How can I count the number of blobs in this image? - image-processing

I have an image which is a result of k-means segmentation. The code to obtain it it's here:
% Read the image and convert to L*a*b* color space
I = imread('Crop.jpg');
% h = ginput(2);
% Diameter = sqrt((h(2)-h(1))^2+(h(4)-h(3))^2);
% MeanArea = 3.14*(diameter^2)/4;
Ilab = rgb2lab(I);
% Extract a* and b* channels and reshape
ab = double(Ilab(:,:,2:3));
nrows = size(ab,1);
ncols = size(ab,2);
ab = reshape(ab,nrows*ncols,2);
% Segmentation usign k-means
nColors = 4;
[cluster_idx, cluster_center] = kmeans(ab,nColors,...
'distance', 'sqEuclidean', ...
'Replicates', 3);
% Show the result
pixel_labels = reshape(cluster_idx,nrows,ncols);
figure(1);
imshow(pixel_labels,[]), title('image labeled by cluster index');
Resulting in this picture:
Now as you can see, most of the elements are connected, so I want to count all of the blobs (besides the background one), then filter them using MeanArea, area of the elements incircle. If the blob has dimensions < MeanArea I do not count it, while if the blob has dimensions > MeanArea I want to divide its area by MeanArea to obtain the number of elements. All of this is to have a measure such that #blobs = #elements. I know that it has something to do with 'bwlabel' and 'regionprops' but I don't know how to code this since I'm a beginner, any coding help is appreciated. Thanks.
EDIT: using the 'trees' approach linked in the comments I got very bad results, so I don't think it's the right method. I don't have objects with same color as the tree example, I just have same shape.
I'm following this other approach. Color segmentation by k-means
I obtained the labeled image above, but how can I save it into a variable so that I can erode it and count the number of blobs? That's my question.
EDIT2: The original picture is this one. I'm trying to detect the number of red green and blue objects.

Related

In ImageJ, how to set pixel value to zero for any pixel intensity greater than some arbitrary value in the whole image?

I have Z-stacks of fluorescently labelled cells.
The samples have an artefact that causes very bright regions inside the cells which are not based on my signal of interest.
Since the intensity (brightness) of these artefacts is far above my signal of interest's intensity, I want to simply zero all those pixels that are above some arbitrary value I will chose.
So I want macro that logically does something like:
For each slice:
For each pixel:
if pixel intensity>150 then set pixel=0
I am coding in imageJ macro language. I want to avoid using ROIs for this part because I already have ROIs representing each cell and am looping through them in my script.
I think this should be really simple but right now my attempted solution is super cumbersome; going through thresholding, analyze particles, generating ROIs, selecting each ROI, and subtracting the value (e.g 150) from each ROI.
Any idea how this is done in simple way?
The problem is resolved using selection and thresholding:
HotPix = 150; Stack.getStatistics(voxelCount, mean, min, StackMax, stdDev); setThreshold(HotPix, StackMax); //your thresholds here for (i = 1; i <= nSlices; i++) { setSlice(i); run("Create Selection"); if (selectionType() != -1) { run("Set...", "value=0"); } run("Select None"); } resetThreshold;
the olsution comes from #antonis on imageJ forum: https://forum.image.sc/t/how-to-delete-all-pixels-or-set-to-zero-in-a-roi-which-are-above-a-certain-value/51173/5

How to classify images based on the amount of colors in the image?

