BIWT Test Data

AnnData object used in the BIWT example, provided here for reproducibility and reference. To use this dataset, first install PhysiCell Studio following their instructions here. Second, launch PhysiCell Studio using the following command from a terminal: ```sh cd path/to/studio/folder python ./bin/studio.py --biwt ``` In the `Config Basics` tab that the GUI opens up on, set the `Xmin` and `Xmax` values to `-750` and `750`, respectively. Set `Ymin` and `Ymax` to the same values. Navigate to the `ICs > BIWT` subtab and click the `Import` button. Select the file downloaded from here. The first window that will pop up lists all the features of the samples (Visium spots in this dataset). Select `mle_cell_type`. The next window will ask if you want to use the spatial data found in `imagerow` and `imagecol`. Select `Yes` and click `Continue`. Curate the cell types as follows: Merge: B cell, Endocrine, Endothelial, Fibroblast, Macrophage, Neutrophil, Stellate, iCAF, myCAF Merge: all Epithelial subtypes Keep: T cell Click `Continue`. Rename the groups: `other`, `cancer`, and `cd8`, respectively. Click `Continue`. Click `Plot` and then `Continue`. Choose the name of the desired output file and `Overwrite`. Then `Finish`. The generated file is ready for initializing the PhysiCell model provided here.