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help > Stitching Procedure
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Jul 7, 2015 08:07 PM | Armaan Singh
Stitching Procedure
Hello,
I am stitching together 30 or so slices of a mouse brain, going from lateral to medial with a sagittal view. The images are not necessarily aligned, and a few are actually flipped over or have very different orientations. I want to reconstruct these images, but I have no clue how to do so. I have tried using pairwise stitching on test data, but I could only stitch images side-by-side, not stacked upon each other. I also tried using terastitcher with its test data, but after the merging step, I couldn't find a final, reconstructed image. I've read almost all the online protocols (i.e. Github, Nature Protocols), but I didn't find any of those resources that helpful.
What plugin do you think would be best? Furthermore, what should my exact procedure be with that plugin? Most of the plugins that I have played around with have caused Vaa3d to crash. Being able to stitch together these mouse brain images is critical to my work, so I've started become quite frustrated with my lack of progress. I would greatly appreciate any advice.
I am stitching together 30 or so slices of a mouse brain, going from lateral to medial with a sagittal view. The images are not necessarily aligned, and a few are actually flipped over or have very different orientations. I want to reconstruct these images, but I have no clue how to do so. I have tried using pairwise stitching on test data, but I could only stitch images side-by-side, not stacked upon each other. I also tried using terastitcher with its test data, but after the merging step, I couldn't find a final, reconstructed image. I've read almost all the online protocols (i.e. Github, Nature Protocols), but I didn't find any of those resources that helpful.
What plugin do you think would be best? Furthermore, what should my exact procedure be with that plugin? Most of the plugins that I have played around with have caused Vaa3d to crash. Being able to stitch together these mouse brain images is critical to my work, so I've started become quite frustrated with my lack of progress. I would greatly appreciate any advice.
Jul 8, 2015 05:07 PM | Hanbo Chen - the university of georgia
RE: Stitching Procedure
Hi, Armaan
You may try neuron_stitcher. See my response in your other post. But right now, it can only stitch adjacent reconstructions pair-wisely. And you need to know the order of the reconstruction. Flip issue can be manually corrected by using manually_affine_neuron_SWC or rightclick on the reconsruction and choose "lock scene and adjust this object" option to adjust.
As for the other plugins that crashed Vaa3D, could you offer more details. If you are using linux system, please make sure you launch Vaa3D by running start_vaa3d.sh
Hanbo
You may try neuron_stitcher. See my response in your other post. But right now, it can only stitch adjacent reconstructions pair-wisely. And you need to know the order of the reconstruction. Flip issue can be manually corrected by using manually_affine_neuron_SWC or rightclick on the reconsruction and choose "lock scene and adjust this object" option to adjust.
As for the other plugins that crashed Vaa3D, could you offer more details. If you are using linux system, please make sure you launch Vaa3D by running start_vaa3d.sh
Hanbo
Sep 2, 2017 03:09 AM | wu chuanchao - Beijing Insitute of Technology
RE: Stitching Procedure
Hi ,all
Recently I am working on 3D stitching in Z direction with 2D slices. Two 3D stacks are not aligned , one is obtained from mouse brain belly, the other is obtained back reversed.
Maybe they have x,y,z offset. So i need to stitch them in three directions.I've tired plug-inFlyWorkstation_utilities of Janelia_istitch of Pairwise Image Stitching.It only support 2D stitching ,but not precisely.when I've tried use 3D stacks ,A window pops up,there is somthing wrong with code.Then I've tried TeraStitcher plugin ,it can not stitch correctly.
Then ,I see this post, I want to know how generate swc file when using manually_affine_neuron_SWC.
I would greatly appreciate any advice.
Recently I am working on 3D stitching in Z direction with 2D slices. Two 3D stacks are not aligned , one is obtained from mouse brain belly, the other is obtained back reversed.
Maybe they have x,y,z offset. So i need to stitch them in three directions.I've tired plug-inFlyWorkstation_utilities of Janelia_istitch of Pairwise Image Stitching.It only support 2D stitching ,but not precisely.when I've tried use 3D stacks ,A window pops up,there is somthing wrong with code.Then I've tried TeraStitcher plugin ,it can not stitch correctly.
Then ,I see this post, I want to know how generate swc file when using manually_affine_neuron_SWC.
I would greatly appreciate any advice.