I have a problem where all images have the same object; however, these objects can either have number_of_colors<=3 OR number_of_colors>3 and images are not labeled.
My attempt starts by converting RGB to LAB and Consider only the A & B to find the color coverage of that image. I was thinking of it as an area on the AB space. So for every image, I found the range of A and B (i.e max(A)-min(A), max(B)-min(B)) and multiplied them together to get the area, assuming it's a rectangle. Then I threshold using this feature.
Please let me know if intuition is correct and why it isn't working. Here is the confusion matrix:
TP: 0.41935483871, FN: 0.0645161290323
FP: 0.0967741935484, TN: 0.41935483871
Here is the basic routine the should work per image
LAB = rgb_to_lab(data_rgb[...,0],data_rgb[...,1],data_rgb[...,2])
A = LAB[1]
B = LAB[2]
minA,maxA = np.min(A),np.max(A)
minB,maxB = np.min(B),np.max(B)
diff_A = maxA - minA
diff_B = maxB - minB
area = diff_A * diff_B
# p is the normalized area
p = area/(200*200.)
# Found 0.53 to be the best possible threshold
if p >0.53:
print 'class 1 - colors > 3'
else:
print 'class 2 - colors <= 3'
Edit 1:
Here is an image to show how the threshold separates positive and negative images
Edit 2:
This shows the same plot but only considering A and B values with luminance between 16 and 70 which seems to increase the area of separation reduces the FP by 1.

Eliminating various backgrounds from image and segmenting object?

Let say I have this input image, with any number of boxes. I want to segment out these boxes, so I can eventually extract them out.
input image:
The background could anything that is continuous, like a painted wall, wooden table, carpet.
My idea was that the gradient would be the same throughout the background, and with a constant gradient. I could turn where the gradient is about the same, into zero's in the image.
Through edge detection, I would dilate and fill the regions where edges detected. Essentially my goal is to make a blob of the areas where the boxes are. Having the blobs, I would know the exact location of the boxes, thus being able to crop out the boxes from the input image.
So in this case, I should be able to have four blobs, and then I would be able to crop out four images from the input image.
This is how far I got:
segmented image:
query = imread('AllFour.jpg');
gray = rgb2gray(query);
[~, threshold] = edge(gray, 'sobel');
weightedFactor = 1.5;
BWs = edge(gray,'roberts');
%figure, imshow(BWs), title('binary gradient mask');
se90 = strel('disk', 30);
se0 = strel('square', 3);
BWsdil = imdilate(BWs, [se90]);
%figure, imshow(BWsdil), title('dilated gradient mask');
BWdfill = imfill(BWsdil, 'holes');
figure, imshow(BWdfill);
title('binary image with filled holes');
What a very interesting problem! Here's my solution in an attempt to solve this problem for you. This is assuming that the background has the same colour distribution throughout. First, transform your image from RGB to the HSV colour space with rgb2hsv. The HSV colour space is an ideal transform for analyzing colours. After this, I would look at the saturation and value planes. Saturation is concerned with how "pure" the colour is, while value is the intensity or brightness of the colour itself. If you take a look at the saturation and value planes for the image, this is what is shown:
im = imread('http://i.stack.imgur.com/1SGVm.jpg');
out = rgb2hsv(im);
figure;
subplot(2,1,1);
imshow(out(:,:,2));
subplot(2,1,2);
imshow(out(:,:,3));
This is what I get:
By taking a look at some locations in the gray background, it looks like the majority of the saturation are less than 0.2 as well as the elements in the value plane are greater than 0.3. As such, we want to find the opposite of those pixels to get our objects. As such, we find those pixels whose saturation is greater than 0.2 or those pixels with a value that is less than 0.3:
seg = out(:,:,2) > 0.2 | out(:,:,3) < 0.3;
This is what we get:
Almost there! There are some spurious single pixels, so I'm going to perform an opening with imopen with a line structuring element.
After this, I'll perform a dilation with imdilate to close any gaps, then use imfill with the 'holes' option to fill in the gaps, then use erosion with imerode to shrink the shapes back to their original form. As such:
se = strel('line', 3, 90);
pre = imopen(seg, c);
se = strel('square', 20);
pre2 = imdilate(pre, se);
pre3 = imfill(pre2, 'holes');
final = imerode(pre3, se);
figure;
imshow(final);
final contains the segmented image with the 4 candy boxes. This is what I get:
Try resizing the image. When you make it smaller, it would be easier to join edges. I tried what's shown below. You might have to tune it depending on the nature of the background.
close all;
clear all;
im = imread('1SGVm.jpg');
small = imresize(im, .25); % resize
grad = (double(imdilate(small, ones(3))) - double(small)); % extract edges
gradSum = sum(grad, 3);
bw = edge(gradSum, 'Canny');
joined = imdilate(bw, ones(3)); % join edges
filled = imfill(joined, 'holes');
filled = imerode(filled, ones(3));
imshow(label2rgb(bwlabel(filled))) % label the regions and show
If you have a recent version of MATLAB, try the Color Thresholder app in the image processing toolbox. It lets you interactively play with different color spaces, to see which one can give you the best segmentation.
If your candy covers are fixed or you know all the covers that are coming into the scene then Template matching is best for this. As it is independent of the background in the image.
http://docs.opencv.org/doc/tutorials/imgproc/histograms/template_matching/template_matching.html

