3D Viewing with multiple channels

[Celeste Eno]

Hello,
Thank you in advance. I am sure this is quite easy, but I am struggling with opening a multichannel, multi-z .lsm into 3D Viewer and getting multiple channels. I also tried Image5D, but I must not be doing the correct things.

How do I open multi-channel, Z-stack so as to look at a 3D rendering?

Thank you,
Celeste Eno

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[ctrueden]

Hi Celeste,

> I am struggling with opening a multichannel, multi-z .lsm into 3D
> Viewer and getting multiple channels.

Bene Schmid, the author of the 3D Viewer, may have other suggestions, but
here is one way:

1. Open your data as a normal hyperstack.
2. Run Image > Color > Make Composite and ensure it is in Composite mode.
3. Optionally, use the Image > Lookup Tables for each channel to assign the
desired color table to each channel.
4. Flatten the channels using Image > Type > RGB Color (note: this will
force each channel to 8-bit, which may be lossy depending on your data)
5. Run Plugins > 3D Viewer to get a color 3D visualization.

Regards,
Curtis


On Fri, May 3, 2013 at 12:45 PM, Celeste Eno <[hidden email]> wrote:

> Hello,
> Thank you in advance. I am sure this is quite easy, but I am struggling
> with opening a multichannel, multi-z .lsm into 3D Viewer and getting
> multiple channels. I also tried Image5D, but I must not be doing the
> correct things.
>
> How do I open multi-channel, Z-stack so as to look at a 3D rendering?
>
> Thank you,
> Celeste Eno
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[gankaku]

Hi Celeste,

Another suggestion would be to actually separate the individual channels either by the command >Image>Color>Split Channels if you have only red, green and blue or any combination of two of them. Starting with a .lsm file should give you directly a composite stack or you can convert it in one, as Curtis already suggested using and split the channels thereafter using the >Image>Color>Channels Tool...

Once you have the individual channel stacks you can add them individually to the 3D viewer. Thanks to this extremely powerful tool from Benjamin Schmid you now have the advantage that you can individually change their properties in the 3D viewer e.g. assign arbitrary colors or display one channel as volume another as ortho-slices and the third as a surface reconstruction with a certain transparency. Like this you can create very nice views.

Hope it helped, have fun and success!
Jan

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