I am very new to this, and am completely overwhelmed and confused. I’ve been trying to read up on what to do here but am totally at a loss. Have tried using the recorder tool but to no avail. I would be SO grateful if someone could help me with this. Here is what I have going on:
I have many 4-channel z-stacks (with between 16-70 slices each). They are currently .lsm files but can easily be saved as .tif files.
I am trying to find a macro that does the following things:
-Splits the channels into four individual channels
-Runs the stack to images function on each channel
-Saves EACH slice from EACH channel with an indication of its channel AND z-position, preferably to a specific folder (ie one folder per channel, within a larger folder. But even one folder with all the slices for all the channels would be fine at this point)
Ex: my image is called “Male Control”, and has four channels (DAPI, 488, rhodamine, 633), and 12 slices. I need it to become…
-“Ch-1-Male Control” (or DAPI-Male Control, or whatever)
And then to have each of those channels split into its component slices, becoming:
-“Ch-1-Male Control-z3” (etc, for all 12 slices).
It’s the renaming and saving that I am having particular trouble with. Currently, even if I can get the channels to split and the get individual images, I still have to go through and rename each one individually, which will take hundreds of hours.
If someone could walk me through this I would be so happy.