Posted by
Kenneth Sloan-2 on
URL: http://imagej.273.s1.nabble.com/Find-missing-spots-in-a-grid-of-spots-tp5019879p5019880.html
As usual, my mind goes immediately to a full Java solution. It you don't have anyone capable
of writing custom Java plugins for FIJI, my comments may not be useful.
As you say - it should be easy to find many of the existing particles. That's a relatively straightforward,
bottom-up use of standard image analysis tools.
Given a collection of high-probability (easily found) particles, you can form a theory about the nature of the grid. With enough data, you can create a set of *predictions* about where particles should (and should not) exist. This may cause you to reject some of the particles found in the first step, because they don't fit the pattern. Your parameter space seems to have 3 parameters:
a) rotation angle
b) spacing in "x" (in quotes because it may not correspond to the horizontal axis of the image)
c) spacing in "y"
plus 2 more parameters to specify a reference particle (x,y location in the image).
One way to tease out the rotation angle is to project the set of known particles onto several rotated lines, and select the rotations (there should be two, at roughly 90 degrees) that gives you the sharpest peaks. This would also allow you to read off the two spacing parameters. If you are sure the grid is rectangular, you can project unto two projection lines at 90 degrees, and perhaps get more robust detection of the angle.
With lots of data, you might consider Fourier analysis.
Now that you have a theory - you can construct a set of points where you *expect* to find a particle. This makes the problem a "verification vision" one. Examine each location, and decide if the image data support the presence, or the absence, of a particle.
Done.
Once you write the Java program, and test it on a few images, the analysis of the "thousands" of images can be easily automated.
--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.
> On 14 Jan 2018, at 12:35 , Cornelius Sicker <
[hidden email]> wrote:
>
> Dear fellow ImageJ users,
>
> a colleague of mine is looking for an automated solution to find missing
> spots in a rectangular grid of small spots. The spots are quite
> uniformly sized and have similar brightness. The grid might be rotated
> slightly. Only a few spots are expected to be missing in each picture
> (<1 % of all grid positions). The grid itself is only virtually created
> by the visible spots. Apart from the visible spots on dark background
> there are no distinguishing features in the images. There are thousands
> of images to be processed, so the solution has to be fully automated.
>
> I think it should be not hard to find the coordinates of the existing
> spots by some particle analysis plugins in ImageJ. However, given a list
> of coordinates of visible spots, how would you identify the missing
> ones? Does anybody know of an existing solution to solve this?
>
> I can provide an example image if it helps, but was not sure how the
> mailing list policy is about attachments.
>
> Best regards
> Cornelius
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html