CN112557285A - Automatic gating method and device for flow cytometry detection data - Google Patents
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Abstract
The application provides a method and a device for automatically setting a gate of flow cytometry detection data, wherein the method comprises the following steps: acquiring an original cell sampling event matrix and a flow cell gating template; judging whether the channel rule of the current gating channel is empty or not based on the dependency relationship graph of the flow cytometry gating template, and if so, calculating the number of cells and the percentage of the cells; if not, judging the channel rule identifier of the currently set door channel; and if the first channel rule identifier is the first channel rule identifier, executing a static gate setting method; and if the channel is the second channel rule identifier, executing a dynamic gate setting method. The channel rule identification can be adjusted according to different samples, and the method combining dynamic gate setting and static gate setting is adopted, so that the adaptability and the accuracy of abnormal samples are improved.
Description
Technical Field
The invention relates to the field of data processing, in particular to a method and a device for automatically setting a gate for flow cytometry detection data.
Background
Flow cytometry is a technique that can accurately and rapidly perform multi-parameter quantitative analysis on physicochemical and biological properties of biological cells and sort specific cell populations. The flow cytometry is used for classifying, analyzing and identifying cells by receiving various optical signals of the cells in the liquid flow after laser irradiation. The data recorded by the flow cytometer typically includes scattered light intensity and fluorescence intensity, among other data. Typically, the scattered and fluorescent signals induced by a single cell are recorded as a single event, and all events are assembled into complete flow cytometer data for the cell population being tested. The flow cytometer collects the optical signals of each channel and analyzes the cells by using a gating technique. Gating requires that a range of target cell populations be specified in certain dimensions and analyzed. In the existing analysis method of flow cytometry data, professionals generally project each event into a two-dimensional or three-dimensional domain, and analyze the event in a manual gating mode to judge whether each cell group is normal or abnormal. The main problems of manual analysis are low speed, low efficiency and easy error. For the existing automatic programming method, it is generally assumed that the cells are good and the grouping is obvious. However, this method is not suitable for cases where the cell population distributions overlap each other or the target cell population is not easily determined, and is liable to cause a large error or to make it difficult to achieve the uniformity of the results.
Disclosure of Invention
The technical problem that this application will be solved overcomes the not enough that exists among the above-mentioned prior art, provides one kind through computer software algorithm, and the accuracy is to flow formula cell detection data and is carried out quick automatic gate setting, contains sample class crowd figure and all kinds of crowd total numbers in the data that obtain.
The method combines the data characteristics of the flow cytometer, provides an automatic gate setting method for flow cytometry detection data, and can quickly obtain the classification information of the samples in the data by adjusting the channel rule marks of different samples and adopting a method combining static gate setting and dynamic gate setting. The analysis method has high accuracy of the result of analyzing the flow cytometry detection data, and the analysis time is far shorter than the time of manually analyzing the data and other analysis methods at present.
The technical scheme adopted by the application comprises the following steps:
a flow cytometry data automatic gating method comprises the following steps:
step 1: reading the fcs flow cytometry file and the gating template file, and acquiring an original cell sampling event matrix and a flow cytometry gating template;
step 2, judging whether the channel rule of the current gating channel is empty or not based on the dependency graph of the flow cytometry gating template; and the number of the first and second groups,
if not, entering the step 3;
if yes, entering step 4;
and step 3: judging a channel rule identifier of a current door channel; and the number of the first and second groups,
if the first channel rule identifier is the first channel rule identifier, executing a static gate setting method;
if the channel is the second channel rule identifier, executing a dynamic gate setting method;
and 4, step 4: calculating the number of cells and the percentage of the cells;
wherein the channel rule identification comprises no expression, low expression, high expression, interval or threshold;
the first channel rule identification comprises a region or threshold; the second channel rule identification comprises no expression, low expression, expression or high expression;
the static door setting method comprises the following steps: judging a first channel rule identifier of a current door channel; and the number of the first and second groups,
if the first channel rule of the current gating channel is identified as an interval, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is not in the interval range, updating the current cell sampling event matrix, and returning to the step 2;
if the first channel rule identifier of the current gating channel is a threshold value, deleting all rows in the current cell sampling event matrix, of which the current gating channel values do not meet the threshold value requirement, updating the current cell sampling event matrix, and returning to the step 2;
the dynamic door setting method comprises the following steps:
a: digitizing the current gating channel value in the current cell sampling event matrix to generate a histogram, and then finding out all wave crests and wave troughs based on the histogram;
b: judging a second channel rule identifier of the current door channel; and the number of the first and second groups,
if the second channel rule identifier of the current gating channel is high expression, selecting a wave trough with the largest channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the step 2;
if the second channel rule identifier of the current gating channel is low expression or expression, selecting a wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the step 2;
if the second channel rule mark of the current gating channel is not expressed, selecting a wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is greater than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the step 2;
counting the number of rows of a current cell sampling event matrix; the percentage calculation method is the number of rows of the current cell sampling event matrix divided by the number of rows of the original cell sampling event matrix.
