Systems and methods for analyses of biological samples

Abstract

Disclosed are methods, systems, and articles of manufacture for performing a process on biological samples. An analysis of biological samples in multiple regions of interest in a microfluidic device and a timeline correlated with the analysis may be identified. One or more region-of-interest types for the multiple regions of interest may be determined; and multiple characteristics may be determined for the biological samples based at least in part upon the one or more region-of-interest types. Associated data that respectively correspond to the multiple regions of interest in a user interface for at least a portion of the biological samples in the user interface based at least in part upon the multiple identifiers and the timeline. A count of the biological samples in a region of interest may be determined based at least in part upon a class or type of data using a convolutional neural network (CNN).

1 - 50 . (canceled) 
     
     
         51 . A method for analyzing biological samples, comprising:
 identifying an analysis of biological samples in multiple regions of interest in a microfluidic device;   identifying, by a processor, filtered regions of interest by applying a filter to reduce the multiple regions of interest to include single biological sample regions of interest that each have single biological samples disposed within and not include multiple biological sample regions of interest that each include more than one biological samples disposed within;   determining, by the processor, multiple characteristics for the single biological samples in the filtered regions of interest, wherein the multiple characteristics respectively correspond to an attribute, a property, or a quantifiable metric for the single biological samples; and   arranging and rendering, by the processor, associated data from the analysis that respectively correspond to the filtered regions of interest in a user interface for at least a portion of the biological samples based at least in part upon the multiple characteristics.   
     
     
         52 . The method of  claim 51 , wherein the biological samples are T cells. 
     
     
         53 . The method of  claim 52 , wherein the analysis is a multiplex cytokine assay, and the multiple characteristics includes a plurality of cytokines secreted from the T cells. 
     
     
         54 . The method of  claim 53 , wherein arranging and rendering the associated data comprises determining a gallery structure having a plurality of gallery sub-structures for the analysis results based at least in part upon an allocable space in the user interface for rendering the analysis results, and wherein determining the gallery structure comprises:
 determining, by the processor, a first sequence of data correlated with a set of time points or time periods for a first biological sample obtained from a first region of interest of the multiple regions of interest from the gallery structure stored in an addressable space in a non-transitory computer accessible storage medium, wherein the first sequence of data corresponds to at least a first characteristic of the multiple characteristics;   determining, by the processor, a second sequence of data correlated with the set of time points or time periods for a second biological sample obtained from a second region of interest of the multiple regions of interest from the gallery structure, wherein the second sequence of data corresponds to at least a second characteristic of the multiple characteristics;   in response to a selection of the at least the first characteristic from the multiple characteristics with a first selection widget in the user interface, extracting, by the processor, a first value of at least the first characteristic from a plurality of values for the first biological sample or for the analysis; and   extracting, by the processor, a second value of at least the first characteristic from the plurality of values for the second biological sample or for the analysis.   
     
     
         55 . The method of  claim 54 , wherein rendering the analysis results comprises:
 rendering, by the processor, a first interactive object and a second interactive object respectively corresponding to the first sequence of data and the second sequence of data into the gallery view, wherein the first interactive object is representative of the first value for the first biological sample or for the analysis, and the second interactive object is representative of the second value for the second biological sample or for the analysis.   
     
     
         56 . The method of  claim 51 , further comprising:
 in response to an invocation of a timeline view through a timeline view activation interactive widget in the user interface based at least in part upon the timeline, rendering, by the processor, the timeline view and a matching grid portion in the user interface.   
     
     
         57 . The method of  claim 56 , wherein:
 the timeline view comprises a respective progress of multiple workflow tasks in the analysis of the biological samples, and   the respective progress graphically indicates respective temporal durations of the multiple workflow tasks.   
     
     
         58 . The method of  claim 51 , further comprising:
 associating, by the processor, a first region of interest of the multiple regions of interest with one or more graphical elements illustrated in a timeline view.   
     
     
         59 . The method of  claim 58 , wherein rendering the analysis results comprises:
 determining, by the processor, a timeline based at least in part upon a pipeline or a workflow comprising the multiple workflow tasks for the analysis of the biological samples.   
     
     
         60 . The method of  claim 59 , wherein rendering the analysis results comprises:
 determining, by the processor, a plurality of stages for the analysis based at least in part upon the timeline, wherein the plurality of stages respectively corresponds to a plurality of timepoints or time periods for the analysis of the biological samples.   
     
     
         61 . The method of  claim 60 , wherein rendering the analysis results comprises:
 respectively determining, by the processor, a plurality of graphic representations for the plurality of stages based at least in part upon the plurality of timepoints or time periods.   
     
     
         62 . The method of  claim 51 , further comprising rendering, by the processor, a data control view in the user interface, rendering the data control view comprising:
 generating a microfluidic device data structure having a plurality of fields for the microfluidic device, wherein the microfluidic device has a plurality of chambers.   
     
