I would like to find a zoomed microscopy image in a dozen of overview images. I would prefer to find some python/numpy/scipy solution.
My knowledge about pattern recognition is negligible. Anyway, here is what I tried:
My first idea was to get the most important structures out of the images by
setting eveything greater[smaller] than some threshold to 255[0] in the greyscaled image.
For example, I then have the following pattern:
The overview image might then look like this:
Here is a version where the region of the pattern is highlighted:
I would now like to find a way to get the pixel number, at which the pattern occurs in the overview image.
It is very important to note, that I do not have information about:
the orientation of the two images with respect to each other
the scaling of the images
in principle, there might even be some stretching between the images, but this might be too hard to implement.
I do no know if the pattern is on the image. There I have to check about 20 images.
For a fixed scaling, my attempt was to use
result = scipy.signal.fftconvolve()
and see how the maximum of result then varies when I rotate the pattern before doing the convolution.
Taking the maximum value gives me the correct angle at which the images overlap.
However this is not a nice solution because it already takes some minutes. Also varying the scaling and even doing further transformations would take forever.
I guess there are better approaches out there!
Related
for my school project, I need to find images in a large dataset. I'm working with python and opencv. Until now, I've managed to find an exact match of an image in the dataset but it takes a lot of time even though I had 20 images for the test code. So, I've searched few pages of google and I've tried the code on these pages
image hashing
building an image hashing search engine
feature matching
Also, I've been thinking to search through the hashed dataset, save their paths, then find the best feature matching image among them. But most of the time, my narrowed down working area is so much different than what is my query image.
The image hashing is really great. It looks like what I need but there is a problem: I need to find an exact match, not similar photos. So, I'm asking you guys, if you have any suggestion or a piece of code might help or improve the reference code that I've linked, can you share it with me? I'd be really happy to try or research what you guys send or suggest.
opencv is probably the wrong tool for this. The algorithms there are geared towards finding similar matches, not exact ones. The general idea is to use machine learning to teach the code to recognize what a car looks like so it can detect cars in videos, even when the color or form changes (driving in the shadow, different make, etc).
I've found two approaches work well when trying to build an image database.
Use a normal hash algorithm like SHA-256 plus maybe some metadata (file or image size) to find matches
Resize the image down to 4x4 or even 2x2. Use the pixel RGB values as "hash".
The first approach is to reduce the image to a number. You can then put the number in a look up table. When searching for the image, apply the same hashing algorithm to the image you're looking for. Use the new number to look in the table. If it's there, you have a match.
Note: In all cases, hashing can produce the same number for different pictures. So you have to compare all the pixels of two pictures to make sure it's really an exact match. That's why it sometimes helps to add information like the picture size (in pixels, not file size in bytes).
The second approach allows to find pictures which very similar to the eye but in fact slightly different. Imagine cropping off a single pixel column on the left or tilting the image by 0.01°. To you, the image will be the same but for a computer, they will by totally different. The second approach tries to average small changes out. The cost here is that you will get more collisions, especially for B&W pictures.
Finding exact image matches using hash functions can be done with the undouble library (Disclaimer: I am also the author). It works using a multi-step process of pre-processing the images (grayscaling, normalizing, and scaling), computing the image hash, and the grouping of images based on a threshold value.
I am generating images (thumbnails) from a video every 3 seconds. Now I need to discard/remove all the similar images. Is there a way I could this?
I generate thumbnails using FFMPEG. I read about various image-diff solutions like given in this SO post, but I do not want to do this manually. How and what parameters should be considered that could tell if a particular image is similar to other images present.
You can calculate the Structural Similarity Index between images and based on the score keep or discard an image. There are other measures you can use, but basically a method that returns a score. Try PIL or OpenCV
https://pillow.readthedocs.io/en/3.1.x/reference/ImageChops.html?highlight=difference
https://www.pyimagesearch.com/2017/06/19/image-difference-with-opencv-and-python/
I dont have enough reputation to comment my idea on your problem, so i will just go ahead and post it as an answer in hope of helping you.
I am quite confused about the term "similar" but since you are reffering on video frames i am going to assume that you want to avoid having "similar" frames that have been captured because of poor camera movement. If that's the case you might want to consider using salient point descriptors.
To be more specific you can detect salient points (using for instance Harris) and then use a point descriptor algorithm (such as SURF) and discard the frames that have been found to have "too many" similar points with a pre-selected frame.
Keep in mind that in order for the above process to be successful, the frames must be as sharp as possible, i guess you don't want to extract as a thubnail a blurred frame anyway. So applying a blurred images detection might be useful in your case.
I am trying to obtain a radius and diameter distribution from some AFM (Atomic force microscopy) measurements. So far I am trying out Gwyddion, ImageJ and different workflows in Matlab.
At the moment the best results I have found is to use Gwyddion and to take the Phase image, high pass filter it and then try an edge detection with 'Laplacian of Gaussian'. The result is shown in figure 3. However this image is still too noisy and doesnt really capture the edges of all the particles. (some are merged together others do not have a clear perimeter).
In the end I need an image which segments each of the spherical particles which I can use for blob detection/analysis to obtain size/radius information.
Can anyone recommend a different method?
[
I would definitely try a Granulometry, it was designed for something really similar. There is a good explanation of granulometry here starting page 158.
The granulometry will perform consecutive / increasing openings that will erase the different patterns according to their dimensions. The bigger the pattern, the latter it will be erased. It will give you a curve that represent the pattern dimension distributions in your image, so exactly what you want.
However, it will not give you any information about the position inside the image. If you want to have a rough modeling of the blobs present in your image, you can take a look to the Ultimate Opening.
