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Hi,
The counts.csv files are missing for the HDST datasets and the adj.csv file is missing for the MERFISH dataset. Is this intentional? Since these are publicly available it would facilitate to ru…
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Hi Chao,
Thanks a lot for developing this great tool. It really helps my project. I recently got some data from the Vizgen merFish platform. When I run the pipeline, there are some bugs and I modify…
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Dear developers,
I have a question regarding computing niche cell type composition from following tutorial.
[https://scenvi.readthedocs.io/en/latest/tutorial/MOp_MERFISH_tutorial.html](tut)
I…
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Hi!
I have an issue with loading the public dataset from Vizgen that is used in [this vignette](https://satijalab.org/seurat/articles/seurat5_spatial_vignette_2).
To give you a view of what the data…
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Hello,
For the analysis of various datasets, spatial domains were used to evaluate BASS's accuracy. However, I can't see it anywhere in the repo. For example, the mouse hypo data in "data/MERFISH_A…
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Hi I am on scanpy=1.9.3 squidpy=1.2.3 tangram=1.0.4 torch=1.13.1+cu117
I am trying to integrate single cell and merfish data.
A marker list of 104 genes was correctly prepared and I have verifie…
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### Project short name:
MerfishCorticalLayer
### Primary Wrangler:
Ida
### Secondary Wrangler:
### Associated files:
* Google Drive:
* Publication: [Spatial Single-cell Analysis Decodes Cortical L…
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Hi! Really nice tool. I found the ssam is really interesting and I am a new starter with the R. When I am trying to run the MERFISH_POA.ipynb within the Jupyter notebook, there throw me serval errors …
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Hi Anna,
I want to use NCEM for other MERFISH data to compare with other tools that how the information differs. I followed your tutorial
https://github.com/theislab/spatial_scog_workshop_2022/b…
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We need some sort of mechanism for learning scale factors from an Experiement. Ideally the output of this method should be a multiplication matrix so that we can take advantage of the ElementWiseMulti…