How to define the markers for Watershed in OpenCV?

I'm writing for Android with OpenCV. I'm segmenting an image similar to below using marker-controlled watershed, without the user manually marking the image. I'm planning to use the regional maxima as markers.
minMaxLoc() would give me the value, but how can I restrict it to the blobs which is what I'm interested in? Can I utilize the results from findContours() or cvBlob blobs to restrict the ROI and apply maxima to each blob?
First of all: the function minMaxLoc finds only the global minimum and global maximum for a given input, so it is mostly useless for determining regional minima and/or regional maxima. But your idea is right, extracting markers based on regional minima/maxima for performing a Watershed Transform based on markers is totally fine. Let me try to clarify what is the Watershed Transform and how you should correctly use the implementation present in OpenCV.
Some decent amount of papers that deal with watershed describe it similarly to what follows (I might miss some detail, if you are unsure: ask). Consider the surface of some region you know, it contains valleys and peaks (among other details that are irrelevant for us here). Suppose below this surface all you have is water, colored water. Now, make holes in each valley of your surface and then the water starts to fill all the area. At some point, differently colored waters will meet, and when this happen, you construct a dam such that they don't touch each other. In the end you have a collection of dams, which is the watershed separating all the different colored water.
Now, if you make too many holes in that surface, you end up with too many regions: over-segmentation. If you make too few you get an under-segmentation. So, virtually any paper that suggests using watershed actually presents techniques to avoid these problems for the application the paper is dealing with.
I wrote all this (which is possibly too naïve for anyone that knows what the Watershed Transform is) because it reflects directly on how you should use watershed implementations (which the current accepted answer is doing in a completely wrong manner). Let us start on the OpenCV example now, using the Python bindings.
The image presented in the question is composed of many objects that are mostly too close and in some instances overlapping. The usefulness of watershed here is to separate correctly these objects, not to group them into a single component. So you need at least one marker for each object and good markers for the background. As an example, first binarize the input image by Otsu and perform a morphological opening for removing small objects. The result of this step is shown below in the left image. Now with the binary image consider applying the distance transform to it, result at right.
With the distance transform result, we can consider some threshold such that we consider only the regions most distant to the background (left image below). Doing this, we can obtain a marker for each object by labeling the different regions after the earlier threshold. Now, we can also consider the border of a dilated version of the left image above to compose our marker. The complete marker is shown below at right (some markers are too dark to be seen, but each white region in the left image is represented at the right image).
This marker we have here makes a lot of sense. Each colored water == one marker will start to fill the region, and the watershed transformation will construct dams to impede that the different "colors" merge. If we do the transform, we get the image at left. Considering only the dams by composing them with the original image, we get the result at right.
import sys
import cv2
import numpy
from scipy.ndimage import label
def segment_on_dt(a, img):
border = cv2.dilate(img, None, iterations=5)
border = border - cv2.erode(border, None)
dt = cv2.distanceTransform(img, 2, 3)
dt = ((dt - dt.min()) / (dt.max() - dt.min()) * 255).astype(numpy.uint8)
_, dt = cv2.threshold(dt, 180, 255, cv2.THRESH_BINARY)
lbl, ncc = label(dt)
lbl = lbl * (255 / (ncc + 1))
# Completing the markers now.
lbl[border == 255] = 255
