I want to quantify the flourescence intensity of an intracellular dye in single cells over (a relatively long period of) time. My problems are:
a) the cell movement --> no static ROIs possible
b) cell division
(see uploaded example)
So what i would need is cell tracking over time (like TrackMate) in combination with ROI setting or mask creation for each image of the time series.
Is there a PlugIn for Fiji available or can give somebody input for an suitable workflow?
Thanks a lot in advance
Guido
Dear Guido A Drexler ,
You might want to try the following (although the success and results might differ). You should open the stack in ImageJ and duplicate it. You should set an appropriate threshold and apply it. That will make your stack binary. Now you can run a watershed on it to divide adjacent cells. When you now go with the binar stack activated to the particle analyzer you should be able check sent roi to manager. You might want to check also get outlines and set a certain minimum size.
After the successful analysis all image might should have the same max intensity (because its binary) but what you really wanted is to create moving ROIs within the manager.
Now you should activate your 16 bit image and apply over the ROI manager a multi measurement of all created ROIs.
The problem will be, that you now have to sort your data more or less manually (but they should be in some logical order). If you are able to crop your time series (into single cells without compromising them) this might be a faster way to success.
Best wishes Soenke
Dear Sönke Weinert,
thank you very much for your helpful input.
Best, Guido
- Badges
- Science topic