counting objects

[yaronberger]

Hi everybody,

I would like to find a way to count objects (dots) on my microscope images. I was trying to use matlab but results weren't satisfying.

here is a link to an image as an example of what I need to deal with. Did any of you used some function that could be helpful here? maybe using VBAI?

http://dl.dropbox.com/u/24633651/point-detection-sample.tif

Thanks,

Yaron

[falkpl]

in labview and the VDM this should be relativly easy

1.  threshold the image, can be as simple as a binary threshold or more complex using an adaptive threshold algorithm

2.  particle analysis, here you can get count, size and many other parameters for each dot.

[falkpl]

after looking at your image, the "dots" are no very clear, this will limit you in your ques for an accurate count.  I would add a step (or several) before the binary threshold and count for filtering the image.  when filtering you can correct for known issues with lighting or edges you wish to ignore, as well as clean up the image some to improve the chances of counting these dots.  Always your processing is limited by the image quality so minimizing the signal to noise is critical.

[yaronberger]

Thank you falkpl,

another thing that is bothering me is that VBAI won't read my image as it's 16-bit. Is there a way to solve that?

[falkpl]

I typically use vision assistant instead of vbai but I was able to open this as a 16-bit image, I did have to select all extensions to open it, not sure why it didnt show as a tif.

A prewitt filter appeared to clean up the edges of the dots some but wou will have to do some more advanced filtering in addition.

[TiTou]

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@yaronberger wrote:

Thank you falkpl,

another thing that is bothering me is that VBAI won't read my image as it's 16-bit. Is there a way to solve that?

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The easiest is to open you image with another application and save it in a different format (one that VBAI will tolerate), I think you can also do this in VBAI by using a Vision Assistant Step but I'm not 100% sure about that.

Hope this helps

[Brad]

I would recommend using the Vision Assistant step in VBAI (located on the second tab). Make sure to select the "Full Image" for your Region of Interest, and then press Edit. You're image is pretty hard to pick out the particles. I would recommend getting an image without any "dots" from your microscope so you can take the absolute difference (also located in the Vision Assistant step under Operators). Here are some steps to help you get started with this:

1. Create a new Image Variable from VBAI menu bar Tools>>Variable Manager.

2. Add Vision Assistant Step that uses your current dot image.

3. In Vision Assistant script use the "Image Buffer" step from the first tab to store the current dot image in the image variable you created.

4. Add a "Get Image" Step to read the image without dots from disk.

5. Use the "Operators" step towards the bottom of the Greyscale tab in Vision Assistant.  Take the Absolute Difference between the current image and the image variable. Hopefully now your dots are easier to see.

6. Use the threshold Step in Vision Assistant (since this one supports 16-bit images) and look for the bright objects since these are the differences. You may also want to use some particle filtering on the last tab of vision assistant to clean up your image after thresholding to remove small particles or skinny lines resulting from the images not being exactly aligned.

Hope that helps,

Brad

[TiTou]

Any idea if VBAI will fully support 16bit images in near futur Brad?

[Brad]

If you could provide a list of steps that are most important to you to support 16-bit images, that would be helpful for us to understand which steps to update first.

Thanks,

Brad