Methods and apparatus related to gate boundaries within a data space

• US 9,183,237 B2
• Filed: 11/26/2012
• Issued: 11/10/2015
• Est. Priority Date: 07/10/2008
• Status: Expired due to Fees

• Current Assignee: Nodality Inc.
• Original Assignee: Nodality Inc.
• Inventors: Banville, Steven C., Putta, Santosh K., Spellmeyer, David C., Wale, Nikil, Evensen, Erik, Purvis, Norman, Friedland, Greg
• Primary Examiner(s): Raymond, Edward
• Application Number:
  US13/685,110
• Publication Number:
  US 20130173618A1
• Time in Patent Office: 1,079 Days
• Field of Search: 702/179, 702182-185
• US Class Current: 1/1
• CPC Class Codes: G06F 16/22 Indexing; Data structures therefor; Storage structures
• CPC Class Codes: G06F 18/40 Software arrangements specially adapted for pattern recognition, e.g. user interfaces or toolboxes therefor
• CPC Class Codes: G06V 20/69 Microscopic objects, e.g. biological cells or cellular parts

Abstract

In one embodiment, one or more processor-readable media storing code representing instructions that when executed by one or more processors cause the one or more processors to receive a set of parameter values defining a boundary within a data space associated with a dataset. The dataset can represent signaling related to a test substance. A first metric can be defined based on a first portion of the dataset associated with a first region defined by the boundary. A second metric can be defined based on a second portion of the dataset associated with a second region defined by the boundary after the boundary is modified. The second region can be different than the first region.

Claims

1. One or more non-transitory processor readable-media storing code representing instructions that when executed by one or more processors cause the one or more processors to:

maintain a database having at least one user-provided cell population definition and at least one associated definition of a well;

define logic to describe the at least one user-provided cell population;

receive data associated with at least one experiment;

generate a plurality of boundaries to a plurality of separate regions to define gating data associated with the data associated with the at least one experiment;

identify outlying data points from the data associated with the at least one experiment for manual review using statistical analysis on the gating data;

highlight and tag a boundary from the plurality of boundaries that is likely to be incorrect based on the gating data;

adjust the boundary from the plurality of boundaries;

provide, to a user, data associated with the at least one experiment and the boundary such that the user can visualize the effect on the data associated with the at least one experiment and the boundary before and after adjusting the boundary; and

store a user preference associated with the adjusting the boundary.

2. The one or more non-transitory processor-readable media of claim 1, wherein the code to cause the one or more processors to adjust includes code to cause the one or more processors to adjust the boundary based on a gating sensitivity algorithm, biological knowledge, the user preference, or a signal from a user associated with adjusting the boundary.

3. The one or more non-transitory processor-readable media of claim 1, wherein the code to cause the processor to receive includes code to cause the processor to receive data from at least one of a flow cytometry experiment or a mass spectrometry experiment.

4. The one or more non-transitory processor-readable media of claim 1, wherein the code further comprises code to cause the one or more processors to:

derive a population hierarchy based on the at least one user-provided cell population.

5. The one or more non-transitory processor-readable media of claim 1, wherein the code to cause the processor to generate includes code to cause the processor to generate the plurality of boundaries using intracellular markers, surface markers, scatter patterns, or expression markers.

6. One or more non-transitory processor-readable media storing code representing instructions that when executed by one or more processors cause the one or more processors to:

receive a set of parameter values defining a boundary within a data space associated with a dataset, the dataset representing signaling related to a test substance;

define a first metric based on a first portion of the dataset associated with a first region defined by the boundary;

modify the boundary; and

define a second metric based on a second portion of the dataset associated with a second region defined by the boundary after the boundary is modified, the second region being different than the first region.

7. The one or more non-transitory processor-readable media of claim 6, wherein the boundary is modified based on a random number.

8. The one or more non-transitory processor-readable media of claim 6, wherein the boundary includes a vertex, the modifying of the boundary includes modifying the vertex of the boundary.

9. The one or more non-transitory processor-readable media of claim 6, wherein the modifying of the boundary includes scaling the boundary along an axis.

10. The one or more non-transitory processor-readable media of claim 6, further storing code representing instructions that when executed by the one or more processors cause the one or more processors to:

define an axis of the boundary based on an Eigenvector, the boundary being modified along the axis based on a random number.

11. The one or more non-transitory processor-readable media of claim 6, further storing code representing instructions that when executed by the one or more processors cause the one or more processors to:

define an axis based on an orientation of the dataset within the data space, the modifying of the boundary is based on the axis.

12. The one or more non-transitory processor-readable media of claim 6, wherein the boundary includes a vertex,

the one or more processor-readable media further storing code representing instructions that when executed by the one or more processors cause the one or more processors to:

define an axis based on a shape mathematically fitted to the boundary, the modifying of the boundary includes modifying the vertex of the boundary based on the axis.

13. The one or more non-transitory processor-readable media of claim 6, wherein the modifying of the boundary is performed based on a user preference.

14. The one or more non-transitory processor-readable media of claim 6, wherein the first portion of the dataset includes a plurality of datapoints outside of the data space.

15. The one or more non-transitory processor-readable media of claim 6, wherein the boundary is a first boundary, the dataset is defined based on a second boundary within the data space, the first boundary being logically related to the second boundary.

16. The one or more non-transitory processor-readable media of claim 6, wherein the boundary is a first boundary, the first region is based on a combination of the first boundary and a second boundary,

the one or more non-transitory processor-readable media further storing code representing instructions that when executed by the one or more processors cause the one or more processors to:

modify the second boundary, the second region is based on a combination of the second boundary after the second boundary is modified and the first boundary after the first boundary is modified.

17. One or more non-transitory processor-readable media storing code representing instructions that when executed by one or more processors cause the one or more processors to:

receive a set of parameter values defining a first boundary within a data space associated with a dataset, the first boundary defining a region inside the first boundary, the dataset representing signaling related to a test substance;

receive a set of parameter values defining a second boundary circumscribing the first boundary, the second boundary being within the data space; and

define a plurality of metrics based on a portion of the dataset included in the region and based on a plurality of relationships between a plurality of perturbations of the second boundary and a portion of the dataset outside of the region.

18. The one or more non-transitory processor-readable media of claim 17, further storing code representing instructions that when executed by the one or more processors cause the one or more processors to:

receive a set of parameter values defining a third boundary circumscribing the second boundary, each perturbation from the plurality of perturbations of the second boundary being within a region between the first boundary and the third boundary.

19. The one or more non-transitory processor-readable media of claim 17, wherein the region is a first region,

further storing code representing instructions that when executed by the one or more processors cause the one or more processors to:

receive a set of parameter values defining a third boundary circumscribing the second boundary, the portion of the dataset outside of the first region is within a second region between the second boundary and the third boundary.

20. The one or more non-transitory processor-readable media of claim 17, wherein the region is a first region,

further storing code representing instructions that when executed by the one or more processors cause the one or more processors to:

receive a set of parameter values defining a third boundary circumscribing the second boundary, each perturbation from the plurality of perturbations is defined by a vertex located within a second region between the second boundary and the third boundary.