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aristoteleo / spateo-release

Spatiotemporal modeling of spatial transcriptomics
https://spateo-release.readthedocs.io/
BSD 2-Clause "Simplified" License
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Multi-slice alignment during 3D reconstruction, Z-axis #287

Open yxs-124 opened 1 week ago

yxs-124 commented 1 week ago

Spateo is an interesting and useful tool. But I observed that the Spateo tutorial in the article seemed to lack input on the Z-axis after Reconstruction. Multi-slice splicing and alignment I did not find.

In addition, there are two files that seem to lack content when opened（https://github.com/aristoteleo/spateo-tutorials/tree/main/3_alignment/5. 3D reconstruction with pairwise alignment.ipynb，3_alignment/6. Global refinement by considering multiple slices.ipynb).

Thanks for your help!

YifanLu2000 commented 1 week ago

Hi, thank you very much for your interest! We will update the tutorial as soon as possible to provide a smoother, more detailed, and comprehensive guide for users. However, as I have been quite busy and would like to make the tutorial as perfect as possible, there has been some delay. I hope you can understand, and thank you again for your patience.

Additionally, I’d like to mention something related to your first question: Spateo does not modify the z-axis during alignment—it only adjusts the xy-axis coordinates. Therefore, I suggest using only the xy-axis as input. After alignment, you can append the z-axis back to the aligned xy-axis coordinates.n Spateo.