Maybe you can use Avizo, it's a powerful software for dealing with image issues, especially for three D data (CT)
I have a grid on pictures (they are from camera). After binarization they look like this (red is 255, blue is 0):
What is the best way to detect grid nodes (crosses) on these pictures?
Note: grid is distorted from cell to cell non-uniformly.
Update:
Some examples of different grids and thier distortions before binarization:
In cases like this I first try to find the best starting point.
So, first I thresholded your image (however I could also skeletonize it and just then threshold. But this way some data is lost irrecoverably):
Then, I tried loads of tools to get the most prominent features emphasized in bulk. Finally, playing with Gimp's G'MIC plugin I found this:
Based on the above I prepared a universal pattern that looks like this:
Then I just got a part of this image:
To help determine angle I made local Fourier freq graph - this way you can obtain your pattern local angle:
Then you can make a simple thick that works fast on modern GPUs - get difference like this (missed case):
When there is hit the difference is minimal; what I had in mind talking about local maximums refers more or less to how the resulting difference should be treated. It wouldn't be wise to weight outside of the pattern circle difference the same as inside due to scale factor sensitivity. Thus, inside with cross should be weighted more in used algorithm. Nevertheless differenced pattern with image looks like this:
As you can see it's possible to differentiate between hit and miss. What is crucial is to set proper tolerance and use Fourier frequencies to obtain angle (with thresholded images Fourier usually follows overall orientation of image analyzed).
The above way can be later complemented by Harris detection, or Harris detection can be modified using above patterns to distinguish two to four closely placed corners.
Unfortunately, all techniques are scale dependent in such case and should be adjusted to it properly.
There are also other approaches to your problem, for instance by watershedding it first, then getting regions, then disregarding foreground, then simplifying curves, then checking if their corners form a consecutive equidistant pattern. But to my nose it would not produce correct results.
One more thing - libgmic is G'MIC library from where you can directly or through bindings use transformations shown above. Or get algorithms and rewrite them in your app.
I suppose that this can be a potential answer (actually mentioned in comments): http://opencv.itseez.com/2.4/modules/imgproc/doc/feature_detection.html?highlight=hough#houghlinesp
There can also be other ways using skimage tools for feature detection.
But actually I think that instead of Hough transformation that could contribute to huge bloat and and lack of precision (straight lines), I would suggest trying Harris corner detection - http://docs.opencv.org/2.4/doc/tutorials/features2d/trackingmotion/harris_detector/harris_detector.html .
This can be further adjusted (cross corners, so local maximum should depend on crossy' distribution) to your specific issue. Then some curves approximation can be done based on points got.
Maybe you cloud calculate Hough Lines and determine the intersections. An OpenCV documentation can be found here
How do you detect the location of an image within a larger image? I have an unmodified copy of the image. This image is then changed to an arbitrary resolution and placed randomly within a much larger image which is of an arbitrary size. No other transformations are conducted on the resulting image. Python code would be ideal, and it would probably require libgd. If you know of a good approach to this problem you'll get a +1.
There is a quick and dirty solution, and that's simply sliding a window over the target image and computing some measure of similarity at each location, then picking the location with the highest similarity. Then you compare the similarity to a threshold, if the score is above the threshold, you conclude the image is there and that's the location; if the score is below the threshold, then the image isn't there.
As a similarity measure, you can use normalized correlation or sum of squared differences (aka L2 norm). As people mentioned, this will not deal with scale changes. So you also rescale your original image multiple times and repeat the process above with each scaled version. Depending on the size of your input image and the range of possible scales, this may be good enough, and it's easy to implement.
A proper solution is to use affine invariants. Try looking up "wide-baseline stereo matching", people looked at that problem in that context. The methods that are used are generally something like this:
Preprocessing of the original image
Run an "interest point detector". This will find a few points in the image which are easily localizable, e.g. corners. There are many detectors, a detector called "harris-affine" works well and is pretty popular (so implementations probably exist). Another option is to use the Difference-of-Gaussians (DoG) detector, it was developed for SIFT and works well too.
At each interest point, extract a small sub-image (e.g. 30x30 pixels)
For each sub-image, compute a "descriptor", some representation of the image content in that window. Again, many descriptors exist. Things to look at are how well the descriptor describes the image content (you want two descriptors to match only if they are similar) and how invariant it is (you want it to be the same even after scaling). In your case, I'd recommend using SIFT. It is not as invariant as some other descriptors, but can cope with scale well, and in your case scale is the only thing that changes.
At the end of this stage, you will have a set of descriptors.
Testing (with the new test image).
First, you run the same interest point detector as in step 1 and get a set of interest points. You compute the same descriptor for each point, as above. Now you have a set of descriptors for the target image as well.
Next, you look for matches. Ideally, to each descriptor from your original image, there will be some pretty similar descriptor in the target image. (Since the target image is larger, there will also be "leftover" descriptors, i.e. points that don't correspond to anything in the original image.) So if enough of the original descriptors match with enough similarity, then you know the target is there. Moreover, since the descriptors are location-specific, you will also know where in the target image the original image is.
You probably want cross-correlation. (Autocorrelation is correlating a signal with itself; cross correlating is correlating two different signals.)
What correlation does for you, over simply checking for exact matches, is that it will tell you where the best matches are, and how good they are. Flip side is that, for a 2-D picture, it's something like O(N^3), and it's not that simple an algorithm. But it's magic once you get it to work.
EDIT: Aargh, you specified an arbitrary resize. That's going to break any correlation-based algorithm. Sorry, you're outside my experience now and SO won't let me delete this answer.
http://en.wikipedia.org/wiki/Autocorrelation is my first instinct.
Take a look at Scale-Invariant Feature Transforms; there are many different flavors that may be more or less tailored to the type of images you happen to be working with.