calculate diameter by using pixel size - image-processing

actually I don't really know how to calculate the diameter of red blood cells by applying image processing techniques? Assume 1 pixel is has a diameter of 100 nm, and 1 RBC has around 3850 pixels.

Assuming you know OpenCV, then you should be able to process the image to identify each individual red blood cells as a contour, or an ellipse, then you can measure the long axis of the contour/ellipse as the red blood cell's diameter in pixels. If you already know the width of 1 pixel represents 100nm, then you can convert the diameter in pixels to diameter in nm.
When you say "1 RBC has around 3850 pixels", does that mean the contour or ellipse has 3850 pixels? Then you still need to measure the "length" of this group of 3850 pixels.
Please show some sample pictures to help people understand and help you.

well..first try find area of a cell as the number of pixels contained in the cell. Then use formula Area= pi* diametr^2/4.

Related

Where exactly does the bounding box start or end?

In OpenCV or object detection models, they represent bounding box as 4 numbers e.g. x,y,width,height or x1,y1,x2,y2.
These numbers seem to be ill-defined but it's fine when the resolution is big.
But it causes me to think when the image has very low resolution e.g. 8x8, the one-pixel error can cause things to go very wrong.
So I want to know, what exactly does it mean when you say that a bounding box has x1=0, x2=100?
Specifically, I want to clear these confusions when understood well:
Does the bounding box border occupy the 0th pixel or is it surrounding 0th pixel (its border is at x=-1)?
Where is the exact end of the bounding box? If the image have shape=(8,8), would the end be at 7 or 8?
If you want to represent a bounding box that occupy the entire image, what should be its values?
So I think the right question should be, how do I think about bounding box intuitively so that these are not confusing for me?
OK. After many days working with bounding boxes, I have my own intuition on how to think about bounding box coordinates now.
I divide coordinates in 2 categories: continuous and discrete. The mental problems usually arise when you try to convert between them.
Suppose the image have width=100, height=100 then you can have a continuous point with x,y that can have any real value in the range [0,100].
It means that points like (0,0), (0.5,7.1,39.83,99.9999) are valid points.
Now you can convert a continuous point to a discrete point on the image by taking the floor of the number. E.g. (5.5, 8.9) gets mapped to pixel number (5,8) on the image. It's very important to understand that you should not use the ceiling or rounding operation to convert it to the discrete version. Suppose you have a continuous point (0.9,0.9) this point lies in the (0,0) pixel so it's closest to (0,0) pixel, not (1,1) pixel.
From this foundation, let's try to answer my question:
So I want to know, what exactly does it mean when you say that a bounding box has x1=0, x2=100?
It means that the continuous point 1 has x value = 0, and continuous point 2, has x value = 100. Continuous point has zero size. It's not a pixel.
Does the bounding box border occupy the 0th pixel or is it surrounding 0th pixel (its border is at x=-1)?
In continuous-space, the bounding box border occupy zero space. The border is infinitesimally slim. But when we want to draw it onto an image, the border will have the size of at least 1 pixel thick. So if we have a continuous point (0,0), it will occupy 0th pixel of the image. But theoretically, it represents a slim border at the left side and top side of the 0th pixel.
Where is the exact end of the bounding box? If the image have shape=(8,8), would the end be at 7 or 8?
The biggest x,y value you can have is 7.999... but when converted to discrete version you will be left with 7 which represent the last pixel.
If you want to represent a bounding box that occupy the entire image, what should be its values?
You should represent bounding box coordinates in continuous space instead of discrete space because of the precision that you have. It means the largest bounding box starts at (0,0) and ends at (100,100). But if you want to draw this box, you need to convert it to discrete version and draws the bounding box at (0,0) and end at (99,99).
In OpenCv the bounding rectangle can be defined in many ways. One way is its top-left corner and bottom-right corner. In case of constructor Rect(int x1, int y1, int x2, int y2) it defines those two points. The rectangle starts exactly on that pixel and coordinate. For subpixel rectangles there are also variants holding the floating point coordinates.
So I want to know, what exactly does it mean when you say that a bounding box has x1=0, x2=100?
That means the top-left corner x-coordinate starts at 0 and bottom-right x-coordinate
starts at 100.
Does the bounding box border occupy the 0th pixel or is it surrounding 0th pixel (its border is at x=-1)?
The border starts exactly on the 0-th pixel. Meaning that rectangle with width and height of 1px when drawn is just a signle dot (1px)
Where is the exact end of the bounding box? If the image have shape=(8,8), would the end be at 7 or 8?
The end would be at 7, see below.
If you want to represent a bounding box that occupy the entire image, what should be its values?
Lets have an image size of 100,100. The around the image rectangle defined by two points would be Rect(Point(0,0), Point(99,99)) by starting point and size Rect(0, 0, 100, 100)
The basic is to know that image of size X,Y has a minimum top-left coordinate at (0,0) and maximum at bottom-right (X-1,Y-1)

