Re: Help writing a macro-with pictures!

Posted by Gabrielle Van Patten on
URL: http://imagej.273.s1.nabble.com/Help-writing-a-macro-with-pictures-tp3688441p3688443.html

Hey thanks for responding so quickly. I'll try to answer you questions in an efficient way.

We are studying the effects of spinal cord injury on 5HT2A and 5HT2C receptors in mice. Our hypothesis is that because spinal cord injury results in a loss of serotonin (5HT) caudal to the injury site, there is an upregulation in the number and/or size of serotonin receptors.

Each image I have is taken from a specific region of either an intact or spinal cord injured mouse spinal cord, so I want to compare the size, brightness (pixel density) and number of receptors in intact and spinal cord injured mice.

For the density question, yes, I would like to use density to define the boundary and use the total density as part of my results. I think as long is the density threshold is kept constant for the whole image and the images that are being compared, it should be ok. I figured I could just experiment with different thresholds and see what works best.

For my end results, I would like to give the average cluster size, density and total number of clusters per image. 

Sorry about the pixel confusion. Each dot in my picture was supposed to represent one pixel.

For the find maxima function, if you wanted to try it out yourself in ImageJ, I have attached the .tif version of the image I posted (it's the first one). You just go to process, then binary, then find maxima. I set the noise tolerance by eye, then use the same tolerance for every image I'm comparing the original to.

The only way the image I posted has be altered is I used a deconvolving filter to blur out the background noise. I also attached what the image looks like when you use find maxima (it's the one called point selection).

To designate the center of each cluster, the best way I can think of is to just use the point that the find maxima function designates. That is a good point that the brightest pixels may not be in the center, but I can't think of any other way to do it.

Thank you again for your response. Hopefully I've answered all of your questions and have a nice weekend!

Gabrielle

On Sat, Mar 27, 2010 at 3:24 PM, EHB2010 [via ImageJ] <[hidden email]> wrote:

also how do you propose to designate the centre of each cluster, as opposed to a bright pixel(s) off-centre?

out of interest: what is the hypothesis you are testing?

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