     
         63 . The method of  claim 62 , wherein rendering the data control view comprises:
 populating first data correlated with the microfluidic device into a first field in the microfluidic device data structure, wherein the first data comprises a first identifier of the microfluidic device.   
     
     
         64 . The method of  claim 51 , further comprising rendering, by the processor, a filter view in the user interface, wherein rendering the filter view comprises:
 determining a first filter type for a first filter based at least in part upon an execution of one or more instructions triggered by an interaction with a first filter selector switch in a filter generation module.   
     
     
         65 . The method of  claim 64 , wherein rendering the filter view further comprises:
 dynamically determining and displaying, by the processor, in the filter view for the microfluidic device, a first total number of regions of interest for a first set of filtered regions of interest that satisfies a first dynamic constraint of the first filter applied to the multiple regions of interest.   
     
     
         66 . The method of  claim 64 , wherein rendering the filter view further comprises:
 generating, by the processor, at a filter generation module, a logical combination of at least a second filter of a second filter type and the first filter of the first filter type.   
     
     
         67 . The method of  claim 51 , further comprising generating, by the processor, a bioinformatics pipeline view, wherein generating the bioinformatics pipeline view comprises:
 determining a sequencing dataset for the biological samples in a plurality of chambers or the multiple regions of interest of the microfluidic device, wherein the biological samples each comprise a sequence of nucleotides or amino acids.   
     
     
         68 . The method of  claim 67 , wherein generating the bioinformatics pipeline view further comprises:
 in response to a first interaction with a first sequencing view widget in the user interface, rendering, by the processor, a first sequencing view in the bioinformatics pipeline view that illustrates a distribution of an attribute of a sequence of first biological samples including at least one of a sequence of nucleotides, a sequence of amino acids, or a sequence of macromolecules in the plurality of chambers or the multiple regions of interest of the microfluidic device.   
     
     
         69 . The method of  claim 68 , wherein generating the bioinformatics pipeline view further comprises:
 overlaying the first sequencing view with first information that comprises one or more statistical measures of the distribution of the attribute of multiple sequences of first biological samples, the multiple sequences of first biological samples including the sequence of first biological samples, wherein the user interface comprises a total number of the multiple sequences of first biological samples, a total number of regions of interest having the sequence of first biological samples, and a respective total number of one or more sequences of first biological samples in a respective region of interest of the array of regions of interest.   
     
     
         70 . The method of  claim 51 , wherein the multiple characteristics correspond to one or more attributes that further comprise at least one of an identifier of a region of interest in the microfluidic device, a size attribute of the biological samples, a maximum brightness attribute for the biological samples, a minimum brightness attribute for the biological samples, a first pixel count attribute in a first direction for a centroid of a first biological sample, a second pixel count attribute in a second direction for the centroid of the biological sample, a size attribute for the centroid of the biological sample, a time lapse index attribute, a device identifier for the microfluidic device, a biological sample count attribute, a verified biological sample count attribute, a biological sample type attribute, a score attribute of the plurality of regions of interest, a gate path index, an area pixel attribute, a background pixel attribute, or a median brightness attribute for the plurality of biological samples. 
     
     
         71 . A computer program product, comprising one or more non-transitory computer-readable media having computer program instructions stored therein, the computer program instructions being configured such that, when executed by one or more computing devices, the computer program instructions cause the one or more computing devices to:
 identify an analysis of biological samples in multiple regions of interest in a microfluidic device;   identify filtered regions of interest by applying a filter to reduce the multiple regions of interest to include single biological sample regions of interest that each have single biological samples disposed within and not include multiple biological sample regions of interest that each include more than one biological samples disposed within;   determine multiple characteristics for the single biological samples in the filtered regions of interest, wherein the multiple characteristics respectively correspond to an attribute, a property, or a quantifiable metric for the single biological samples; and   arrange and render associated data from the analysis that respectively correspond to the filtered regions of interest in a user interface for at least a portion of the biological samples based at least in part upon the multiple characteristics.   
     
     
         72 . A system, comprising:
 one or more processors;   a memory coupled with the one or more processors, wherein the memory is configured to provide the one or more processors with instructions which when executed cause the one or more processors to:   identify an analysis of biological samples in multiple regions of interest in a microfluidic device;   identify filtered regions of interest by applying a filter to reduce the multiple regions of interest to include single biological sample regions of interest that each have single biological samples disposed within and not include multiple biological sample regions of interest that each include more than one biological samples disposed within;   determine multiple characteristics for the single biological samples in the filtered regions of interest, wherein the multiple characteristics respectively correspond to an attribute, a property, or a quantifiable metric for the single biological samples; and arrange and render associated data from the analysis that respectively correspond to the filtered regions of interest in a user interface for at least a portion of the biological samples based at least in part upon the multiple characteristics.