Yuling Zhu

Hi @LucaMarconato, I have questions about alignment and stacking. I have noticed that spatialData used H&E image and landmarks to do alignment instead of using gene expression data and spatial...

I have clicked "3D reconstruction with pairwise alignment", but 404 page not found. Thanks.

> Hi @yuling999666, apologies, the current link is indeed invalid. You can refer to this [page](https://spateo-release.readthedocs.io/en/latest/tutorials/notebooks/3_alignment/5.%203D%20reconstruction%20workflow.html) instead, and we will update it as soon as possible. > > Regarding when...

Hi Yifan, one more question. When you did 3D reconstruction in figure 3 for human metastatic lymph node, did you use non-rigid alignment? Thanks.

> Hi @yuling999666, I think we didn't use the nonrigid alignment for 3D reconstruction for human metastatic lymph node dataset Thanks for quick response. I appreciate it.

Hi @YifanLu2000, I would like to ask how can I reproduce the result of pairwise alignment since you have multiple randomness generator in your st.align.morph_align () function. I tried to...

Hi @YifanLu2000 , thank you for your reply. It seems that you have used np.random.choice() multiple times in the morpho_pairwise(). If I just set seed before applying st.align.morph_align(), the first...

Hi @YifanLu2000 , thanks for reply. I appreciate it. I can generate the same results using the same conda environment, but when I change to another conda environment, it changes....

Hi @YifanLu2000 , thank you for your quick response. Got it. It really helps!

> Hi [@yuling999666](https://github.com/yuling999666), the affine mapping has been derived with the aim of aligning the full resolution H&E image for Visium and the two full resolution IF images for Xenium....