Wrong channel names when opening .lif files with Icy

[IcyLyd]

Hi,

I would like to warn you about the fact (as mentionned in my previous post, 20th may concerning 1.5.0.0 release) that the channel names are still wrong when opening .lif file with the new release (1.5.2.0).

I think it does not come from Bioformat, since .lif file are correctly open in Image J.

Channel names :

channel 1 is wrongly indicating the name of the channel 4

Channel 2 is wrongly indicating the name of the channel 3

Channel 3 is wrongly indicating the name of the channel 2

Channel 4 is wrongly indicating the name of the channel 1

Colormap

imbedded lut is not respected. The colormap imposed is stille Red-Green blue and transparency.

I agree that colormap is a detail (and can be adapt manually, even if it's a little bit time consuming), but the channel name is to me a major problem and can be really misleading. If you could look at that, it would be great.

Thanks a lot.

Lydia.

[Alexandre Dufour]

I agree,

I'm having the same issue, plus I'd really like to store the current viewer's color map via the persistence mechanism (e.g. via an option in the color map panel). 

I know that everything is always high priority, but this one should really climb up the todo list :-)

@Stephane: if you're interested I can have a look and prepare a pull request for you to speed things up a bit

Alexandre

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[Stephane]

Hi Lydia,

Unfortunately i don't have the images you sent me sometime ago, they are on my personal notebook but still i tried to open another lif image in ImageJ and i don't see where you can retrieve the channel name ?
Honestly I don't see any reason why ImageJ can display them correctly if they use Bio-Formats to open the LIF file as the metadata is probably referencing them in wrong order... but maybe i am missing something.
About the channel color we can indeed fix it !

Best,

- Stephane

[IcyLyd]

Hi Stephane,

I send you by ftp a .lif file if you want to try.

The channel name is not retrieve in ImageJ, but the order of the channel is kept and LUT is conform to the Leica software.

The channel names reported in Icy seem to be the emission spectra chosen in the leica software. In my case: Leica 488, leica CY3, Leica 488 and Leica CY5.