Measure horizontal lengths of multiple ROI

I would like to measure the horizontal lengths of multiple ROI. I tried Feret's diameter, but it only gives the longest distance between any two points along the selection boundary. I tried bounding rectangle, but I suppose the rectangles are tilted to obtain the minimum bounding rectangle.
Does anyone have another idea? Because clearly, the selection boundaries fit nicely to the ROI - so how could I extract that information, i.e. the xy-coordinates of the fits? Thanks in advance
PS: I did not write ROIs because 'Region of Interests' makes no sense

How does meanshift tracking work? (using histograms)

I know, that the Meanshift-Algorithm calculates the mean of a pixel density and checks, if the center of the roi is equal with this point. If not, it moves the new ROI center to the mean center and checks again... . Like in this picture:
For density, it is clear how to find the mean point. But it can't simply calculate the mean of a histogram and get the new position by this point. How can this algorithm work using color histogram?
The feature space in your image is 2D.
Say you have an intensity image (so it's 1D) then you would just have a line (e.g. from 0 to 255) on which the points are located. The circles shown above would just be line segments on that [0,255] line. Depending on their means, these line segments would then shift, just like the circles do in 2D.
You talked about color histograms, so I assume you are talking about RGB.
In that case your feature space is 3D, so you have a sphere instead of a line segment or circle. Your axes are R,G,B and pixels from your image are points in that 3D feature space. You then still look where the mean of a sphere is, to then shift the center towards that mean.

Display 3D matrix with its thickness information

I have a problem about plotting 3D matrix. Assume that I have one image with its size 384x384. In loop function, I will create about 10 images with same size and store them into a 3D matrix and plot the 3D matrix in loop. The thickness size is 0.69 between each size (distance between two slices). So I want to display its thickness by z coordinate. But it does not work well. The problem is that slice distance visualization is not correct. And it appears blue color. I want to adjust the visualization and remove the color. Could you help me to fix it by matlab code. Thank you so much
for slice = 1 : 10
Img = getImage(); % get one 2D image.
if slice == 1
image3D = Img;
else
image3D = cat(3, image3D, Img);
end
%Plot image
figure(1)
[x,y,z] = meshgrid(1:384,1:384,1:slice);
scatter3(x(:),y(:),z(:).*0.69,90,image3D(:),'filled')
end
The blue color can be fixed by changing the colormap. Right now you are setting the color of each plot point to the value in image3D with the default colormap of jet which shows lower values as blue. try adding colormap gray; after you plot or whichever colormap you desire.
I'm not sure what you mean by "The problem is that slice distance visualization is not correct". If each slice is of a thickness 0.69 than the image values are an integral of all the values within each voxel of thickness 0.69. So what you are displaying is a point at the centroid of each voxel that represents the integral of the values within that voxel. Your z scale seems correct as each voxel centroid will be spaced 0.69 apart, although it won't start at zero.
I think a more accurate z-scale would be to use (0:slice-1)+0.5*0.69 as your z vector. This would put the edge of the lowest slice at zero and center each point directly on the centroid of the voxel.
I still don't think this will give you the visualization you are looking for. 3D data is most easily viewed by looking at slices of it. you can check out matlab's slice which let's you make nice displays like this one:
slice view http://people.rit.edu/pnveme/pigf/ThreeDGraphics/thrd_threev_slice_1.gif

Pixel-Milimeter Proportion

I have a digital image, and I want to make some calculation based on distances on it. So I need to get the Milimeter/Pixel proportion. What I'm doing right now, is to mark two points wich I know the real world distance, to calculate the Euclidian distance between them, and than obtain the proportion.
The question is, Only with two points can I make the correct Milimeter/Pixel's proportion, or do I need to use 4 points, 2 for the X-Axis and 2 for Y-axis?
If your image is of a flat surface and the camera direction is perpendicular to that surface, then your scale factor should be the same in both directions.
If your image is of a flat surface, but it is tilted relative to the camera, then marking out a rectangle of known proportions on that surface would allow you to compute a perspective transform. (See for example this question)
If your image is of a 3D scene, then of course there is no way in general to convert pixels to distances.
If you know the distance between the points A and B measured on the picture(say in inch) and you also know the number of pixels between the points, you can easily calculate the pixels/inch ratio by dividing <pixels>/<inches>.
I suggest to take the points on the picture such that the line which intersects them is either horizontal either vertical such that calculations do not have errors taking into account the pixels have a rectangular form.

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