Open TobiasKletter opened 5 years ago
@TobiasKletter Could you play a bit with the different auto-thresholding methods in ImageJ?
[ Image > Adjust > Auto Threshold ]
[ Image > Adjust > Auto Local Threshold ]
(unfortunately I don't think they are really implemented in 3D thoughIs there one that works well for all examples?
I could imagine as an algorithm:
Step (2) is important because most algorithms change their output depending on the fraction of pixels that should be above threshold. So, if we can keep this kind of constant it would be a good thing.
Representative central slices:
Judging by eye, I think Otsu does a good job on all of them. These are montages of all slices in the stack:
The "Default" also gives a nice output, might actually be even identical to Otsu.
In that case maybe we can go for the Otsu and then we can cite Julius' paper (see discussion on the forum).
Agreed, we should give it a shot like this.
Some testing data with different degrees of signal-to-noise in the DNA channel:
https://www.dropbox.com/s/03plpdjott78voy/Dim_DNA_signal.tif?dl=0 https://www.dropbox.com/s/133xnp5ses6ugpz/Mid_DNA_signal.tif?dl=0 https://www.dropbox.com/s/tr3oabu8jm2mv6h/Bright_DNA_signal.tif?dl=0