splitting 4 color .LSM confocal stack

[Jaime21]

Dear List members

I have a 4 color confocal .LSM stack (12 bit, 2048 X 2048 pixels) want to split it and save it as a .TIF stack.
I tried the LOCI stack importer and it keeps giving me the same result: a 3 color stack with a slider for the red, green and blue channels and another one for the Z slices. Also, dragging and dropping the file to the Fiji bar gives me the same result as in LOCI. I checked the file and it has the 4 channels, it seems that the default for Image J is to open everything as RGB.

Thanks in advance for the help and suggestions.

Jaime

[G. Esteban Fernandez]

Hi Jaime,

I open >3 channel LSM files all the time with no trouble, even 34-channel
lambda + T-PMT stacks. Is your Fiji up to date?  Can you somehow make your
file available to download so we can see this behavior on our own? Maybe
crop it in XY to something small like 128x128 for download.

Thanks,
Esteban
On May 21, 2013 6:34 AM, "Jaime21" <[hidden email]> wrote:

> Dear List members
>
> I have a 4 color confocal .LSM stack (12 bit, 2048 X 2048 pixels) want to
> split it and save it as a .TIF stack.
> I tried the LOCI stack importer and it keeps giving me the same result: a 3
> color stack with a slider for the red, green and blue channels and another
> one for the Z slices. Also, dragging and dropping the file to the Fiji bar
> gives me the same result as in LOCI. I checked the file and it has the 4
> channels, it seems that the default for Image J is to open everything as
> RGB.
>
> Thanks in advance for the help and suggestions.
>
> Jaime
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/splitting-4-color-LSM-confocal-stack-tp5003058.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[ctrueden]

Hi Jaime,

> I tried the LOCI stack importer and it keeps giving me the same
> result: a 3 color stack

If the dataset is 4-channel, Bio-Formats is supposed to open it as
4-channel. If not, it is probably a bug.

As Esteban suggests, if you are willing to upload a sample dataset
demonstrating as the problem, we can investigate further. You can upload a
file (up to ~500MB) using the following link:
http://qa.openmicroscopy.org.uk/qa/upload/

Thanks,
Curtis


On Tue, May 21, 2013 at 3:30 AM, Jaime21 <[hidden email]> wrote:

> Dear List members
>
> I have a 4 color confocal .LSM stack (12 bit, 2048 X 2048 pixels) want to
> split it and save it as a .TIF stack.
> I tried the LOCI stack importer and it keeps giving me the same result: a 3
> color stack with a slider for the red, green and blue channels and another
> one for the Z slices. Also, dragging and dropping the file to the Fiji bar
> gives me the same result as in LOCI. I checked the file and it has the 4
> channels, it seems that the default for Image J is to open everything as
> RGB.
>
> Thanks in advance for the help and suggestions.
>
> Jaime
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/splitting-4-color-LSM-confocal-stack-tp5003058.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html