Preferably, the method for searching the peak in the dynamic gating method is to determine values of the left and right sides of each point of the histogram, and when the values are greater than the values of the left and right sides, the values are regarded as the peak; the method for searching the wave trough is to judge the values of the left side and the right side of each point of the histogram, and when the values are smaller than the values of the left side and the right side, the values are regarded as the wave trough.
Preferably, step 2 is preceded by performing fluorescence compensation on the obtained raw cell sampling event matrix.
Preferably, the fluorescence compensation method is to subtract the sum of the products of all other fluorescence channel values and the corresponding fluorescence matrix from the current gating channel value.
In order to achieve the above object, the present application further provides an automatic gate setting device for flow cytometry data, comprising:
a data collection unit: the system is used for reading the fcs flow cytometry file and the gating template file, and acquiring an original cell sampling event matrix and a flow cytometry gating template;
the judging unit is used for judging whether the channel rule of the current gating channel is empty or not based on the flow cytometry gating template dependency graph;
setting a door unit: the channel rule identifier is used for determining the current door channel; if the first channel rule identifier is the first channel rule identifier, executing a static door setting module; if the channel is the second channel rule identifier, executing a dynamic door setting module;
the statistical unit is used for calculating the number of the cells and the percentage of the cells;
wherein the static set door module is further configured to:
judging a first channel rule identifier of a current door channel; and the number of the first and second groups,
if the first channel rule of the current gating channel is identified as an interval, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is not in the interval range, updating the current cell sampling event matrix, and returning to the judging unit;
if the first channel rule identifier of the current gating channel is a threshold value, deleting all rows in the current cell sampling event matrix, the current gating channel value of which does not meet the requirement of the threshold value, updating the current cell sampling event matrix, and returning to the judging unit;
the dynamic door setting module is further configured to:
digitizing the current gating channel value in the current cell sampling event matrix to generate a histogram, and then finding out all wave crests and wave troughs based on the histogram;
judging a second channel rule identifier of the current door channel; and the number of the first and second groups,
if the second channel rule identifier of the current gating channel is high expression, selecting a wave trough with the largest channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the judging unit;
if the second channel rule identifier of the current gating channel is low expression or expression, selecting a wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the judging unit;
if the second channel rule mark of the current gating channel is not expressed, selecting a wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is greater than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the judging unit;
counting the number of rows of a current cell sampling event matrix; the percentage calculation method is the number of rows of the current cell sampling event matrix divided by the number of rows of the original cell sampling event matrix.
The method comprises the steps that a set of flow cell detection data is analyzed, aiming at the specificity of a detected sample, a channel rule identifier can be adjusted according to different samples, a method combining dynamic gating and static gating is adopted, when the boundary point of a positive peak and a negative peak is not obvious, a method of manually setting an interval or a threshold value is adopted, the channel rule identifier of a current gated channel is a first channel rule identifier, and a static gating method is executed; when the positive peak and the negative peak are clearly separated, the current channel rule identification of the gating channel is the second channel rule identification, and a dynamic gating method is executed, so that the defects caused by a fixed boundary classification method are overcome, and the adaptability and the accuracy of the abnormal sample are improved.
Drawings
Fig. 1 is a flowchart of an automatic gating method for flow cytometry data according to an embodiment of the present disclosure;
fig. 2 is a flowchart of a static gating method for flow cytometry data according to an embodiment of the present disclosure;
FIG. 3 is a flowchart of a method for dynamically gating flow cytometry data according to an embodiment of the present disclosure;
fig. 4 is a schematic diagram of an automatic gate setting device for flow cytometry data according to an embodiment of the present disclosure.
Detailed Description
The technical solutions of the embodiments of the present application are clearly and completely described below with reference to the drawings in the embodiments of the present application, and it is obvious that the described embodiments are only a part of the embodiments of the present application, and not all of the embodiments. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present application.
Fig. 1 is a flowchart illustrating an automatic gating method for flow cytometry data according to an embodiment of the present disclosure. As shown in fig. 1, the automatic gating method for flow cytometry data comprises the following steps:
Wherein, the fluorescence compensation is carried out on the obtained original cell sampling event matrix. The fluorescence compensation method is that the sum of the products of all other fluorescence channel values and the corresponding fluorescence matrix is subtracted from the current set gate channel value.
