Posted by
Doc Watson on
Feb 24, 2019; 12:21pm
URL: http://imagej.273.s1.nabble.com/Hyperplexing-multi-channel-immunofluorescence-images-tp5021831.html
My apologies if this has been asked before, but I wasn't able to find
previous threads that really answered this. Here's what I'm trying to do:
I have tissue sections imaged on a Zeiss slide scanner that produces large,
tiled and stiched, pyramid composites with 20x magnification, and 5
fluorescent channels (.czi format). Then I'm doing pretty standard
cyclic-IF where I strip the fluorphores from the tissue, stain with new
markers, and image again. This leaves me with 8-10 5-channels images of the
same tissue that I then want to align and merge together to create one image
with ~40 channels.
So I need to align every channel from each staining round to the images from
the first round of staining, and probably perform small local deformations
in case the tissue is warped during the stainings. Ideally, I'd like to use
the DAPI channel from each 5-channel image to perform alignment and
registration, so that any image deformation is also applied to the other
channels from that round of staining.
I'm looking at using TrakEM2, but does anyone have other suggestions for how
to approach this?
And does anyone know a way to keep the pyramid structure of the .czi file,
or will I have to convert the whole thing to a BigTIFF image?
Thanks!
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