lbl = lbl.astype(numpy.int32)
cv2.watershed(a, lbl)
lbl[lbl == -1] = 0
lbl = lbl.astype(numpy.uint8)
return 255 - lbl
img = cv2.imread(sys.argv[1])
# Pre-processing.
img_gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
_, img_bin = cv2.threshold(img_gray, 0, 255,
cv2.THRESH_OTSU)
img_bin = cv2.morphologyEx(img_bin, cv2.MORPH_OPEN,
numpy.ones((3, 3), dtype=int))
result = segment_on_dt(img, img_bin)
cv2.imwrite(sys.argv[2], result)
result[result != 255] = 0
result = cv2.dilate(result, None)
img[result == 255] = (0, 0, 255)
cv2.imwrite(sys.argv[3], img)
I would like to explain a simple code on how to use watershed here. I am using OpenCV-Python, but i hope you won't have any difficulty to understand.
In this code, I will be using watershed as a tool for foreground-background extraction. (This example is the python counterpart of the C++ code in OpenCV cookbook). This is a simple case to understand watershed. Apart from that, you can use watershed to count the number of objects in this image. That will be a slightly advanced version of this code.
1 - First we load our image, convert it to grayscale, and threshold it with a suitable value. I took Otsu's binarization, so it would find the best threshold value.
import cv2
import numpy as np
img = cv2.imread('sofwatershed.jpg')
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
ret,thresh = cv2.threshold(gray,0,255,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
Below is the result I got:
( even that result is good, because great contrast between foreground and background images)
2 - Now we have to create the marker. Marker is the image with same size as that of original image which is 32SC1 (32 bit signed single channel).
Now there will be some regions in the original image where you are simply sure, that part belong to foreground. Mark such region with 255 in marker image. Now the region where you are sure to be the background are marked with 128. The region you are not sure are marked with 0. That is we are going to do next.
A - Foreground region:- We have already got a threshold image where pills are white color. We erode them a little, so that we are sure remaining region belongs to foreground.
fg = cv2.erode(thresh,None,iterations = 2)
fg :
B - Background region :- Here we dilate the thresholded image so that background region is reduced. But we are sure remaining black region is 100% background. We set it to 128.
bgt = cv2.dilate(thresh,None,iterations = 3)
ret,bg = cv2.threshold(bgt,1,128,1)
Now we get bg as follows :
C - Now we add both fg and bg :
marker = cv2.add(fg,bg)
Below is what we get :
Now we can clearly understand from above image, that white region is 100% foreground, gray region is 100% background, and black region we are not sure.
Then we convert it into 32SC1 :
marker32 = np.int32(marker)
3 - Finally we apply watershed and convert result back into uint8 image:
cv2.watershed(img,marker32)
m = cv2.convertScaleAbs(marker32)
m :
4 - We threshold it properly to get the mask and perform bitwise_and with the input image:
ret,thresh = cv2.threshold(m,0,255,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
res = cv2.bitwise_and(img,img,mask = thresh)
res :
Hope it helps!!!
ARK
Foreword
I'm chiming in mostly because I found both the watershed tutorial in the OpenCV documentation (and C++ example) as well as mmgp's answer above to be quite confusing. I revisited a watershed approach multiple times to ultimately give up out of frustration. I finally realized I needed to at least give this approach a try and see it in action. This is what I've come up with after sorting out all of the tutorials I've come across.
Aside from being a computer vision novice, most of my trouble probably had to do with my requirement to use the OpenCVSharp library rather than Python. C# doesn't have baked-in high-power array operators like those found in NumPy (though I realize this has been ported via IronPython), so I struggled quite a bit in both understanding and implementing these operations in C#. Also, for the record, I really despise the nuances of, and inconsistencies in most of these function calls. OpenCVSharp is one of the most fragile libraries I've ever worked with. But hey, it's a port, so what was I expecting? Best of all, though -- it's free.
