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Reference of the library and data used

Libraries:

Seen during the course: * SpaGE: * Paper * GitHub

* Tangram:
    * [Paper](https://doi.org/10.1038/s41592-021-01264-7)
    * [GitHub](https://github.com/broadinstitute/Tangram)

* Banksy:
    * [Paper](https://doi.org/10.1038/s41588-024-01664-3)
    * [GitHub](https://github.com/prabhakarlab/Banksy)

Additional tools mentioned during the course for image analysis:

* Stardist:
    * [Paper](https://arxiv.org/abs/2203.02284)
    * [GitHub](https://github.com/stardist/stardist)
* Cellpose:
    * [Paper](https://doi.org/10.1038/s41592-020-01018-x)
    * [GitHub](https://github.com/MouseLand/cellpose)
    * [Website](https://www.cellpose.org/)

Analysis container

  • To retrieve the singularity image used for the analyses of Day 3, you can use this singularity command that will pull the image from dockerhub : singularity pull docker://alessiavalenti/courses:brainomics2_day3-0.0.1

Data:

* MERFISH spatial transcriptomics dataset of a single adult mouse brain:
    * [Paper](https://www.nature.com/articles/s41586-023-06808-9)
    * [Code](https://github.com/AllenInstitute/abc_atlas_access/blob/main/notebooks/zhuang_merfish_tutorial.ipynb)
    * [Data availability](https://knowledge.brain-map.org/data/5C0201JSVE04WY6DMVC/collections)