multichannel 3D viewing problem with Fluoview500 tiffs

Posted by Katinka Wouters on Jul 23, 2010; 10:39am
URL: http://imagej.273.s1.nabble.com/multichannel-3D-viewing-problem-with-Fluoview500-tiffs-tp3687386.html

Hi All,

For a while, I've been using ImageJ 3D viewer or volume viewer to visualize bacterial biofilms scanned with an Olympus Fluoview 500. It works perfectly for single channel images, thanks a lot to the developers!

But, when I'm using it for multichannel images (so in my case: multispecies biofilms), my '3D' images appear 'flat' (like 2D), in both the 3D viewer and the volume viewer. When I rotate them, I get just one plane. This is particularly strange, since I can still browse through the Z-slices in the stack from which the 3D-image originate: all the (over 40) z-slices are there. So, I have a perfect 8 bit z-stack of each channel, but get a 2D image from them, both from the separate channels as from a stack in which the channels have been merged first.

Because this problem occurs in two separate plugins (both 3D Viewer as Volume Viewer), I wonder whether it's a problem with my tiff-series. An image stack originates from a Fluoview500 tiff file, which was converted for use with ImageJ using the Save_8bit_MultiCH plugin in combination with the LOCI plugin. This generates a separate tiff stack for each channel. So everything seems perfect, untill I try to render them to 3D. I used the same plugin to convert the single channel images to a tiff stack, without any 3D viewing problems.

I noticed before that I can not use the LOCI plugin as such to import my FV tiffs, because channels and z-position get mixed up: I always get a stack with repeatedly CH1; CH2; CH3; CH1; CH2; CH3... as if these are the z-slices, and this divided over 3 'channels', which are in fact not the channels. This happens with every setting I tried (e.g. changing the xyzct order). Luckily, this problem was solved when using the Save_8bit_MultiCH plugin, but now I wonder there is maybe some error left in the metadata that gets the 3D/Volume Viewer confused about the stack.

Does anyone recognize this problem? Or is there something obvious that I'm missing here? I would be very gratefull if I could find a solution for it, since I'm promoting ImageJ towards my colleagues who are now using  the very expensive program from Zurich...

Thanks a lot!

Katinka