How to export pixel coordinates of point objects from an image (with imagej?)

Question

Dear all,

I am on a project where I am interested in the spacing & distribution of point objects in an microscope image.

So the image consists of darker, circular small dots from a rather complex background. It would be nice to do this with an feature extraction script automatically some day, but for now I am just hand-picking the points... Because I trust my own eyes :)

I looked through a couple different softwares and so far I liked imagej, which has a multi-point select feature. But I couldn't figure out after selecting the points by hand, how to export the coordinates. All I need is the X's and Y's for each point (for about a hundred points for each image).

Any pointers?

Or if you have alternative ideas on how to do this, suggest me another program (matlab?), or even point me to other useful readings, etc...

Thanks immensely!

Answer 1

OK. With some help I discovered that I can do this with just CTRL-M in imagej...

Answer 2

Though it doesn't seem to be the same process you're after there is something similar written in ImageJ for analysing 'Dot Blots'

http://image.bio.methods.free.fr/dotblot.html

It has a number of methods for identifying the dots and can also export the results as a CSV. The code itself is available at the bottom of the above page so you should be able to work with it if you're interested in automation.