[ome-users] Problems with Leica SP5 Confocal files

[Paulo Almeida]

Hi,

A couple of users have made some comments regarding Leica SP5 confocal images:

 - The colors are not the same as in the microscope (green becomes red, for 
instance).
 - Individual .lif files that contain several pictures are split and it is no 
longer possible to differentiate them because all the sub-pictures are named 
after the filename of the parent picture. (Leica software manages this by 
creating a tree structure) 
 - One of our users listed some items in the metadata that would be useful to 
her, which I am including here:

Format  512x512
Zoom, Obj       z1.7/Obj20xIM
view/system     12BA 
PMT1 488nm, Gain/%      600V/40
PMT2 561 nm, Gain/%     400V/40%
Depth/Step size/nr sections (this is already there, but not associated as in 
Leica software)        153um/0.64/239
Pinhole (airy)  1.32
Line Av/ Frame Av       Lav:8
Scan Speed      8000Hz


I have already given some example files to Jean Marie, but if it is necessary 
I can provide some more.

Thank you,
Paulo Almeida
Instituto Gulbenkian de Ciência