Wherein the channel rule identification comprises no expression, low expression, high expression, interval or threshold;
the first channel rule identification comprises a region or threshold; the second channel rule identification comprises no expression, low expression, expression or high expression.
As shown in fig. 2, a flowchart of a static gating method for flow cytometry data according to an embodiment of the present application includes, in step 400, the static gating method includes the following steps:
And step 420, deleting all rows in the current cell sampling event matrix, of which the current gating channel values are not in the interval range, updating the current cell sampling event matrix, and returning to the step 200.
And 430, deleting all rows in the current cell sampling event matrix, the current gating channel values of which do not meet the threshold requirement, updating the current cell sampling event matrix, and returning to the step 200.
As shown in fig. 3, a flowchart of a dynamic gating method for flow cytometry data according to an embodiment of the present application, in step 500, the dynamic gating method includes the following steps:
and 510, if the cell sampling event matrix is identified by the second channel rule, digitizing the current gating channel value in the compensated current cell sampling event matrix to generate a histogram, and then finding out all wave crests and wave troughs based on the histogram.
The method for searching the wave crest is to judge the values of the left side and the right side of each point of the histogram, and when the values are larger than the values of the left side and the right side, the values are regarded as the wave crest; the method for searching the wave trough is to judge the values of the left side and the right side of each point of the histogram, and when the values are smaller than the values of the left side and the right side, the wave trough is regarded as the wave trough.
And 530, selecting a trough with the largest channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected trough, updating the current cell sampling event matrix, and returning to 200.
And 540, selecting the wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, wherein the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to 200.
And 550, selecting the wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is greater than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the step 200.
Counting the number of rows of a current cell sampling event matrix; the percentage calculation method is the number of rows of the current cell sampling event matrix divided by the number of rows of the original cell sampling event matrix.
As shown in fig. 4, a schematic diagram of an automatic gate setting device for flow cytometry data according to an embodiment of the present disclosure includes:
a data collection unit: the system is used for reading the fcs flow cytometry file and the gating template file, and acquiring an original cell sampling event matrix and a flow cytometry gating template;
the judging unit is used for judging whether the channel rule of the current gating channel is empty or not based on the flow cytometry gating template dependency graph;
setting a door unit: the channel rule identifier is used for determining the current door channel; if the first channel rule identifier is the first channel rule identifier, executing a static door setting module; if the channel is the second channel rule identifier, executing a dynamic door setting module;
the statistical unit is used for calculating the number of the cells and the percentage of the cells;
wherein the static set door module is further configured to:
judging a first channel rule identifier of a current door channel; and
if the first channel rule mark of the gating channel is an interval, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is not in the interval range, updating the current cell sampling event matrix, and returning to the judging unit;
and if the first channel rule identifier of the current gating channel is a threshold value, deleting all rows in the current cell sampling event matrix, the current gating channel value of which does not meet the threshold value requirement, updating the current cell sampling event matrix, and returning to the judging unit.
The dynamic door setting module is further configured to:
digitizing the current gating channel value in the current cell sampling event matrix to generate a histogram, and then finding out all wave crests and wave troughs based on the histogram;
judging a second channel rule identifier of the current door channel; and the number of the first and second groups,
if the second channel rule identifier of the current gating channel is high expression, selecting a wave trough with the largest channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the judging unit;
if the second channel rule identifier of the current gating channel is low expression or expression, selecting a wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the judging unit;
if the second channel rule mark of the current gating channel is not expressed, selecting a wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is greater than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the judging unit;
the counting unit counts the number of the current cell sampling event matrix lines; the percentage calculation method is the number of rows of the current cell sampling event matrix divided by the number of rows of the original cell sampling event matrix.
It will be understood by those skilled in the art that all or part of the steps of the methods in the above embodiments may be implemented by a program instructing associated hardware, and the program may be stored in a computer-readable storage medium, which may include a read-only memory, a random access memory, a magnetic or optical disk, and the like.
The present application has been described above with reference to specific examples, which are provided only to aid understanding of the present application and are not intended to limit the present application. Variations of the above-described embodiments may occur to those of ordinary skill in the art in light of the teachings of this application.
