopulation based on the second subset of parameters associated with the second levels, and displaying the second tree plot.

21. The article of manufacture of claim 20, wherein the method further comprises:

displaying a third plot of parameters for a plurality of cells in the sample;

receiving user inputs indicating a boundary of a gate for the parameters on the third plot; and

determining whether a cell is positive or negative for a parameter is based, at least in part, on the gate for the parameter.

22. The article of manufacture of claim 20, wherein at least one of the plurality of parameters is a presence of a marker, the marker being a cell-surface protein detectable using a labeled antibody, and wherein measurements of the plurality of parameters include measurements of fluorescence of the labeled antibody.

23. The article of manufacture of claim 20, wherein the method further comprises:

receiving a third user input on the second tree plot to select or deselect a second parameter of the second subset of parameters;

responsive to the third user input, selecting or deselecting the second parameter from the second subset of parameters; and

responsive to selecting or deselecting the second parameter from the second subset of parameters, altering the second tree plot to reflect adding or removing a level corresponding to the second parameter.