Matlab - distinguish overlapping low contrast objects in a RGB or Grayscale Image

Question

I have a big problem detecting objects within an image - I know this topic was already highly discusses in many forums, but I spend the last 4 days searching for an answer and was not able.

In fact: I have a picture from a branch (http://cl.ly/image/343Y193b2m1c). My goal is to count every single needle in this picture. So I have to face several problems:

Separate the branch with its needles from the background (which in this case is no problem).

Select the borders of the needles. This is a huge problem; I tried different ways including all edges() functions but the problem is always the same - the borders around the needles are not closed and - which leads to the last problem:

Needles are overlapping! This leads in "squares between the needles" which are, if I use imfill() or equal formula, filled in instead of the needles. And: the places where the needles are concentrated (many needles at one place) are nearly impossible to distinguish.

I tried watershed, I tried to enhance the contrast, Kmeans clustering, I tried imerose, imdilate and related functions with subsequent edge detection. I tried as well to filter and smooth the picture a bit in order to "unsharp" the needles a bit so that not every small change in color is recognized as a border (which is another problem).

I am relatively new to matlab, so I dont know what I have to look for. I tried to follow the MatLab tutorial used for Nuclei detection - but with this I just can get all the green objects (all needles at once).

I hope this questions did not came up before - if yes, I apologize deeply for the double post. If anybody has an idea what to do or what methods to use, it would be awesome and would safe this really bad beginning of the week.

Thank you very much in advance,

Phillip

Answer 1

I agree with @Jonas = you got yourself one HUGE problem.

Let me make a few suggestions.

First, along @Jonas' direction, instead of getting an accurate count, another way of getting a rough estimate is by counting the tips of the needles. Obviously, not all the tips are clearly visible. But, if you can get a clear mask of the branch it might be relatively easy to identify the tips of the needles using some of the morphological operations you mentioned yourself.

Second, is there any way you can get more information? For example, if you could have depth information it might help a little in distinguishing the needles from one another (it will not completely solve the task but it may help). You may get depth information from stereo - that is, taking two pictures of the branch while moving the camera a bit. If you have a Kinect device at your disposal (or some other range-camera) you can get a depth map directly...

Answer 2

Distinguishing overlapping objects is very, very hard, particularly if you do not know how many objects you have to distinguish. Your brain is much better at distinguishing overlapping objects than any segmentation algorithm I'm aware of, since it is able to integrate a lot of information that is difficult to encode. Therefore: If you're not able to distinguish some of the features yourself, forget about doing it via code.

Having said that, there may be a way for you to be able to get an approximate count of the needles: If you can segment the image pixels into two classes: "needle" versus "not needle", and you know how much area in your picture is covered by a needle (it may help to include a ruler when you take the picture), you can then divide number of "needle"-pixels by the number of pixels covered by a single needle to estimate the total number of needles in the image. This will somewhat underestimate the needle count due to overlaps, and it will underestimate more the denser the needles are (due to more overlaps), but it should allow you to compare automatically between branches with lots of needles and branches with few needles, as well as to identify changes in time, should that be one of your goals.