help > Image stitching in the Z direction
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Jul 29, 2015 06:07 PM | sumeer brar
Image stitching in the Z direction
Dear all,
Is there any way to stitch images together in the z direction? I have several images with similar but not identical x/y dimensions that need to be stitched in z. I used the pairwise stitching plugin to stitch the individual images together in x and y but this does not work for the z direction.
To clarify, I am trying to stitch consecutive confocal images that were taken of the same part of a mouse brain. The slices are 50 microns thick and are taken with a saggital view, starting laterally and going medial. Unfortunately, the stacks do not have the exact same X and Y dimensions, nor the same number of z-slices (they range from 10-16 slices). There's also no true landmark present in all of the images. It would be really useful to be able to combine these images so that I can visualize this section of the brain and do neuron tracing.
Thank you for your time and help!
Sumeer
Is there any way to stitch images together in the z direction? I have several images with similar but not identical x/y dimensions that need to be stitched in z. I used the pairwise stitching plugin to stitch the individual images together in x and y but this does not work for the z direction.
To clarify, I am trying to stitch consecutive confocal images that were taken of the same part of a mouse brain. The slices are 50 microns thick and are taken with a saggital view, starting laterally and going medial. Unfortunately, the stacks do not have the exact same X and Y dimensions, nor the same number of z-slices (they range from 10-16 slices). There's also no true landmark present in all of the images. It would be really useful to be able to combine these images so that I can visualize this section of the brain and do neuron tracing.
Thank you for your time and help!
Sumeer
Jul 29, 2015 07:07 PM | Hanbo Chen - the university of georgia
RE: Image stitching in the Z direction
Hi, Sumeer
Are these z stacks from physically sectioned slices? If not, are there overlap between them?
If there is not overlap between stacks in Z direction, you can:
1st. Do the reconstruction within each stack to generate SWC file (using any reconstructions algorithm in Vaa3D or Right Click Tool in Vaa3D 3D view);
2nd. Use Plugin>neuron_stitch>auto/live_stitch_neuron_SWC to stich the reconstruction in adjacent stacks.
This will give you a complete reconstruction. But currently the image cannot be stitched in this way. I am working an extension of the tool to allow stitch images as well.
Hanbo
Are these z stacks from physically sectioned slices? If not, are there overlap between them?
If there is not overlap between stacks in Z direction, you can:
1st. Do the reconstruction within each stack to generate SWC file (using any reconstructions algorithm in Vaa3D or Right Click Tool in Vaa3D 3D view);
2nd. Use Plugin>neuron_stitch>auto/live_stitch_neuron_SWC to stich the reconstruction in adjacent stacks.
This will give you a complete reconstruction. But currently the image cannot be stitched in this way. I am working an extension of the tool to allow stitch images as well.
Hanbo
Aug 3, 2015 04:08 PM | sumeer brar
RE: Image stitching in the Z direction
Hi Hanbo, thanks for the response. To clarify, if it's the images I
want to stitch together (not just the neuron structures
themselves), there is currently no way to do this? The neurons that
I'm tracing are not necessarily connected to each other, so I don't
want to assume that they are. My main goal is to trace the
dendrites through z-planes so that I can more accurately define
their morphology.
Thanks again, Sumeer.
Thanks again, Sumeer.
Sep 2, 2017 03:09 AM | wu chuanchao - Beijing Insitute of Technology
RE: Image stitching in the Z direction
Hi ,sumeer brar
I met the same problem like u . I have sevral 3D stacks which formed by 2D slices.they have overlaps.
I need to stitch them in Z-direction. I tried plugin FlyWorkstation_utilities of Janelia_istitch of Pairwise Image Stitching.
it can achieve 2D stitching not much precisely and correctly. But when I try 3D stitching , a bug comes up .there is somthing wrong with the code.
So I am writing to ask whether I use a right plug-in.
At the same time , I tried TeraStitcher plugin, how can i generate .xml files ?
I met the same problem like u . I have sevral 3D stacks which formed by 2D slices.they have overlaps.
I need to stitch them in Z-direction. I tried plugin FlyWorkstation_utilities of Janelia_istitch of Pairwise Image Stitching.
it can achieve 2D stitching not much precisely and correctly. But when I try 3D stitching , a bug comes up .there is somthing wrong with the code.
So I am writing to ask whether I use a right plug-in.
At the same time , I tried TeraStitcher plugin, how can i generate .xml files ?
Sep 25, 2017 08:09 PM | Yang Yu - Allen Institute for Brain Science
RE: Image stitching in the Z direction
Hi,
Thanks for being interested in using our plugins. The istitch plugin we've developed for stitching 2D/3D/4D images with merely "translations" (x,y, and z shifts). From your messages, it looks like there might be also rotations and possibly deformable transformations between the consecutive sections. Your "stitching" issues are more like "alignment/registration" problems instead of image stitching problems we solved here. To clarify your real problems, you can send us a link of your data or screen shots so that we can further help.
Best,
Yang
Thanks for being interested in using our plugins. The istitch plugin we've developed for stitching 2D/3D/4D images with merely "translations" (x,y, and z shifts). From your messages, it looks like there might be also rotations and possibly deformable transformations between the consecutive sections. Your "stitching" issues are more like "alignment/registration" problems instead of image stitching problems we solved here. To clarify your real problems, you can send us a link of your data or screen shots so that we can further help.
Best,
Yang