Claims (5)
1. A flow cytometry data automatic gating method is characterized by comprising the following steps:
step 1: reading the fcs flow cytometry file and the gating template file, and acquiring an original cell sampling event matrix and a flow cytometry gating template;
step 2, acquiring a channel rule of the current gating channel based on the flow cytometry gating template dependency relationship diagram, and judging whether the channel rule of the current gating channel is empty; and the number of the first and second groups,
if not, entering the step 3;
if yes, entering step 4;
and step 3: judging a channel rule identifier of a current door channel; and the number of the first and second groups,
if the first channel rule identifier is the first channel rule identifier, executing a static gate setting method;
if the channel is the second channel rule identifier, executing a dynamic gate setting method;
and 4, step 4: calculating the number of cells and the percentage of the cells;
wherein the channel rule identification comprises no expression, low expression, high expression, interval or threshold;
the first channel rule identification comprises a region or threshold; the second channel rule identification comprises no expression, low expression, expression or high expression;
the static door setting method comprises the following steps: judging a first channel rule identifier of a current door channel; and the number of the first and second groups,
if the first channel rule of the current gating channel is identified as an interval, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is not in the interval range, updating the current cell sampling event matrix, and returning to the step 2;
if the first channel rule identifier of the current gating channel is a threshold value, deleting all rows in the current cell sampling event matrix, of which the current gating channel values do not meet the threshold value requirement, updating the current cell sampling event matrix, and returning to the step 2;
the dynamic door setting method comprises the following steps:
a: digitizing the current gating channel value in the current cell sampling event matrix to generate a histogram, and then finding out all wave crests and wave troughs based on the histogram;
b: judging a second channel rule identifier of the current door channel; and the number of the first and second groups,
if the second channel rule identifier of the current gating channel is high expression, selecting a wave trough with the largest channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the step 2;
if the second channel rule identifier of the current gating channel is low expression or expression, selecting a wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the step 2;
if the second channel rule mark of the current gating channel is not expressed, selecting a wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is greater than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the step 2;
counting the number of rows of a current cell sampling event matrix; the percentage calculation method is the number of rows of the current cell sampling event matrix divided by the number of rows of the original cell sampling event matrix.
2. The method of claim 1, wherein the peak is found by determining the values of the histogram on the left and right sides of each point, and when the values are greater than the values on the left and right sides, the peak is determined; the method for searching the wave trough is to judge the values of the left side and the right side of each point of the histogram, and when the values are smaller than the values of the left side and the right side, the values are regarded as the wave trough.
3. The flow cytometry data automatic gating method of claim 1, wherein step 2 is preceded by fluorescence compensating the acquired raw cell sampling event matrix.
4. The flow cytometry data auto-gating method of claim 3, wherein the fluorescence compensation method is the current gating channel value minus the sum of the products of all other fluorescence channel values and their corresponding fluorescence matrix.
5. A flow cytometry data automatic gate setting device is characterized by comprising:
a data collection unit: the system is used for reading the fcs flow cytometry file and the gating template file, and acquiring an original cell sampling event matrix and a flow cytometry gating template;
the judging unit is used for judging whether the channel rule of the current gating channel is empty or not based on the flow cytometry gating template dependency graph;
setting a door unit: the channel rule identifier is used for determining the current door channel; if the first channel rule identifier is the first channel rule identifier, executing a static door setting module; if the channel is the second channel rule identifier, executing a dynamic door setting module;
the statistical unit is used for calculating the number of the cells and the percentage of the cells;
wherein the static set door module is further configured to:
judging a first channel rule identifier of a current door channel; and the number of the first and second groups,
if the first channel rule of the current gating channel is identified as an interval, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is not in the interval range, updating the current cell sampling event matrix, and returning to the judging unit;
if the first channel rule identifier of the current gating channel is a threshold value, deleting all rows in the current cell sampling event matrix, the current gating channel value of which does not meet the requirement of the threshold value, updating the current cell sampling event matrix, and returning to the judging unit;
the dynamic door setting module is further configured to:
digitizing the current gating channel value in the current cell sampling event matrix to generate a histogram, and then finding out all wave crests and wave troughs based on the histogram;
judging a second channel rule identifier of the current door channel; and the number of the first and second groups,
if the second channel rule identifier of the current gating channel is high expression, selecting a wave trough with the largest channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the judging unit;
if the second channel rule identifier of the current gating channel is low expression or expression, selecting a wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is smaller than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the judging unit;
if the second channel rule mark of the current gating channel is not expressed, selecting a wave trough with the minimum channel value as a boundary point, deleting all rows in the current cell sampling event matrix, of which the current gating channel value is greater than the channel value of the selected wave trough, updating the current cell sampling event matrix, and returning to the judging unit;
counting the number of rows of a current cell sampling event matrix; the percentage calculation method is the number of rows of the current cell sampling event matrix divided by the number of rows of the original cell sampling event matrix.
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| TANG SHANJIANG: "An Adaptive Efficiency-Fairness Meta-Scheduler for DATA-Intensive Computing", 《TRANSACTIONS ON SERVICES COMPUTING》 * |
| 柴晓静: "网织血小板在急性白血病中的检测和临床意义", 《国际检验医学杂志》 * |
| 汤善江: "FJRR：一种基于阵列型数据划分应用的并行设计模式", 《计算机应用研究》 * |
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