Identifying and extracting clusters of points from image

조회 수: 54 (최근 30일)
Rebecca
Rebecca 2024년 12월 5일 19:43
댓글: Image Analyst 2024년 12월 8일 19:39
I have images containing different groups of points, as in the attached image (example for two groups). I need to identify the distinct groups of points, and extract the information into separate files for each group. The groups vary in size and location across images, and the distance between groups also varies. Can anyone suggest a method(s) of doing so?

이 질문에 답변하려면 로그인하십시오.

채택된 답변

Subhajyoti
Subhajyoti 2024년 12월 5일 20:52
편집: Subhajyoti 2024년 12월 5일 20:54
Ran in:
Hi @Rebecca,
It is my understanding that you are trying to extract and cluster the data points from the image input.
Here, in the following implementation, I have loaded the image into MATLAB and generated the binary image.
% Read the image
imgPath = 'image (2).png';
img = imread(imgPath);
% Convert to grayscale if necessary
if size(img, 3) == 3
img = rgb2gray(img);
end
% Convert to binary image
bw = ~imbinarize(img)
bw = 360x922 logical array
Columns 1 through 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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You can use the 'bwconncomp' function to find and count points (connected components) in the binary image.
cc = bwconncomp(bw);
% Extract properties
stats = regionprops(cc, 'Centroid', 'BoundingBox')
stats = 29x1 struct array with fields:
Centroid BoundingBox
Now, we can perform clustering on the detected points. Since the number of clusters is unknown, I have used 'dbscan' function to perform Density-Based Spatial Clustering of Applications with Noise.
% Initialize an array to store centroids
coordinates = zeros(length(stats), 2);
% Loop through each component to get the centroid
for k = 1:length(stats)
coordinates(k, :) = stats(k).Centroid;
end
% Set parameters for DBSCAN
epsilon = 100; % Maximum distance for two points to be considered as in the same neighborhood
minpts = 1; % Minimum number of points required to form a dense region
% Perform DBSCAN clustering
clusterIndices = dbscan(coordinates, epsilon, minpts);
% Determine the number of clusters (excluding noise)
numClusters = max(clusterIndices);
fprintf('Number of clusters using DBSCAN: %d\n', numClusters);
Number of clusters using DBSCAN: 2
% Optional: Visualize the clusters
gscatter(coordinates(:,1), coordinates(:,2), clusterIndices);
title('DBSCAN Clustering of Binary Image');
ylim([0, size(bw, 1)]);
xlim([0, size(bw, 2)]);
Refer to the following MathWorks Documentations to know about clustering in MATLAB:
  댓글 수: 2
Rebecca
Rebecca 2024년 12월 5일 22:57
Thank you! Running this code on a more complex example didnt work (points in the interior of groups didn't show) so I'm fiddling with the code to see if I can fix that. Thanks again! Will accept your answer.
Image Analyst
Image Analyst 2024년 12월 8일 19:39
You may have to adjust epsilon until it produces a classification that you agree with.

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추가 답변 (2개)

Matt J
Matt J 2024년 12월 5일 20:04
Perhaps clusterdata.
Image Analyst
Image Analyst 2024년 12월 5일 21:45
If you know the number of clusters, then kmeans or knnsearch might be the way to go, or even SVM (support vector machine). If you don't know the number of clusters then I think dbscan is the way to go. It identifies clusters by whether the points can be connected by links (distances) of less than a certain distance. So sometimes the clusters are very compact in shape but other times the shape can look very tortuous/gerrymandered. If a point is farther than the specified distance threshold from any other point, then it's essentially a cluster all by itself (just a single point cluster - it's noise). I'm attaching my dbscan demo:
The red spots are isolated single points not in any other cluster. The yellow spots are centroids of 2 or more clustered points. The ring/circle is showing you the search radius (distance threshold parameter). Any points within that radius will be considered to be the same cluster.
For more info see wikipedia:
https://en.wikipedia.org/wiki/DBSCAN
Note: in the diagram above the red and yellow points are all in the same cluster (because they're all within a radius of at least one other point), while point N is a noise point all by itself (a different group/cluster of just one point).
  댓글 수: 2
Image Analyst
Image Analyst 2024년 12월 5일 21:49
My answer above assumes you know how to get the coordinates of the points. If you have spots in your image and don't yet know how to find the (x,y) centroids of the spots, then see my Image Segmentation Tutorial in my File Exchange:
Image Analyst's File Exchange
It's a generic, general purpose demo of how to threshold an image to find blobs, and then measure things about the blobs, and extract certain blobs based on their areas or diameters.
Rebecca
Rebecca 2024년 12월 5일 22:56
Thanks for the suggestion of dbscan. I'll look into it! I do have the coordindates of each point, so don't need the image segmentation portion, but your tutorial looks great!

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