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Bottom Hat function (in Igor Pro)
Jerome Simons from United States  [1 posts] 		15 year
Hello,
We have a little problem in our lab. When analyzing images of cell traps, the cells usually overlap. And since they are flexible, living objects, the size of such a blob is a function of how many cells there are in each trap. Our goal is to have Image Analysis software count the number of cells. My professor has a pretty good detecting algorithm in Igor Pro, but it still fails occasionally which we want to avoid. Now, I have found a good  algorithm to separate overlapping blobs.
See here: http://ecco2.jpl.nasa.gov/data1/matlab/images/imdemos/examples/morph/morph3.html
Now the problem is that Igor Pro lacks a bottom hat function (it just has the top hat one)
Does anyone know about a public bottom hat function that I could implement in Igor Pro or alternative software that could process this job?

Thank you very much,

Jerome

PS: There is a sample image of the dapi staining attached. These are examples where it is hard to train a program how to separate adjacent cells.



Anonymous 15 year
You should be able to implement a bottom hat from a top hat simply by negating or inverting the image. Not sure how Igor Pro does that but it is a simple function.

Also, how many cells should the count be in the images? 3 in both? Or does the first one only count as 2?

STeven.

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