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Hi,
Thanks for this great tool.
I have been able to successfully run STalign on my cpu, but am coming up against an error when trying to use my NVIDIA GPU.
Specifically, when I run:
```
tra…
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We have found that the on our microscopes, which use Marzhauser stages, the 'Current Position' values in the stage display no longer update periodically. They update if we command a move with Dave or …
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Thank you for developing such a wonderful tool. The tutorial is concise and easy to follow, and I have been trying ELLA on my own dataset. I have a few questions after some preliminary runs.
- Does…
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Excellent work, there's no doubt that CAST would be applied in various spatially resolved multi-omics data analysis tasks.
However, I wanted to know if conducting an alignment between MALDI-MSI and V…
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Hello, this is an excellent piece of work. Based on the code provided in the "MERFISH_scRNAseq_integration.ipynb" notebook, I have combined my MERFISH data with single-cell RNA-seq data and inferred t…
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Hi again,
I am trying to load in our Merfish dataset and I am running into a few problems with `formVoltRon`.
I have
- a dgTMatrix in gene x cell orientation
- a metadata data frame
- a co…
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# Image Alignment
Image alignment in starfish is driven by the need to carry out two tasks:
1. Identify the cell of origin for each spot
2. Identify mRNA molecules whose identity is encoded across…
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Hi,
I am using CellChat-V2 for the analysis of stereo-seq (cell-bin) data. Could you provide guidance on how to estimate the 'spot.diameter' and 'spot' parameters within 'scale.factors', as these a…
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Hi developer,
Thank so much for the package. I'm currently looking for a package can do 3D segmentation and visualizarion on xenium dataset. And also can crop the dataset to the region I'm only in…
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Jorstad, Nikolas L., Jennie Close, Nelson Johansen, Anna Marie Yanny, Eliza R. Barkan, Kyle J. Travaglini, Darren Bertagnolli, et al. 2023. “Transcriptomic Cytoarchitecture Reveals Principles of Human…