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Dear alegiac95,
![123](https://github.com/alegiac95/Imaging-transcriptomics/assets/111960642/70c80529-f188-4d5d-918e-060f447b8838)
Thank you for your toolbox "Imaging-transcriptomics".
I have …
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Hello, when running 'imt_gsea', I encountered an error: 'TypeError: gsea() got an unexpected keyword argument 'perm_index'.' I've tried various methods but still can't resolve it. Can you help me? The…
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### Contact Details
pamela.baker@alleninstitute.org
### Schema Name
Image-based Spatial Transcriptomics Metadata
### Oranizational Usage
BICAN
### General Description
This is a metadata schema …
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https://github.com/alegiac95/Imaging-transcriptomics/blob/46adb1df85c37123c77226d023b6d763edae8aca/imaging_transcriptomics/genes.py#L116C1-L125C36
Hi,
I am wondering if there is some thing wrong w…
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Dear alegiac95,
Thanks for providing this great scripts! I am using this toolbox in my project but meeting a bug.
After PLS analysis, I obtained .pkl file.
When I did imt_gsea (below),
`imt…
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Hi,
First, thanks for developing the Imaging Transcriptomics toolbox—it's been incredibly helpful for my research.
I have a quick question about the models of partial least-squares (PLS) regress…
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Description
Define SLOs for imaging data and scope work to update the DCP for imaging data resulting in an RFC.
See [image-based transcriptomics RFC](https://github.com/HumanCellAtlas/dcp-community/pu…
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We have at least one dataset coming in that uses ST. Should assess what metadata to collect and what file formats to require. There's both imaging and transcriptomics components, so this might require…
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There is an API which allows to easily retrieve pre-calculated tags of PubMed papers, with extracted bioconcepts including gene, chemical, disease, mutation and species:
![Screenshot from 2020-06-1…
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Thank you for this great tool and congratulations on the recent Nature publication!! I am wondering if you would recommend using CellOracle for spatially-resolved data, or would that violate any of th…