Posted by
Majurski, Michael Paul (Fed) on
Oct 21, 2015; 8:17pm
URL: http://imagej.273.s1.nabble.com/Grid-Collection-Stitch-tp5014667p5014711.html
Cheuk,
If you stitch multiple channels such that each channel gets registered independently then it will almost always result in stitched images of different sizes.
The method I usually use is to select a registration channel, typically the one with the most information. I like to use phase contrast, but whatever channel has the more foreground information in the overlap regions between image should be used. By selecting the channel with the most foreground information in the overlapping regions you give the stitching algorithm the best possible chance of stitching correctly. I then take the registration information from the registration channel and assemble the other channels using that information. That results in all of the stitched images being the same size and exactly registered with each other.
I do not know of a way to do this using the Grid/Collection stitching tool. I usually let the Grid/Collection tool generate the global image positions ("TileConfiguration.registered.txt") and then I parse and assemble that file using a function I have written in Matlab. This allows me to stitch a registration channel, have the global image positions file generated, and then parse and assemble all of the channels I am interested in using the global image positions.
If you are inclined to try the MIST stitching tool there is a method to assemble from metadata which allows you to stitch a registration channel and then use that to assemble secondary channels. This link explains how:
https://github.com/NIST-ISG/MIST/wiki/FAQ#stitching-multiple-channels .
I am not sure that I understand what you meant by convert the channels to timepoints. From what I have read (from
http://fiji.sc/Image_Stitching#Register_different_channels_to_each_other ) it seems that only the pairwise stitching from the Grid/Collection tool will handle time series.
If you can post the images to be stitched on dropbox (with the previous results) I would be happy to play with them and figure out what I can get MIST to produce and give you a script.
Thanks,
Michael Majurski
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Cheuk Tam
Sent: Wednesday, October 21, 2015 2:47 PM
To:
[hidden email]
Subject: Re: Grid/Collection Stitch
Dear Dr. Majurski,
Thank you for your suggestions. Lowering the regression threshold gave better alignment to parts of the image. Unfortunately, the nuclei were still misaligned. I was able to have proper alignment when stitching the channels (red for Beta-3 Tubulin and blue for Hoechst) separately. However, it was difficult merge the two channels together after stitching because the fused images are of different sizes. I was wondering there is an issue with registering different channels together. If so, will converting the channels to timepoints (perhaps by designating channels as tandem timepoints) help? Is there a way to do this in MIST? Thank you for your help.
Sincerely,
Cheuk
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