Thanks Stephane, I understand about name parsing. In the end I did it with FIJI and by merging files ordered in a precise way:

file01_ch0

file01_ch1

file01_ch2, etc

and merging files in groups of 3. If they are in the right order it works well.

 

Still, do you think a merge channel bloc would be useful for protocols maybe?

 

Also, another question:

In a protocol, I get a 3D ROI for the whole cell, coming from HK-means, but that has gaps in it. Some of these gaps are filled by ‘Fill in Holes in ROI’, but not all of them.

What is the easiest way of filling all the ROI in?

I got around it by dilating the ROI along x, y and z, and that filled some of the smaller gaps, but not all.

 

Is there a way to get the outline of a 3D ROI (i.e. the 3D border) and then filling it in completely maybe?

 

Many thanks!

 

David