I have two images of yeast plates:
Permissive:
Xgal:
The to images should be in the same spot and roughly the same size. I am trying to use one of the images to generate a grid and then apply that grid to the other image. The grid is made by looking at the colonies on permissive plate, the plate should have 1536 colonies on it. The problem is that the camera that was used to take the images moves a bit up and down and the images can also be shifted slightly due to the other plate not being in exactly the same place.
This then means that when I use the permissive plate to generate the grid on the xgal plate the grid shifts. Does anyone know a way in which I can compensate for this? I am using perl with the gd module. Any advice would be greatly appreciated. Thank you
I've done this in other languages in relation to motion analysis. You can mathematically determine the shift in position between two images using cross correlation.
Fortunately, you may not need to actually do the maths :) You could use something like ImageMagick, which provides a lot of image processing functions for you, and is perl scriptable. Independently scripts already exists for tasks very much like yours -- see.
If you have only a few pairs of images and, as in the examples, they are very different in appearance then an alternative method to Tim Barrass' would be
Open the first image in gimp, find the co-ordinates of a landmark feature
Open the second image in gimp, find the co-ordinates of the same landmark
Calculate the offset
Shift the second image using ImageMagick's convert command with the affine option. Set the parameters sx=sy=1.0, rx=ry=0.0, tx= negative horizontal offset, ty= negative vertical offset
Related
I have seen many tutorials that people blend two images that are placed on top of each other very nicely in Photoshop. For example here are two images that are placed on top of each other:
Then in Photoshop after some work, the edges (around the smaller image) will be erased and two images are nicely mixed.
For example, this is a possible end result:
As it can be seen there is no edge and two images are very nicely blended, without blurring.
Can someone point me to any article or post that shows the math behind it? If there is a MATLAB code that can do it, that would be even better. Or at least if someone can tell me what is the correct term for this so I can do Google search on the topic.
Straight alpha blending alone is not sufficient, as it will perform a uniform mixing of the two images.
To achieve nice-looking results, you will need to define an alpha map, i.e. an image of the same size where you adjust the degree of transparency depending on the image that should dominate.
To obtain the mask, you can draw it by hand, for example as a filled outline, as a path or a polygon. Then you have to strongly blur this mask to get a smooth blend.
It looks very difficult (if not impossible) to automate this, as no software can guess what you want to enhance.
The term you are looking for is alpha blending.
https://en.wikipedia.org/wiki/Alpha_compositing#Alpha_blending
The maths behind it boils down to some alpha weighted sums.
Matlab provides the function imfuse to achieve this:
https://de.mathworks.com/help/images/ref/imfuse.html
Edit: (as it still seems to be unclear)
Let's say you have 2 images A and B wich you want to blend.
You put one image over the other so for each coordinate you have 2 RGB touples.
Now you need to define the weight of both images. Will you only see the colour of image A or B or which ratio will you choose to mix them?
This is done by alpha values.
So all you need is a 2d function that defines the mixing ratio for each pixel.
Usually you have values between 0 and 1 where 0 shows one image, 1 shows the other image, 0.5 will mix them both equally and so on...
Just read the article I have linked. It gives you a clear mathematical definition. I can't provide more detail than that.
If you have problems understanding that I urge you to read a book on image processing fundamentals.
Given are two monochromatic images of same size. Both are prealigned/anchored to one common point. Some points of the original image did move to a new position in the new image, but not in a linear fashion.
Below you see a picture of an overlay of the original (red) and transformed image (green). What I am looking for now is a measure of "how much did the "individual" points shift".
At first I thought of a simple average correlation of the whole matrix or some kind of phase correlation, but I was wondering whether there is a better way of doing so.
I already found that link, but it didn't help that much. Currently I implement this in Matlab, but this shouldn't be the point I guess.
Update For clarity: I have hundreds of these image pairs and I want to compare each pair how similar they are. It doesn't have to be the most fancy algorithm, rather easy to implement and yielding in a good estimate on similarity.
An unorthodox approach uses RASL to align an image pair. A python implementation is here: https://github.com/welch/rasl and it also
provides a link to the RASL authors' original MATLAB implementation.
You can give RASL a pair of related images, and it will solve for the
transformation (scaling, rotation, translation, you choose) that best
overlays the pixels in the images. A transformation parameter vector
is found for each image, and the difference in parameters tells how "far apart" they are (in terms of transform parameters)
This is not the intended use of
RASL, which is designed to align large collections of related images while being indifferent to changes in alignment and illumination. But I just tried it out on a pair of jittered images and it worked quickly and well.
I may add a shell command that explicitly does this (I'm the author of the python implementation) if I receive encouragement :) (today, you'd need to write a few lines of python to load your images and return the resulting alignment difference).
You can try using Optical Flow. http://www.mathworks.com/discovery/optical-flow.html .
It is usually used to measure the movement of objects from frame T to frame T+1, but you can also use it in your case. You would get a map that tells you the "offset" each point in Image1 moved to Image2.