Without further ado, let's talk about my OpenCVSharp implementation of the watershed, and hopefully clarify some of the stickier points of watershed implementation in general.
Application
First of all, make sure watershed is what you want and understand its use. I am using stained cell plates, like this one:
It took me a good while to figure out I couldn't just make one watershed call to differentiate every cell in the field. On the contrary, I first had to isolate a portion of the field, then call watershed on that small portion. I isolated my region of interest (ROI) via a number of filters, which I will explain briefly here:
Start with source image (left, cropped for demonstration purposes)
Isolate the red channel (left middle)
Apply adaptive threshold (right middle)
Find contours then eliminate those with small areas (right)
Once we have cleaned the contours resulting from the above thresholding operations, it is time to find candidates for watershed. In my case, I simply iterated through all contours greater than a certain area.
Code
Say we've isolated this contour from the above field as our ROI:
Let's take a look at how we'll code up a watershed.
We'll start with a blank mat and draw only the contour defining our ROI:
var isolatedContour = new Mat(source.Size(), MatType.CV_8UC1, new Scalar(0, 0, 0));
Cv2.DrawContours(isolatedContour, new List<List<Point>> { contour }, -1, new Scalar(255, 255, 255), -1);
In order for the watershed call to work, it will need a couple of "hints" about the ROI. If you're a complete beginner like me, I recommend checking out the CMM watershed page for a quick primer. Suffice to say we're going to create hints about the ROI on the left by creating the shape on the right:
To create the white part (or "background") of this "hint" shape, we'll just Dilate the isolated shape like so:
var kernel = Cv2.GetStructuringElement(MorphShapes.Ellipse, new Size(2, 2));
var background = new Mat();
Cv2.Dilate(isolatedContour, background, kernel, iterations: 8);
To create the black part in the middle (or "foreground"), we'll use a distance transform followed by threshold, which takes us from the shape on the left to the shape on the right:
This takes a few steps, and you may need to play around with the lower bound of your threshold to get results that work for you:
var foreground = new Mat(source.Size(), MatType.CV_8UC1);
Cv2.DistanceTransform(isolatedContour, foreground, DistanceTypes.L2, DistanceMaskSize.Mask5);
Cv2.Normalize(foreground, foreground, 0, 1, NormTypes.MinMax); //Remember to normalize!
foreground.ConvertTo(foreground, MatType.CV_8UC1, 255, 0);
Cv2.Threshold(foreground, foreground, 150, 255, ThresholdTypes.Binary);
Then we'll subtract these two mats to get the final result of our "hint" shape:
var unknown = new Mat(); //this variable is also named "border" in some examples
Cv2.Subtract(background, foreground, unknown);
Again, if we Cv2.ImShow unknown, it would look like this:
Nice! This was easy for me to wrap my head around. The next part, however, got me quite puzzled. Let's look at turning our "hint" into something the Watershed function can use. For this we need to use ConnectedComponents, which is basically a big matrix of pixels grouped by the virtue of their index. For example, if we had a mat with the letters "HI", ConnectedComponents might return this matrix:
0 0 0 0 0 0 0 0 0
0 1 0 1 0 2 2 2 0
0 1 0 1 0 0 2 0 0
0 1 1 1 0 0 2 0 0
0 1 0 1 0 0 2 0 0
0 1 0 1 0 2 2 2 0
0 0 0 0 0 0 0 0 0
So, 0 is the background, 1 is the letter "H", and 2 is the letter "I". (If you get to this point and want to visualize your matrix, I recommend checking out this instructive answer.) Now, here's how we'll utilize ConnectedComponents to create the markers (or labels) for watershed:
var labels = new Mat(); //also called "markers" in some examples
Cv2.ConnectedComponents(foreground, labels);
labels = labels + 1;
//this is a much more verbose port of numpy's: labels[unknown==255] = 0
for (int x = 0; x < labels.Width; x++)
{
for (int y = 0; y < labels.Height; y++)
{
//You may be able to just send "int" in rather than "char" here:
