I may have found the cause of my problem stitching stacks with 5 planes...

Posted by Gelman, Laurent on Jul 05, 2013; 2:16pm
URL: http://imagej.273.s1.nabble.com/I-may-have-found-the-cause-of-my-problem-stitching-stacks-with-5-planes-tp5003778.html

Hi everybody,


Following my last e-mail (see below), I looked at http://fiji.sc/Image_Stitching#Problems.2C_known_issues_and_solutions (thanks to Pariksheet Nanda) and it is stated that Z-stacks should have at least 3 planes. I tested different numbers (adding empty planes to my stacks), and actually any number equal to or above 8 seem fine. I guess this is because it is now possible to merge 7 channels...??

If this is the answer, then I would find nice, provided that image properties are set correctly, if the plugin could not convert Z-planes into channels. It does happen to make Z-stacks with less than 8 planes...



Many thanks in advance for your help,



Best regards (and have a nice week-end),



Laurent.



From: Gelman, Laurent
Sent: 05 July 2013 13:28
To: '[hidden email]'
Subject: Stitching of Z-stacks converts Z planes into color channels. Is this normal ?

Hi everybody,

I try to stitch 3D stacks (5 planes, 1 channel) with the Grid/Collection stitching plugin but the displayed fused image is a multi-channel one with 1 plane, with new number of channels = number of Z-planes. Obviously Stitching in Z is also wrong.
Does that mean that I can't stitch Z-stacks this way?

Thanks for your help,

Best regards,

Laurent.

___________________________
Laurent Gelman, PhD
Friedrich Miescher Institut
Facility for Advanced Imaging and Microscopy
Head of Light Microscopy
WRO 1066.2.16
Maulbeerstrasse 66
CH-4058 Basel
[phone]
[phone]


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