Saving cell segmentation output as a TMAP or Anndata object without running cell type annotations

[bradgigax]

Thank you very much for ENACT! I am new to analyzing HD Visium data so this is very helpful. However, I was wondering if there was a way to save the output from running ENACT as an h5ad file, anndata, or as the tmap output without having to run the cell type annotation steps for easy export to programs like Seurat?

[Mena-SA-Kamel]

ENACT v0.1.2 now saves the output segmentation masks under cells_layer.png within the cache folder you specified in your configurations. This is aligned to cropped whole slide image (where the Visium bins are located). Both files are now located under the /tmap directory within your cache. Currently, ENACT only generates the Anndata object after you ran cell annotation. Adding an option to dump the bin-to-cell assignment results to an Anndata object separately could be a viable option that can be added in the next release.