var labelPixel = (int)labels.At<char>(y, x); //note: x and y are inexplicably
var borderPixel = (int)unknown.At<char>(y, x); //and infuriatingly reversed
if (borderPixel == 255)
labels.Set(y, x, 0);
}
}
Note that the Watershed function requires the border area to be marked by 0. So, we've set any border pixels to 0 in the label/marker array.
At this point, we should be all set to call Watershed. However, in my particular application, it is useful just to visualize a small portion of the entire source image during this call. This may be optional for you, but I first just mask off a small bit of the source by dilating it:
var mask = new Mat();
Cv2.Dilate(isolatedContour, mask, new Mat(), iterations: 20);
var sourceCrop = new Mat(source.Size(), source.Type(), new Scalar(0, 0, 0));
source.CopyTo(sourceCrop, mask);
And then make the magic call:
Cv2.Watershed(sourceCrop, labels);
Results
The above Watershed call will modify labels in place. You'll have to go back to remembering about the matrix resulting from ConnectedComponents. The difference here is, if watershed found any dams between watersheds, they will be marked as "-1" in that matrix. Like the ConnectedComponents result, different watersheds will be marked in a similar fashion of incrementing numbers. For my purposes, I wanted to store these into separate contours, so I created this loop to split them up:
var watershedContours = new List<Tuple<int, List<Point>>>();
for (int x = 0; x < labels.Width; x++)
{
for (int y = 0; y < labels.Height; y++)
{
var labelPixel = labels.At<Int32>(y, x); //note: x, y switched
var connected = watershedContours.Where(t => t.Item1 == labelPixel).FirstOrDefault();
if (connected == null)
{
connected = new Tuple<int, List<Point>>(labelPixel, new List<Point>());
watershedContours.Add(connected);
}
connected.Item2.Add(new Point(x, y));
if (labelPixel == -1)
sourceCrop.Set(y, x, new Vec3b(0, 255, 255));
}
}
Then, I wanted to print these contours with random colors, so I created the following mat:
var watershed = new Mat(source.Size(), MatType.CV_8UC3, new Scalar(0, 0, 0));
foreach (var component in watershedContours)
{
if (component.Item2.Count < (labels.Width * labels.Height) / 4 && component.Item1 >= 0)
{
var color = GetRandomColor();
foreach (var point in component.Item2)
watershed.Set(point.Y, point.X, color);
}
}
Which yields the following when shown:
If we draw on the source image the dams that were marked by a -1 earlier, we get this:
Edits:
I forgot to note: make sure you're cleaning up your mats after you're done with them. They WILL stay in memory and OpenCVSharp may present with some unintelligible error message. I should really be using using above, but mat.Release() is an option as well.
Also, mmgp's answer above includes this line: dt = ((dt - dt.min()) / (dt.max() - dt.min()) * 255).astype(numpy.uint8), which is a histogram stretching step applied to the results of the distance transform. I omitted this step for a number of reasons (mostly because I didn't think the histograms I saw were too narrow to begin with), but your mileage may vary.

Extracting image of words from a scanned paper

I want get a small image of every word in a lot of scanned books (that is in Persian (Arabic-script)).
I have no experiment in image prossessing.
How can I do that in most efficient way?
I suggest you write a script in MATLAB something like this.
a : half of the maximum distance between the letters.(in pixels)
b : half of the minimum distance between the words.(in pixels)
(lets hope a < b )
Threshold the scanned image of the page.
I(I < Th) = 0;I(I > Th) = 1;
Choose 'Th' by experimenting. You should get a binary image 'I' having 1's where letters are.
Dilate the image.
imdilate(I,a);
This will connect the letters together.
Remove noise.
I = bwareaopen(I,n);
this will remove all connected components with less that n pixels.
Do connected component analysis.
CC = bwconncomp(I);
Rect = regionprops(I,'BoundingBox');
This will return a list of co-ordinates of a rectangle containing a single word.
Extract the sub-matrix from original copy and write the image using imwrite().

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