Posted by
Ed Simmons on
Oct 18, 2013; 9:11am
URL: http://imagej.273.s1.nabble.com/deleting-uneventful-frames-in-a-tif-stack-tp5005238p5005239.html
On 18/10/2013 11:00, jehangir cama wrote:
> Hi,
>
> I would appreciate any help with this- I have data stored as tif stacks
> (eg., a single tif file with 5000 images saved). I want to define two
> regions of interest that I can define in the first frame, and which stay
> the same throughout the 5000 frames.
>
> Each roi is bright except when dark (approximately) circular objects pass
> through (these are the events I want to study). I want to use ImageJ to
> delete all the frames in which these dark objects are* absent* (so I want
> to modify the tif stack to only keep those frames in which I have these
> events).
>
> Is this possible in ImageJ? Ideally, I need to also detect the radius and
> intensity of the objects, but the first thing I need to do is get rid of
> the extra frames. I'm new to using macros/plugins so if there is anything
> close to what I need, I would be grateful for a link.
>
> Thanks and regards
>
> Jehangir
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.htmlHi Jehangir,
This is certainly possible...
If you difference each image with the previous one, you will obtain
images that show only what has changed. You can then use these images of
the movement to determine what, if anything, is going on inside the ROIs.
In a macro you could do something like this:
Check for the presence of a stack of images with the required ROIs,
Perform the differencing to obtain a new stack of movement images,
Using the locations of the ROIs on the master stack, perform some simple
analysis of the movement stack to get the location of the object(s) of
interest,
Perform further analysis on the frames that show objects of interest
using the images from the master stack...
Do you really need to get rid of the extra frames? Or would you rather
skip past them silently?
Using the Macro recorder in IJ, you can record your actions in the GUI
to simplify wiring a macro in the first place.
Hope that helps,
Ed
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