ROIs based on intensity

[ojharding]

Hi so I'm really new to ImageJ but I'm analyzing time lapse images from calcium transients and I'm wondering whether there is a way to create (or single out) ROIs/objects from intensity profiles of the regions. I have a stack of 500 images and I could search visually for flashes in image set and use Plot Z Profile to determine the slice with the highest intensity, but for one thing, a code that searches for the approximate profile of a calcium transient would be empirical and for another, it would save me time and mistakes.
Thanks!

[dscho]

Hi ojharding,

On Tue, 23 Jul 2013, ojharding wrote:

> I'm analyzing time lapse images from calcium transients and I'm
> wondering whether there is a way to create (or single out) ROIs/objects
> from intensity profiles of the regions. I have a stack of 500 images and
> I could search visually for flashes in image set and use Plot Z Profile
> to determine the slice with the highest intensity, but for one thing, a
> code that searches for the approximate profile of a calcium transient
> would be empirical and for another, it would save me time and mistakes.

If you want to make a ROI given a range of intensities, this is very easy
by calling Adjust>Threshold..., click the "Set" button and specifying the
range, then calling Edit>Selection>Create Selection.

To help you with analyzing a lot of images, you should try to record a
macro from your operations: Plugins>Macros>Record...

Ciao,
Johannes

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