Posted by
Katinka Wouters on
URL: http://imagej.273.s1.nabble.com/multichannel-3D-viewing-problem-with-Fluoview500-tiffs-tp3687386p3687388.html
Hi Bene,
Thanks for your very fast reply. I checked the image properties, and indeed, the voxel depth is at 0.0000000. So, problem solved! Any idea why the macro changes the voxel depths for multichannel images this dramatically?
I will now try to use a SetVoxelDepth macro, in order to keep the process automated.
Thanks a lot, you made my day!
Katinka
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Benjamin Schmid
Sent: Friday, July 23, 2010 1:09 PM
To:
[hidden email]
Subject: Re: multichannel 3D viewing problem with Fluoview500 tiffs
Hi Katinka,
>
> 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...
>
My first thought is that the calibration in the z direction may be wrong/to
small. Can you check this? (->Image->Properties: Voxel depth).
If the voxel depth seems to make sense, could you post the dimensions of
the image, i.e. what you see in the dialog when clicking
Image->Hyperstacks->Stack to Hyperstack.
Best wishes,
Bene