Getting started

Three pages, in order:

1. Installation — the pip extras, and the conda recipe for the R stack if you need Seurat .rds support.
2. Your first walkthrough — run the wizard end to end on a small CSV, so you have seen every step before you point it at real data.
3. Troubleshooting — when .rds import fails, which it usually does for one of six reasons.

The short version

pip install "biwt[anndata,gui]"

That covers .csv and .h5ad with the Qt UI. Seurat .rds support needs a working R alongside the pip extra — see installation.

If you are using BIWT through a host application such as PhysiCell Studio, the host may already install it for you. Check the host's documentation first.

Which format should I bring?

BIWT reads whatever your analysis already produced; there is no advantage to converting.

You have	Extension	Extra needed
Scanpy / AnnData object	.h5ad	biwt[anndata]
Seurat object	.rds	biwt[seurat] + R
SingleCellExperiment / SpatialExperiment	.rds	biwt[seurat] + R
R workspace containing one of the above	.rda, .rdata	biwt[seurat] + R
A flat table of cells	.csv	none

If you are only trying BIWT out, a CSV is by far the least friction — see your first walkthrough for a file you can paste.