Then, if you want a metric that gives you a "distance" between the images, you can perhaps average the pixel values or something similar.
I have several binary images which represent a partial map of an area (~4m radius) and were taken ~0.2m apart, for example:
(Sorry for the different axis limit).
If you look closely, you'll see that the first image is about 20cm to the right.
I want to be able to create a map of the area from several pictures like this.
I've tried several methods, such as Matlab's register but couldn't find any good algorithm for this purpose. Any ideas on how to approach this?
Thanks in advance!
Two possible routes:
Use imregister. This does registration based on image intensity. You will probably want a rigid transform.
However, this will require your data to be an image (matrix), which it doesn't look like it currently is.
Alternatively, you can use control points. These are common (labelled) points in each image which provide a reference to determine the transform.
Matlab has a built in function to determine control points, cpselect. However, again this requires image data. You may be better of writing your own function to do this or just selecting control points manually.
Once you have control points you can determine the transform between them using fitgeotrans
At image i need find "table" - simple rectangle.
Problem is with edge recognition, because potencial photos will be "dark".
I tried edge - sobel, canny, log, .... - recognition and after that Hough transformation and line finding. But this algorithms are not enough for this task.
Something what can help me:
- it is rectangle!, only in perspective view (something like fitting perspective rectangle?)
- that object MUST cover atleast for example 90% of photo (i know i need looking near photo edges)
- that rectangle have fast same color (for example wood dining table)
- i need find atleast "only" 4 corners..(but yes, better will be find the edges of that table)
I know how for example sobel, canny or log algorithms works and Hough as well. And naturally those algorithms fail at dark or non-contrast images. But is there some another method for example based at "fitting"?
Images showing photo i can get (you see it would be dark) and what i need find:
and this is really "nice" picture (without noise). I tested it on more noise pictures and the result was..simply horrible..
Result of this picture with actual algorithm log (with another ones it looks same):
I know image and edge recognition is not simple challenge but are there some new better methods or something like that what i can try to use?
In one of posts in here i found LSD algorithm. It seems very nice descripted and it seems it is recognizing really nice straight lines as well. Do you think it would be better to use it insted of the canny or sobel detection?
Another solution will be corner detection, on my sample images it works better but it recognize too much points and there will problem with time..i will need to connect all the points and "find" the table..
Another solution:
I thought about point to point mapping. That i will have some "virtual" table and try to map that table above with that "virtual" table (simple 2d square in painting :] )..But i think point to point mapping will give me big errors or it will not working.
Does someone have any advice what algorithm use to?
I tried recognize edges in FIJI and then put the edge detected image in matlab, but with hough it works bad as well..:/..
What do you think it would be best to use? In short i need find some algorithm working on non contrast, dark images.
I'd try some modified snakes algorithm:
you parameterize your rectangle with 4 points and initialize them somewhere in the image corners. Then you move the points towards image features using some optimization algorithm (e.g. gradient descent, simulated annealing, etc.).
The image features could be a combination of edge features (e.g. sobel directly or sobel of some gaussian filtered image) to be evaluated on the lines between those four points and corner features to be evaluated at those 4 points.
Additionally you can penalize unlikely rectangles (maybe depending on the angles between the points or on the distance to the image boundary).
I have two images. In one of the images, my eye is in the center position and in the other image, it is in the left. How do I find out whether my eye is in the left or the right?
I am using MATLAB. Are there any functions for this?
A simple solution is to try to detect the iris using circular Hough Transform.
You can find a lot materials out there. To name a few, these two fileexchange submissions:
Hough Transform for circle
detection
Circle Detection via Standard Hough
Transform
This sounds like Eye tracking implemented in MATLAB which is a fairly popular research topic.
If you want a more detailed answer, please answer the following questions:
Do you know the coordinates of your eye in the first image?
What kind of motion is there between the two images? Rotation/translation/scaling/...?
Do you want this to be real-time?
What is the resolution of the images?
Are there going to be more eyes in the image apart from yours?
If you are willing to select the eye in one image you can use template matching to find it in others (for example you can mark it in the first frame of a video and then find it in all other frames).
Look at the normxcor2 function in matlab:
http://www.nd.edu/~hpcc/solaris8_usr_local/src/matlab6.1/help/toolbox/images/normxcorr2.html
This technique is robust to constant illumination change, but will fail if the appearance of the eye changes significantly between the image you took the template from and the image you are searching in.
If you are going to search for the eye in a lot of frames (for example, eye tracking from a webcam) then you should look at stronger techniques such as the Kalman Filter or the Particle Filter (aka Condensation Filter in computer vision)
By using Color Distance Maps, the skin and non skin area can be differentiated and thus the non skin area contains the iris. From the iris, the whole eye could be detected. Hope it works.
You should also have a look at Eye Ball Detection in MATLAB , they have detected eyes first and then detected the EyeBall.